diff --git a/DevelopmentExamples/DevEx1_CustomModule/README.md b/DevelopmentExamples/DevEx1_CustomModule/README.md
index e611766..0734fde 100644
--- a/DevelopmentExamples/DevEx1_CustomModule/README.md
+++ b/DevelopmentExamples/DevEx1_CustomModule/README.md
@@ -20,12 +20,24 @@ The main MIA documentation can be found at https://mianalysis.github.io and the
 
 Adding MIA as a dependency
 --------------------------
-MIA can be added to Maven projects using the following dependency:
+MIA can be added to Maven projects using the following dependencies:
 ```
 <dependency>
     <groupId>io.github.mianalysis</groupId>
-    <artifactId>mia</artifactId>
-    <version>1.2.10</version>
+    <artifactId>mia-core</artifactId>
+    <version>1.5.1</version>
+</dependency>
+
+<dependency>
+    <groupId>io.github.mianalysis</groupId>
+    <artifactId>mia-modules</artifactId>
+    <version>1.5.1</version>
+</dependency>
+
+<dependency>
+    <groupId>io.github.mianalysis</groupId>
+    <artifactId>mia-plugin</artifactId>
+    <version>1.5.1</version>
 </dependency>
 ```
 
diff --git a/DevelopmentExamples/DevEx1_CustomModule/pom.xml b/DevelopmentExamples/DevEx1_CustomModule/pom.xml
index e061258..a00ba69 100644
--- a/DevelopmentExamples/DevEx1_CustomModule/pom.xml
+++ b/DevelopmentExamples/DevEx1_CustomModule/pom.xml
@@ -43,8 +43,20 @@
 
         <dependency>
             <groupId>io.github.mianalysis</groupId>
-            <artifactId>mia</artifactId>
-            <version>1.4.2</version>
+            <artifactId>mia-core</artifactId>
+            <version>1.5.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>io.github.mianalysis</groupId>
+            <artifactId>mia-modules</artifactId>
+            <version>1.5.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>io.github.mianalysis</groupId>
+            <artifactId>mia-plugin</artifactId>
+            <version>1.5.1</version>
         </dependency>
     </dependencies>
 </project>
diff --git a/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/ExampleModule.java b/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/ExampleModule.java
index c6ccd13..4ece9fb 100644
--- a/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/ExampleModule.java
+++ b/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/ExampleModule.java
@@ -44,6 +44,7 @@
 import io.github.mianalysis.mia.process.ColourFactory;
 import io.github.mianalysis.mia.process.math.CumStat;
 import net.imagej.ImageJ;
+import net.imagej.patcher.LegacyInjector;
 
 /**
  * An example of a MIA Module.
@@ -115,11 +116,14 @@ public interface Measurements {
      * @param args Can be left blank
      */
     public static void main(String[] args) {
+        // The following must be called before initialising ImageJ
+        LegacyInjector.preinit();
+        
         // Creating a new instance of ImageJ
         new ij.ImageJ();
 
         // Launching MIA
-        new ImageJ().command().run("io.github.mianalysis.mia.MIA", false);
+        new ImageJ().command().run("io.github.mianalysis.mia.MIA_", false);
 
         // Adding the current module to MIA's list of available modules.
         AvailableModules.addModuleName(ExampleModule.class);
@@ -218,7 +222,7 @@ public Status process(Workspace workspace) {
         // Measuring intensity for each centroid object.  Iterating over each output centroid object.
         for (Obj outputObject : outputObjects.values()) {
             // The MeasureObjectIntensity module has a public method that allows the intensity of a single object to be measured for a specified image.  This returns a cumulative statistic (CumStat) object, from which we can extract statistics about the intensities of all coordinates in the specified object.  Here, the object only has a single point, so mean, min, max and sum will all have the same value.
-            CumStat cs = MeasureObjectIntensity.measureIntensity(outputObject, inputImage, false);
+            CumStat cs = MeasureObjectIntensity.measureIntensity(outputObject, inputImage, false, false);
 
             // Creating a new "Measurement" object to store the intensity of the centroid object.  As noted above, all statistics (bar the standard deviation) will have the same value, so the "mean" is used.
             Measurement intensity = new Measurement(Measurements.INTENSITY, cs.getMean());
diff --git a/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/TemplateModule.java b/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/TemplateModule.java
index d803ae9..eeb54b3 100644
--- a/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/TemplateModule.java
+++ b/DevelopmentExamples/DevEx1_CustomModule/src/main/java/io/github/mianalysis/example/TemplateModule.java
@@ -17,30 +17,43 @@
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
 import net.imagej.ImageJ;
+import net.imagej.patcher.LegacyInjector;
 
 /**
  * A template MIA module.
- */ 
+ */
 @Plugin(type = Module.class, priority = Priority.LOW, visible = true)
 
 public class TemplateModule extends Module {
     /**
-     * (Optional) If we wish to put our new module into a different category to the default categories, we need to create it here. Leaving it till the {@link getCategory} method is called is too late.  Here, we create a new module category called "Examples" which will be in the first level of the available modules list.
+     * (Optional) If we wish to put our new module into a different category to the
+     * default categories, we need to create it here. Leaving it till the
+     * {@link getCategory} method is called is too late. Here, we create a new
+     * module category called "Examples" which will be in the first level of the
+     * available modules list.
      */
     private static final Category category = new Category("Examples", "Modules used in examples", Categories.ROOT,
             true);
 
+    
+
     /**
-     * (Optional) This main function allows us to launch a new copy of Image, start MIA and add the current module to MIA.  These steps are only necessary when running the MIA and the new module from a main function.  When run as part of  distribution, the module will be automatically included in MIA.
+     * (Optional) This main function allows us to launch a new copy of Image, start
+     * MIA and add the current module to MIA. These steps are only necessary when
+     * running the MIA and the new module from a main function. When run as part of
+     * distribution, the module will be automatically included in MIA.
      * 
      * @param args Can be left blank
      */
     public static void main(String[] args) {
+        // The following must be called before initialising ImageJ
+        LegacyInjector.preinit();
+
         // Creating a new instance of ImageJ
         new ij.ImageJ();
 
         // Launching MIA
-        new ImageJ().command().run("io.github.mianalysis.mia.MIA", false);
+        new ImageJ().command().run("io.github.mianalysis.mia.MIA_", false);
 
         // Adding the current module to MIA's list of available modules.
         AvailableModules.addModuleName(TemplateModule.class);
@@ -59,7 +72,11 @@ public TemplateModule(Modules modules) {
     }
 
     /**
-     * The module category within MIA in which this module will be placed. We can choose any of the default categories available in io.github.mianalysis.mia.module.Categories or use one created along with this module. This template uses the "Example" category created at the top of this class.
+     * The module category within MIA in which this module will be placed. We can
+     * choose any of the default categories available in
+     * io.github.mianalysis.mia.module.Categories or use one created along with this
+     * module. This template uses the "Example" category created at the top of this
+     * class.
      */
     @Override
     public Category getCategory() {
@@ -67,15 +84,25 @@ public Category getCategory() {
     }
 
     /**
-     * Since MIA v1.4.0, each Module has been given a version number returned by this function.  The intention is that these version numbers follow the standard semantic versioning format, where the numbers indicate changes in the form major.minor.patch.  When loading a workflow, MIA checks the version number of a module against the version number of the module used to create the workflow.  Based on any differences in version number, MIA will display a warning to users about the likelihood of results coming from that module being different.
+     * Since MIA v1.4.0, each Module has been given a version number returned by
+     * this function. The intention is that these version numbers follow the
+     * standard semantic versioning format, where the numbers indicate changes in
+     * the form major.minor.patch. When loading a workflow, MIA checks the version
+     * number of a module against the version number of the module used to create
+     * the workflow. Based on any differences in version number, MIA will display a
+     * warning to users about the likelihood of results coming from that module
+     * being different.
      */
     @Override
     public String getVersionNumber() {
         return "1.0.0";
     }
-    
+
     /**
-     * Each module should include a description which will be included in the GUI (accessible by going to View / Show help panel) as well as in the automatically-generated online documentation at https://mianalysis.github.io/modules.
+     * Each module should include a description which will be included in the GUI
+     * (accessible by going to View / Show help panel) as well as in the
+     * automatically-generated online documentation at
+     * https://mianalysis.github.io/modules.
      */
     @Override
     public String getDescription() {
@@ -83,9 +110,13 @@ public String getDescription() {
     }
 
     /**
-     * The method which is run as part of a workflow.  This method contains all the code for loading items from the MIA workspace, performing the action of this module and exporting any new items to the workspace.
+     * The method which is run as part of a workflow. This method contains all the
+     * code for loading items from the MIA workspace, performing the action of this
+     * module and exporting any new items to the workspace.
      * 
-     * @param workspace The current workspace containing all available images and objects (i.e. those previously output by earlier modules in the workflow).
+     * @param workspace The current workspace containing all available images and
+     *                  objects (i.e. those previously output by earlier modules in
+     *                  the workflow).
      */
     @Override
     public Status process(Workspace workspace) {
@@ -94,7 +125,10 @@ public Status process(Workspace workspace) {
     }
 
     /**
-     * Creates an instance of each parameter, each of which is stored in the "parameters" variable of the module.  Each new instance of the module will have a new set of parameters.  This method runs once, when the module is first created.
+     * Creates an instance of each parameter, each of which is stored in the
+     * "parameters" variable of the module. Each new instance of the module will
+     * have a new set of parameters. This method runs once, when the module is first
+     * created.
      */
     @Override
     protected void initialiseParameters() {
@@ -102,7 +136,10 @@ protected void initialiseParameters() {
     }
 
     /**
-     * Returns the currently-active parameters for this module.  The returned parameters will change depending on what other parameters are set to.  The output of this module determines the parameters that are displayed in the GUI.
+     * Returns the currently-active parameters for this module. The returned
+     * parameters will change depending on what other parameters are set to. The
+     * output of this module determines the parameters that are displayed in the
+     * GUI.
      */
     @Override
     public Parameters updateAndGetParameters() {
@@ -111,7 +148,12 @@ public Parameters updateAndGetParameters() {
     }
 
     /**
-     * Measurements added to any images by this module are reported by adding their reference to an ImageMeasurementRefs collection.  When no measurements are added by this module, this method can simply return "null".  These references tell downstream modules what measurements are available for each image.  Returned references should be the original copies stored in the local "imageMeasurementRefs" object.
+     * Measurements added to any images by this module are reported by adding their
+     * reference to an ImageMeasurementRefs collection. When no measurements are
+     * added by this module, this method can simply return "null". These references
+     * tell downstream modules what measurements are available for each image.
+     * Returned references should be the original copies stored in the local
+     * "imageMeasurementRefs" object.
      */
     @Override
     public ImageMeasurementRefs updateAndGetImageMeasurementRefs() {
@@ -119,16 +161,27 @@ public ImageMeasurementRefs updateAndGetImageMeasurementRefs() {
     }
 
     /**
-     * Measurements added to any objects by this module are reported by adding their reference to an ObjMeasurementRefs collection.  When no measurements are added by this module, this method can simply return "null".  These references tell downstream modules what measurements are available for each object of a specific object collection.  Returned references should be the original copies stored in the local "objectMeasurementRefs" object.
+     * Measurements added to any objects by this module are reported by adding their
+     * reference to an ObjMeasurementRefs collection. When no measurements are added
+     * by this module, this method can simply return "null". These references tell
+     * downstream modules what measurements are available for each object of a
+     * specific object collection. Returned references should be the original copies
+     * stored in the local "objectMeasurementRefs" object.
      */
     @Override
     public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
-       return null;
+        return null;
 
     }
 
     /**
-     * Values added to the workspace's metadata collection by this module are reported by adding their reference to a MetadataRefs collection.  When no metadata values are added by this module, this method can simply return "null".  Metadata values are single values within a workspace that specify information such as the root filename or series number.  These references tell downstream modules what metadata is available.  Returned references should be the original copies stored in the local "metadataRefs" object.
+     * Values added to the workspace's metadata collection by this module are
+     * reported by adding their reference to a MetadataRefs collection. When no
+     * metadata values are added by this module, this method can simply return
+     * "null". Metadata values are single values within a workspace that specify
+     * information such as the root filename or series number. These references tell
+     * downstream modules what metadata is available. Returned references should be
+     * the original copies stored in the local "metadataRefs" object.
      */
     @Override
     public MetadataRefs updateAndGetMetadataReferences() {
@@ -136,7 +189,12 @@ public MetadataRefs updateAndGetMetadataReferences() {
     }
 
     /**
-     * Any parent-child relationships established between objects by this module are reported by adding their reference to a ParentChildRefs collection.  When no parent-child relationships are added by this module, this method can simply return "null".  These references tell downstream modules what parent-child relationships are available.  Returned references should be the original copies stored in the local "parentChildRefs" object.
+     * Any parent-child relationships established between objects by this module are
+     * reported by adding their reference to a ParentChildRefs collection. When no
+     * parent-child relationships are added by this module, this method can simply
+     * return "null". These references tell downstream modules what parent-child
+     * relationships are available. Returned references should be the original
+     * copies stored in the local "parentChildRefs" object.
      */
     @Override
     public ParentChildRefs updateAndGetParentChildRefs() {
@@ -145,15 +203,22 @@ public ParentChildRefs updateAndGetParentChildRefs() {
     }
 
     /**
-     * Any partner-partner relationships established between objects by this module are reported by adding their reference to a PartnerRefs collection.  When no partner-partner relationships are added by this module, this method can simply return "null".  These references tell downstream modules what partner-partner relationships are available.  Returned references should be the original copies stored in the local "partnerRefs" object.
-     */    
+     * Any partner-partner relationships established between objects by this module
+     * are reported by adding their reference to a PartnerRefs collection. When no
+     * partner-partner relationships are added by this module, this method can
+     * simply return "null". These references tell downstream modules what
+     * partner-partner relationships are available. Returned references should be
+     * the original copies stored in the local "partnerRefs" object.
+     */
     @Override
     public PartnerRefs updateAndGetPartnerRefs() {
         return null;
     }
 
     /**
-     * Can be used to perform checks on parameters or other conditions to ensure the module is configured correctly.  This runs whenever a workflow is updated (e.g. a parameter in any module is changed).
+     * Can be used to perform checks on parameters or other conditions to ensure the
+     * module is configured correctly. This runs whenever a workflow is updated
+     * (e.g. a parameter in any module is changed).
      */
     @Override
     public boolean verify() {
diff --git a/Ex1_NucleiSegmentation/Ex1_NucleiSegmentation.mia b/Ex1_NucleiSegmentation/Ex1_NucleiSegmentation.mia
index 0cfc732..f32ffcf 100644
--- a/Ex1_NucleiSegmentation/Ex1_NucleiSegmentation.mia
+++ b/Ex1_NucleiSegmentation/Ex1_NucleiSegmentation.mia
@@ -1 +1 @@
-<?xml version="1.0" encoding="UTF-8"?><ROOT MIA_VERSION="1.4.2"><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.InputControl" DISABLEABLE="false" ENABLED="true" ID="1636961347222" NAME="Input control" NICKNAME="Input control" NOTES="In &quot;Input control&quot; we specify the path to the file we wish to work on.  At this point, no images are actually being loaded into the workspace.  We will load the images in during the main part of the workflow, typically using the &quot;Load image&quot; module.  These can be inserted anywhere in the workflow, meaning we're not wasting memory by opening them before they're needed.&#10;&#10;Here, we can specify a single file or, if we wish to run in batch mode, a folder.  When dealing with folders we may not want to load all the files contained within.  Therefore, it's possible to add filters that will help us process only the images of interest.  In the example here, we've got it set to only load files with .tif extensions and to skip anything with &quot;_overlay&quot; in the name (these will be created by this workflow).&#10;&#10;In MIA, parameters can be made visible for users working in &quot;Processing view&quot; by clicking the button to the right of the parameter.  In this workflow, the &quot;Input path&quot; is one such visible parameter." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input path" NICKNAME="Input path" VALUE="F:\Java Projects\mia-examples\Ex1_NucleiSegmentation" VISIBLE="true"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="All series" VISIBLE="false"/><PARAMETER NAME="Series list" NICKNAME="Series list" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Only load first file per folder" NICKNAME="Only load first file per folder" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only load first matching group" NICKNAME="Only load first matching group" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Pattern" NICKNAME="Pattern" VALUE="" VISIBLE="false"/><PARAMETER NAME="Spatial unit" NICKNAME="Spatial unit" VALUE="Micrometres" VISIBLE="false"/><PARAMETER NAME="Temporal unit" NICKNAME="Temporal unit" VALUE="Milliseconds" VISIBLE="false"/><PARAMETER NAME="Ignore case" NICKNAME="Ignore case" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add filter" NICKNAME="Add filter" VALUE="" VISIBLE="false"><COLLECTION><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Extension" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="tif" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (include)" VISIBLE="false"/></PARAMS><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Filename" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="_overlay" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (exclude)" VISIBLE="false"/></PARAMS></COLLECTION></PARAMETER><PARAMETER NAME="Simultaneous jobs" NICKNAME="Simultaneous jobs" VALUE="1" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Extension" NICKNAME="Extension"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="File" NICKNAME="File"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filename" NICKNAME="Filename"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filepath" NICKNAME="Filepath"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Series name" NICKNAME="Series name"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Series number" NICKNAME="Series number"/></METADATA></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.OutputControl" DISABLEABLE="false" ENABLED="true" ID="1636961347222" NAME="Output control" NICKNAME="Output control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Add variable" NICKNAME="Add variable" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Run macro" NICKNAME="Run macro" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Macro mode" NICKNAME="Macro mode" VALUE="Macro text" VISIBLE="false"/><PARAMETER NAME="Macro text" NICKNAME="Macro text" VALUE="run(&quot;Enable MIA Extensions&quot;);&#10;&#10;// Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID)." VISIBLE="false"/><PARAMETER NAME="Macro file" NICKNAME="Macro file" VALUE="" VISIBLE="false"/><PARAMETER NAME="Export mode" NICKNAME="Export mode" VALUE="All together" VISIBLE="false"/><PARAMETER NAME="Individual save location" NICKNAME="Individual save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Group save location" NICKNAME="Group save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file/folder name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Metadata item for grouping" NICKNAME="Metadata item for grouping" VALUE="" VISIBLE="false"/><PARAMETER NAME="Continuous data export" NICKNAME="Continuous data export" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Save every n files" NICKNAME="Save every n files" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Export summary" NICKNAME="Export summary" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Summary mode" NICKNAME="Summary mode" VALUE="Per input file" VISIBLE="false"/><PARAMETER NAME="Metadata item for summary" NICKNAME="Metadata item for summary" VALUE="" VISIBLE="false"/><PARAMETER NAME="Show object counts" NICKNAME="Show object counts" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Export individual objects" NICKNAME="Export individual objects" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962470785" NAME="GUI separator" NICKNAME="File loading" NOTES="These separators have no direct effect on the workflow.  Instead, they're simply to help visually break the workflow down into easy-to-understand sections.  &#10;&#10;Clicking the power icon to the left of the separator will disable all modules contained within this section.&#10;&#10;Sections can also be collapsed/expanded by clicking the arrows to the left or right of the separator name.  When collapsed, all modules will still be run." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1636961348488" NAME="Load image" NICKNAME="Load image" NOTES="&quot;Load image&quot; is the main module for loading images from file into the workspace.  In most cases, this will be from the &quot;Current file&quot; (i.e. the one selected in &quot;Input control&quot;); however, it is possible to use metadata values to load other images, although this will be covered in a later example.&#10;&#10;For multi-dimensional images it's possible to load of subset of channels, slices or timepoints.  This way we don't need to load the entire image into the computer's memory - something that can be very useful when dealing with largeimage stacks.  For example, we may only want the first channel or a particular subset of slices.&#10;&#10;In this example, &quot;Channels&quot;, &quot;Slices&quot; and &quot;Frames&quot; are all set to &quot;1-end&quot;, which will load every available image; however, subsets can be selected using ranges (e.g. &quot;4-7&quot;), comma-separated lists (e.g. &quot;1,5,6,7&quot;).&#10;&#10;Multiple &quot;Load image&quot; modules can be inserted into the workflow as and when they are required.  This also allows us to manage the memory being used at any time.&#10;&#10;This module will add an image called &quot;Raw&quot; to the workspace.  The image will then be accessible by all subsequent modules.  Although not done in this example workflow, images can be assigned measurement values.  Measurements can be exported to the final Excel file or used by subsequent modules." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="0.75" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="0.75" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962481633" NAME="GUI separator" NICKNAME="Segmentation" NOTES="The modules in this section deal with segmentation of the nuclei in 3D." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.FilterImage" DISABLEABLE="false" ENABLED="true" ID="1636961810491" NAME="Filter image" NICKNAME="Filter image" NOTES="Taking the &quot;Raw&quot; image we loaded earlier in the workflow we apply a 2D median filter to each slice.&#10;&#10;The filtered image will be added to the workspace with the name &quot;Binary&quot;.  While this isn't a binarised image just yet, MIA allows us to change images in the workspace, thus avoiding wasting memory on intermediate images we no longer need." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Median 2D" VISIBLE="false"/><PARAMETER NAME="Filter radius" NICKNAME="Filter radius" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Filter radius 2" NICKNAME="Filter radius 2" VALUE="3.0" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Rolling filter method" NICKNAME="Rolling filter method" VALUE="Average" VISIBLE="false"/><PARAMETER NAME="Window indices" NICKNAME="Window indices" VALUE="-1-1" VISIBLE="false"/><PARAMETER NAME="Contour contrast" NICKNAME="Contour contrast" VALUE="Dark line" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.transform.ProjectImage" DISABLEABLE="false" ENABLED="true" ID="1636961855499" NAME="Project image" NICKNAME="Project image" NOTES="For the purpose of background subtraction we will create a minimum intensity Z-axis projection and subtract this from all slices (subtraction will be done in the next module).&#10;&#10;This module outputs the projected image (which is now a single slice) to the workspace as &quot;MinProjection&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="MinProjection" VISIBLE="false"/><PARAMETER NAME="Projection axis" NICKNAME="Projection axis" VALUE="Z" VISIBLE="false"/><PARAMETER NAME="Projection mode" NICKNAME="Projection mode" VALUE="Minimum" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.ImageCalculator" DISABLEABLE="false" ENABLED="true" ID="1636961888899" NAME="Image calculator" NICKNAME="Image calculator" NOTES="Subtracting the minimum intensity projection image from each slice of the &quot;Binary&quot; image.&#10;&#10;In this instance, &quot;Input image 1&quot; is a Z-stack and &quot;Input image 2&quot; is a single slice.  As such, the single slice will be subtracted from each slice of &quot;Binary&quot;.  If we had provided two Z-stacks of equal dimensions, the corresponding slices would have been subtracted (i.e. slice 5 subtracted from slice 5).&#10;&#10;Rather than create a new, background-subtracted image, the image stored in the workspace as &quot;Binary&quot; will be updated.  This prevents us unnecessarily creating new images and keeps the list of available images tidier." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image 1" NICKNAME="Input image 1" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Input image 2" NICKNAME="Input image 2" VALUE="MinProjection" VISIBLE="false"/><PARAMETER NAME="Overwrite mode" NICKNAME="Overwrite mode" VALUE="Overwrite image 1" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Output 32-bit image" NICKNAME="Output 32-bit image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Calculation method" NICKNAME="Calculation method" VALUE="Subtract image 2 from image 1" VISIBLE="false"/><PARAMETER NAME="Image 2 relative contribution" NICKNAME="Image 2 relative contribution" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set NaN values to zero" NICKNAME="Set NaN values to zero" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.threshold.GlobalAutoThreshold" DISABLEABLE="false" ENABLED="true" ID="1636961828208" NAME="Global auto-threshold" NICKNAME="Global auto-threshold" NOTES="Now binarising the filtered and background-subtracted image called &quot;Binary&quot;.&#10;&#10;As with the &quot;Image calculator&quot; module, we apply the changes from this module to the input image rather than storing them as a new image in the workspace.&#10;&#10;Modules dealing with binary images typically have the &quot;Binary logic&quot; control.  This determines whether objects are considered as white objects on a black background or as black objects on a white background.  In both cases, &quot;black&quot; corresponds to 0-intensity and &quot;white&quot; corresponds to 255 (irrespective of applied LUT)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output mode" NICKNAME="Output mode" VALUE="Calculate and apply" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Algorithm" NICKNAME="Algorithm" VALUE="Huang" VISIBLE="false"/><PARAMETER NAME="Threshold multiplier" NICKNAME="Threshold multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use lower threshold limit" NICKNAME="Use lower threshold limit" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Lower threshold limit" NICKNAME="Lower threshold limit" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Measure on objects" NICKNAME="Measure on objects" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" IMAGE_NAME="Binary" NAME="THRESHOLD // GLOBAL Huang" NICKNAME="THRESHOLD // GLOBAL Huang"/></IMAGE_MEASUREMENTS><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.binary.FillHoles" DISABLEABLE="false" ENABLED="true" ID="1636961945985" NAME="Fill holes" NICKNAME="Fill holes" NOTES="Performing a 3D fill holes operation on the binarised image.&#10;&#10;This module uses of the MorphoLibJ implementation of binary hole filling." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.binary.Watershed" DISABLEABLE="false" ENABLED="true" ID="1636961976414" NAME="Watershed transform" NICKNAME="Watershed transform" NOTES="Performing watershed segmentation to split adjacent nuclei which have become merged during filtering and binarisation.  &#10;&#10;This module uses of the MorphoLibJ implementation of watershed, wlhich allows us to optionally specify markers and the dynamic value (how aggressively regions are split down)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Use markers" NICKNAME="Use markers" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Input marker image" NICKNAME="Input marker image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Intensity mode" NICKNAME="Intensity mode" VALUE="Distance" VISIBLE="false"/><PARAMETER NAME="Intensity image" NICKNAME="Intensity image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Dynamic" NICKNAME="Dynamic" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Match Z to XY" NICKNAME="Match Z to XY" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.IdentifyObjects" DISABLEABLE="false" ENABLED="true" ID="1636962210444" NAME="Identify objects" NICKNAME="Identify objects" NOTES="Using connected components labelling to identify the nuclei as contiguous regions of &quot;foreground&quot; pixels (defined by the &quot;Binary logic&quot; parameter).&#10;&#10;This module takes an image from the workspace, but outputs a collection of objects.  Objects are stored as individual entities within the output collection.  Each object has its own set of coordinates and can be assigned relationships (to other objects) and measurements.&#10;&#10;Object coordinates can be stored using three different systems (Pointlist, Quadtree and Octree), each of which has uinque memory usage characterisics.  Other than memory usage, there should be no difference in between the systems.  Here we'll use &quot;Quadtree&quot; as it's generally more efficient for solid objects.  More information on these is provided at https://mianalysis.github.io.  " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output objects" NICKNAME="Output objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Identify as single object" NICKNAME="Identify as single object" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Volume type" NICKNAME="Volume type" VALUE="Quadtree" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum strip width (px)" NICKNAME="Minimum strip width (px)" VALUE="60" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.spatial.MeasureObjectShape" DISABLEABLE="false" ENABLED="true" ID="1636962319317" NAME="Measure object shape" NICKNAME="Measure object shape" NOTES="Calculating the volume of each object stored in the &quot;Nuclei&quot; collection.&#10;&#10;As with the image processing modules earlier in this workflow, the &quot;Measure object shape&quot; module can take any previously-generated objects as inputs.&#10;&#10;The selected measurements are calculated for each object in the &quot;Nuclei&quot; collection.  These measurements are stored with the relevant object and can be used in subsequent modules." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Measure volume" NICKNAME="Measure volume" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Measure projected area" NICKNAME="Measure projected area" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected diameter" NICKNAME="Measure projected diameter" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected perimeter" NICKNAME="Measure projected perimeter" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure 3D metrics" NICKNAME="Measure 3D metrics" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Surface area method" NICKNAME="Surface area method" VALUE="13 directions" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // BASE_AREA_(PX²)" NICKNAME="SHAPE // BASE_AREA_(PX²)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // BASE_AREA_(µm²)" NICKNAME="SHAPE // BASE_AREA_(µm²)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // HEIGHT_(SLICE)" NICKNAME="SHAPE // HEIGHT_(SLICE)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // HEIGHT_(µm)" NICKNAME="SHAPE // HEIGHT_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // N_VOXELS" NICKNAME="SHAPE // N_VOXELS" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // VOLUME_(PX³)" NICKNAME="SHAPE // VOLUME_(PX³)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // VOLUME_(µm³)" NICKNAME="SHAPE // VOLUME_(µm³)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByMeasurement" DISABLEABLE="true" ENABLED="true" ID="1636962353494" NAME="Based on measurement" NICKNAME="Volume filter" NOTES="With volume measurements now assigned to each object in the &quot;Nuclei&quot; collection, we can apply a filter to remove those smaller than a specified value.&#10;&#10;In this module, any &quot; Nuclei&quot; objects less than the specified &quot;Reference value&quot; will simply be removed from the collection (it is also possible to add them to a new collection using the &quot;Filter mode&quot; control).&#10;&#10;This is a useful operation to be displayed in MIA's &quot;Processing view&quot;, so the &quot;Reference value&quot; parameter has been selected as editable using the toggle to its right.&#10;&#10;By having &quot;Can be disabled&quot; selected at the top of the module page, processing view will display the enable/disable control.&#10;&#10;Finally, this module has been renamed from &quot;Based on measurement&quot; to &quot;Volume filter&quot; as this is more intuitive as to its purpose.  Modules (and parameters) can be renamed by right-clicking on their name." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Less than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="100" VISIBLE="true"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement to filter on" NICKNAME="Measurement to filter on" VALUE="SHAPE // VOLUME_(µm³)" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962497111" NAME="GUI separator" NICKNAME="Measurements" NOTES="Modules in this section are involved with additional measurements assigned to the detectetd nuclei." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.intensity.MeasureObjectIntensity" DISABLEABLE="false" ENABLED="true" ID="1636962461046" NAME="Measure object intensity" NICKNAME="Measure object intensity" NOTES="Measuring the intensity of the &quot;Raw&quot; image coincident with each &quot;Nuclei&quot; object.&#10;&#10;As with the &quot;Measure object shape&quot; module, this will make a separate measurement for each object in the collection.  In this case that measurement is the mean, min, max, sum and standard deviation of all pixel intensities coincident with the coordinates of each object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Measure weighted centre" NICKNAME="Measure weighted centre" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_MAX" NICKNAME="INTENSITY // Raw_MAX" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_MEAN" NICKNAME="INTENSITY // Raw_MEAN" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_MIN" NICKNAME="INTENSITY // Raw_MIN" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_STDEV" NICKNAME="INTENSITY // Raw_STDEV" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_SUM" NICKNAME="INTENSITY // Raw_SUM" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.process.FitLongestChord" DISABLEABLE="false" ENABLED="true" ID="1690970094383" NAME="Fit longest chord" NICKNAME="Fit longest chord" NOTES="Measuring the &quot;longest chord&quot; for each nucleus.  The longest chord is the longest straight line that can be placed between any two points on the surface of an object.  In other words, it is the maximum diameter." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Measure object width" NICKNAME="Measure object width" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure object orientation" NICKNAME="Measure object orientation" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store end points" NICKNAME="Store end points" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="LONGEST_CHORD // LENGTH (PX)" NICKNAME="LONGEST_CHORD // LENGTH (PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="LONGEST_CHORD // LENGTH (µm)" NICKNAME="LONGEST_CHORD // LENGTH (µm)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962505950" NAME="GUI separator" NICKNAME="Image output" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectFill" DISABLEABLE="false" ENABLED="true" ID="1636962635839" NAME="Add object fill" NICKNAME="Add object fill" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Measurement value" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="LONGEST_CHORD // LENGTH (µm)" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectOutline" DISABLEABLE="false" ENABLED="true" ID="1636962596250" NAME="Add object outline" NICKNAME="Add object outline" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.1"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reduce line complexity" NICKNAME="Reduce line complexity" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Line interpolation" NICKNAME="Line interpolation" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Line width" NICKNAME="Line width" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddLabels" DISABLEABLE="false" ENABLED="true" ID="1690970140097" NAME="Add labels" NICKNAME="Add labels" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Label mode" NICKNAME="Label mode" VALUE="ID" VISIBLE="false"/><PARAMETER NAME="Decimal places" NICKNAME="Decimal places" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Use scientific notation" NICKNAME="Use scientific notation" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Label size" NICKNAME="Label size" VALUE="10" VISIBLE="false"/><PARAMETER NAME="X-offset" NICKNAME="X-offset" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Y-offset" NICKNAME="Y-offset" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Centre text" NICKNAME="Centre text" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Child objects for label" NICKNAME="Child objects for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for label" NICKNAME="Parent object for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for label" NICKNAME="Partner objects for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for label" NICKNAME="Measurement for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Prefix" NICKNAME="Prefix" VALUE="" VISIBLE="false"/><PARAMETER NAME="Suffix" NICKNAME="Suffix" VALUE="" VISIBLE="false"/><PARAMETER NAME="Label position" NICKNAME="Label position" VALUE="Centre of object" VISIBLE="false"/><PARAMETER NAME="X-position measurement" NICKNAME="X-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Y-position measurement" NICKNAME="Y-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Z-position measurement" NICKNAME="Z-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="X-position" NICKNAME="X-position" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Y-position" NICKNAME="Y-position" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Z-position" NICKNAME="Z-position" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Render in all object slices" NICKNAME="Render in all object slices" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.ShowImage" DISABLEABLE="true" ENABLED="true" ID="1636962716078" NAME="Show image" NICKNAME="Show image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="true" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Display image" NICKNAME="Display image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Title mode" NICKNAME="Title mode" VALUE="Image name" VISIBLE="false"/><PARAMETER NAME="Quick normalisation" NICKNAME="Quick normalisation" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageSaver" DISABLEABLE="true" ENABLED="true" ID="1636962735245" NAME="Save image" NICKNAME="Save image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Save location" NICKNAME="Save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="File name (generic)" NICKNAME="File name (generic)" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Append series mode" NICKNAME="Append series mode" VALUE="Series number" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Add filename suffix" NICKNAME="Add filename suffix" VALUE="_overlay" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="File format" NICKNAME="File format" VALUE="TIF" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/><PARAMETER NAME="Save as RGB" NICKNAME="Save as RGB" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Compression mode" NICKNAME="Compression mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Quality (0-100)" NICKNAME="Quality (0-100)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Frame rate (fps)" NICKNAME="Frame rate (fps)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Flatten overlay" NICKNAME="Flatten overlay" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES></ROOT>
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8"?><ROOT MIA_VERSION="1.5.1"><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.InputControl" DISABLEABLE="false" ENABLED="true" ID="1636961347222" NAME="Input control" NICKNAME="Input control" NOTES="In &quot;Input control&quot; we specify the path to the file we wish to work on.  At this point, no images are actually being loaded into the workspace.  We will load the images in during the main part of the workflow, typically using the &quot;Load image&quot; module.  These can be inserted anywhere in the workflow, meaning we're not wasting memory by opening them before they're needed.&#10;&#10;Here, we can specify a single file or, if we wish to run in batch mode, a folder.  When dealing with folders we may not want to load all the files contained within.  Therefore, it's possible to add filters that will help us process only the images of interest.  In the example here, we've got it set to only load files with .tif extensions and to skip anything with &quot;_overlay&quot; in the name (these will be created by this workflow).&#10;&#10;In MIA, parameters can be made visible for users working in &quot;Processing view&quot; by clicking the button to the right of the parameter.  In this workflow, the &quot;Input path&quot; is one such visible parameter." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input path" NICKNAME="Input path" VALUE="/Users/sc13967/Documents/Programming/Java/mia-examples/Ex1_NucleiSegmentation" VISIBLE="true"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="All series" VISIBLE="false"/><PARAMETER NAME="Series list" NICKNAME="Series list" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Only load first file per folder" NICKNAME="Only load first file per folder" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only load first matching group" NICKNAME="Only load first matching group" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Pattern" NICKNAME="Pattern" VALUE="" VISIBLE="false"/><PARAMETER NAME="Spatial unit" NICKNAME="Spatial unit" VALUE="Micrometres" VISIBLE="false"/><PARAMETER NAME="Temporal unit" NICKNAME="Temporal unit" VALUE="Milliseconds" VISIBLE="false"/><PARAMETER NAME="Ignore case" NICKNAME="Ignore case" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add filter" NICKNAME="Add filter" VALUE="" VISIBLE="false"><COLLECTION><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Extension" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="tif" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (include)" VISIBLE="false"/></PARAMS><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Filename" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="_overlay" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (exclude)" VISIBLE="false"/></PARAMS></COLLECTION></PARAMETER><PARAMETER NAME="Simultaneous jobs" NICKNAME="Simultaneous jobs" VALUE="1" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Extension" NICKNAME="Extension"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="File" NICKNAME="File"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filename" NICKNAME="Filename"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filepath" NICKNAME="Filepath"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Series name" NICKNAME="Series name"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Series number" NICKNAME="Series number"/></METADATA></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.OutputControl" DISABLEABLE="false" ENABLED="true" ID="1636961347222" NAME="Output control" NICKNAME="Output control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Add variable" NICKNAME="Add variable" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Run macro" NICKNAME="Run macro" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Macro mode" NICKNAME="Macro mode" VALUE="Macro text" VISIBLE="false"/><PARAMETER NAME="Macro text" NICKNAME="Macro text" VALUE="run(&quot;Enable MIA Extensions&quot;);&#10;&#10;// Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID)." VISIBLE="false"/><PARAMETER NAME="Macro file" NICKNAME="Macro file" VALUE="" VISIBLE="false"/><PARAMETER NAME="Export mode" NICKNAME="Export mode" VALUE="All together" VISIBLE="false"/><PARAMETER NAME="Individual save location" NICKNAME="Individual save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Group save location" NICKNAME="Group save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file/folder name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Metadata item for grouping" NICKNAME="Metadata item for grouping" VALUE="" VISIBLE="false"/><PARAMETER NAME="Continuous data export" NICKNAME="Continuous data export" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Save every n files" NICKNAME="Save every n files" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Export summary" NICKNAME="Export summary" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Summary mode" NICKNAME="Summary mode" VALUE="Per input file" VISIBLE="false"/><PARAMETER NAME="Metadata item for summary" NICKNAME="Metadata item for summary" VALUE="" VISIBLE="false"/><PARAMETER NAME="Show object counts" NICKNAME="Show object counts" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Export individual objects" NICKNAME="Export individual objects" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962470785" NAME="GUI separator" NICKNAME="File loading" NOTES="These separators have no direct effect on the workflow.  Instead, they're simply to help visually break the workflow down into easy-to-understand sections.  &#10;&#10;Clicking the power icon to the left of the separator will disable all modules contained within this section.&#10;&#10;Sections can also be collapsed/expanded by clicking the arrows to the left or right of the separator name.  When collapsed, all modules will still be run." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1636961348488" NAME="Load image" NICKNAME="Load image" NOTES="&quot;Load image&quot; is the main module for loading images from file into the workspace.  In most cases, this will be from the &quot;Current file&quot; (i.e. the one selected in &quot;Input control&quot;); however, it is possible to use metadata values to load other images, although this will be covered in a later example.&#10;&#10;For multi-dimensional images it's possible to load of subset of channels, slices or timepoints.  This way we don't need to load the entire image into the computer's memory - something that can be very useful when dealing with largeimage stacks.  For example, we may only want the first channel or a particular subset of slices.&#10;&#10;In this example, &quot;Channels&quot;, &quot;Slices&quot; and &quot;Frames&quot; are all set to &quot;1-end&quot;, which will load every available image; however, subsets can be selected using ranges (e.g. &quot;4-7&quot;), comma-separated lists (e.g. &quot;1,5,6,7&quot;).&#10;&#10;Multiple &quot;Load image&quot; modules can be inserted into the workflow as and when they are required.  This also allows us to manage the memory being used at any time.&#10;&#10;This module will add an image called &quot;Raw&quot; to the workspace.  The image will then be accessible by all subsequent modules.  Although not done in this example workflow, images can be assigned measurement values.  Measurements can be exported to the final Excel file or used by subsequent modules." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="0.75" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="0.75" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962481633" NAME="GUI separator" NICKNAME="Segmentation" NOTES="The modules in this section deal with segmentation of the nuclei in 3D." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.FilterImage" DISABLEABLE="false" ENABLED="true" ID="1636961810491" NAME="Filter image" NICKNAME="Filter image" NOTES="Taking the &quot;Raw&quot; image we loaded earlier in the workflow we apply a 2D median filter to each slice.&#10;&#10;The filtered image will be added to the workspace with the name &quot;Binary&quot;.  While this isn't a binarised image just yet, MIA allows us to change images in the workspace, thus avoiding wasting memory on intermediate images we no longer need." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Median 2D" VISIBLE="false"/><PARAMETER NAME="Filter radius" NICKNAME="Filter radius" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Filter radius 2" NICKNAME="Filter radius 2" VALUE="3.0" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Rolling filter method" NICKNAME="Rolling filter method" VALUE="Average" VISIBLE="false"/><PARAMETER NAME="Window indices" NICKNAME="Window indices" VALUE="-1-1" VISIBLE="false"/><PARAMETER NAME="Contour contrast" NICKNAME="Contour contrast" VALUE="Dark line" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.transform.ProjectImage" DISABLEABLE="false" ENABLED="true" ID="1636961855499" NAME="Project image" NICKNAME="Project image" NOTES="For the purpose of background subtraction we will create a minimum intensity Z-axis projection and subtract this from all slices (subtraction will be done in the next module).&#10;&#10;This module outputs the projected image (which is now a single slice) to the workspace as &quot;MinProjection&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="MinProjection" VISIBLE="false"/><PARAMETER NAME="Projection axis" NICKNAME="Projection axis" VALUE="Z" VISIBLE="false"/><PARAMETER NAME="Projection mode" NICKNAME="Projection mode" VALUE="Minimum" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.ImageCalculator" DISABLEABLE="false" ENABLED="true" ID="1636961888899" NAME="Image calculator" NICKNAME="Image calculator" NOTES="Subtracting the minimum intensity projection image from each slice of the &quot;Binary&quot; image.&#10;&#10;In this instance, &quot;Input image 1&quot; is a Z-stack and &quot;Input image 2&quot; is a single slice.  As such, the single slice will be subtracted from each slice of &quot;Binary&quot;.  If we had provided two Z-stacks of equal dimensions, the corresponding slices would have been subtracted (i.e. slice 5 subtracted from slice 5).&#10;&#10;Rather than create a new, background-subtracted image, the image stored in the workspace as &quot;Binary&quot; will be updated.  This prevents us unnecessarily creating new images and keeps the list of available images tidier." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image 1" NICKNAME="Input image 1" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Input image 2" NICKNAME="Input image 2" VALUE="MinProjection" VISIBLE="false"/><PARAMETER NAME="Overwrite mode" NICKNAME="Overwrite mode" VALUE="Overwrite image 1" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Output 32-bit image" NICKNAME="Output 32-bit image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Calculation method" NICKNAME="Calculation method" VALUE="Subtract image 2 from image 1" VISIBLE="false"/><PARAMETER NAME="Image 2 relative contribution" NICKNAME="Image 2 relative contribution" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set NaN values to zero" NICKNAME="Set NaN values to zero" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.threshold.GlobalAutoThreshold" DISABLEABLE="false" ENABLED="true" ID="1636961828208" NAME="Global auto-threshold" NICKNAME="Global auto-threshold" NOTES="Now binarising the filtered and background-subtracted image called &quot;Binary&quot;.&#10;&#10;As with the &quot;Image calculator&quot; module, we apply the changes from this module to the input image rather than storing them as a new image in the workspace.&#10;&#10;Modules dealing with binary images typically have the &quot;Binary logic&quot; control.  This determines whether objects are considered as white objects on a black background or as black objects on a white background.  In both cases, &quot;black&quot; corresponds to 0-intensity and &quot;white&quot; corresponds to 255 (irrespective of applied LUT)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output mode" NICKNAME="Output mode" VALUE="Calculate and apply" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Algorithm" NICKNAME="Algorithm" VALUE="Huang" VISIBLE="false"/><PARAMETER NAME="Threshold multiplier" NICKNAME="Threshold multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use lower threshold limit" NICKNAME="Use lower threshold limit" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Lower threshold limit" NICKNAME="Lower threshold limit" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Measure on objects" NICKNAME="Measure on objects" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" IMAGE_NAME="Binary" NAME="THRESHOLD // GLOBAL Huang" NICKNAME="THRESHOLD // GLOBAL Huang"/></IMAGE_MEASUREMENTS><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.binary.FillHoles" DISABLEABLE="false" ENABLED="true" ID="1636961945985" NAME="Fill holes" NICKNAME="Fill holes" NOTES="Performing a 3D fill holes operation on the binarised image.&#10;&#10;This module uses of the MorphoLibJ implementation of binary hole filling." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.binary.Watershed" DISABLEABLE="false" ENABLED="true" ID="1636961976414" NAME="Watershed transform" NICKNAME="Watershed transform" NOTES="Performing watershed segmentation to split adjacent nuclei which have become merged during filtering and binarisation.  &#10;&#10;This module uses of the MorphoLibJ implementation of watershed, wlhich allows us to optionally specify markers and the dynamic value (how aggressively regions are split down)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Use markers" NICKNAME="Use markers" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Input marker image" NICKNAME="Input marker image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Intensity mode" NICKNAME="Intensity mode" VALUE="Distance" VISIBLE="false"/><PARAMETER NAME="Intensity image" NICKNAME="Intensity image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Dynamic" NICKNAME="Dynamic" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Match Z to XY" NICKNAME="Match Z to XY" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.IdentifyObjects" DISABLEABLE="false" ENABLED="true" ID="1636962210444" NAME="Identify objects" NICKNAME="Identify objects" NOTES="Using connected components labelling to identify the nuclei as contiguous regions of &quot;foreground&quot; pixels (defined by the &quot;Binary logic&quot; parameter).&#10;&#10;This module takes an image from the workspace, but outputs a collection of objects.  Objects are stored as individual entities within the output collection.  Each object has its own set of coordinates and can be assigned relationships (to other objects) and measurements.&#10;&#10;Object coordinates can be stored using three different systems (Pointlist, Quadtree and Octree), each of which has uinque memory usage characterisics.  Other than memory usage, there should be no difference in between the systems.  Here we'll use &quot;Quadtree&quot; as it's generally more efficient for solid objects.  More information on these is provided at https://mianalysis.github.io.  " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output objects" NICKNAME="Output objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Identify as single object" NICKNAME="Identify as single object" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Volume type" NICKNAME="Volume type" VALUE="Quadtree" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum strip width (px)" NICKNAME="Minimum strip width (px)" VALUE="60" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.spatial.MeasureObjectShape" DISABLEABLE="false" ENABLED="true" ID="1636962319317" NAME="Measure object shape" NICKNAME="Measure object shape" NOTES="Calculating the volume of each object stored in the &quot;Nuclei&quot; collection.&#10;&#10;As with the image processing modules earlier in this workflow, the &quot;Measure object shape&quot; module can take any previously-generated objects as inputs.&#10;&#10;The selected measurements are calculated for each object in the &quot;Nuclei&quot; collection.  These measurements are stored with the relevant object and can be used in subsequent modules." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Measure volume" NICKNAME="Measure volume" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Measure projected area" NICKNAME="Measure projected area" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected diameter" NICKNAME="Measure projected diameter" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected perimeter" NICKNAME="Measure projected perimeter" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure 3D metrics" NICKNAME="Measure 3D metrics" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Surface area method" NICKNAME="Surface area method" VALUE="13 directions" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // BASE_AREA_(PX²)" NICKNAME="SHAPE // BASE_AREA_(PX²)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // BASE_AREA_(µm²)" NICKNAME="SHAPE // BASE_AREA_(µm²)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // HEIGHT_(SLICE)" NICKNAME="SHAPE // HEIGHT_(SLICE)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // HEIGHT_(µm)" NICKNAME="SHAPE // HEIGHT_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // N_VOXELS" NICKNAME="SHAPE // N_VOXELS" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // VOLUME_(PX³)" NICKNAME="SHAPE // VOLUME_(PX³)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // VOLUME_(µm³)" NICKNAME="SHAPE // VOLUME_(µm³)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByMeasurement" DISABLEABLE="true" ENABLED="true" ID="1636962353494" NAME="Based on measurement" NICKNAME="Volume filter" NOTES="With volume measurements now assigned to each object in the &quot;Nuclei&quot; collection, we can apply a filter to remove those smaller than a specified value.&#10;&#10;In this module, any &quot; Nuclei&quot; objects less than the specified &quot;Reference value&quot; will simply be removed from the collection (it is also possible to add them to a new collection using the &quot;Filter mode&quot; control).&#10;&#10;This is a useful operation to be displayed in MIA's &quot;Processing view&quot;, so the &quot;Reference value&quot; parameter has been selected as editable using the toggle to its right.&#10;&#10;By having &quot;Can be disabled&quot; selected at the top of the module page, processing view will display the enable/disable control.&#10;&#10;Finally, this module has been renamed from &quot;Based on measurement&quot; to &quot;Volume filter&quot; as this is more intuitive as to its purpose.  Modules (and parameters) can be renamed by right-clicking on their name." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Less than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="100" VISIBLE="true"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement to filter on" NICKNAME="Measurement to filter on" VALUE="SHAPE // VOLUME_(µm³)" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962497111" NAME="GUI separator" NICKNAME="Measurements" NOTES="Modules in this section are involved with additional measurements assigned to the detectetd nuclei." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.intensity.MeasureObjectIntensity" DISABLEABLE="false" ENABLED="true" ID="1636962461046" NAME="Measure object intensity" NICKNAME="Measure object intensity" NOTES="Measuring the intensity of the &quot;Raw&quot; image coincident with each &quot;Nuclei&quot; object.&#10;&#10;As with the &quot;Measure object shape&quot; module, this will make a separate measurement for each object in the collection.  In this case that measurement is the mean, min, max, sum and standard deviation of all pixel intensities coincident with the coordinates of each object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Measure median intensity" NICKNAME="Measure median intensity" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure weighted centre" NICKNAME="Measure weighted centre" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_MAX" NICKNAME="INTENSITY // Raw_MAX" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_MEAN" NICKNAME="INTENSITY // Raw_MEAN" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_MIN" NICKNAME="INTENSITY // Raw_MIN" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_STDEV" NICKNAME="INTENSITY // Raw_STDEV" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="INTENSITY // Raw_SUM" NICKNAME="INTENSITY // Raw_SUM" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.process.FitLongestChord" DISABLEABLE="false" ENABLED="true" ID="1690970094383" NAME="Fit longest chord" NICKNAME="Fit longest chord" NOTES="Measuring the &quot;longest chord&quot; for each nucleus.  The longest chord is the longest straight line that can be placed between any two points on the surface of an object.  In other words, it is the maximum diameter." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Measure object width" NICKNAME="Measure object width" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure object orientation" NICKNAME="Measure object orientation" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store end points" NICKNAME="Store end points" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="LONGEST_CHORD // LENGTH (PX)" NICKNAME="LONGEST_CHORD // LENGTH (PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="LONGEST_CHORD // LENGTH (µm)" NICKNAME="LONGEST_CHORD // LENGTH (µm)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1636962505950" NAME="GUI separator" NICKNAME="Image output" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectFill" DISABLEABLE="false" ENABLED="true" ID="1636962635839" NAME="Add object fill" NICKNAME="Add object fill" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Measurement value" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="LONGEST_CHORD // LENGTH (µm)" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Raw" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectOutline" DISABLEABLE="false" ENABLED="true" ID="1636962596250" NAME="Add object outline" NICKNAME="Add object outline" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.1"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reduce line complexity" NICKNAME="Reduce line complexity" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Line interpolation" NICKNAME="Line interpolation" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Line width" NICKNAME="Line width" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddLabels" DISABLEABLE="false" ENABLED="true" ID="1690970140097" NAME="Add labels" NICKNAME="Add labels" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Label mode" NICKNAME="Label mode" VALUE="ID" VISIBLE="false"/><PARAMETER NAME="Decimal places" NICKNAME="Decimal places" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Use scientific notation" NICKNAME="Use scientific notation" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Label size" NICKNAME="Label size" VALUE="10" VISIBLE="false"/><PARAMETER NAME="X-offset" NICKNAME="X-offset" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Y-offset" NICKNAME="Y-offset" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Centre text" NICKNAME="Centre text" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Child objects for label" NICKNAME="Child objects for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for label" NICKNAME="Parent object for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for label" NICKNAME="Partner objects for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for label" NICKNAME="Measurement for label" VALUE="" VISIBLE="false"/><PARAMETER NAME="Prefix" NICKNAME="Prefix" VALUE="" VISIBLE="false"/><PARAMETER NAME="Suffix" NICKNAME="Suffix" VALUE="" VISIBLE="false"/><PARAMETER NAME="Label position" NICKNAME="Label position" VALUE="Centre of object" VISIBLE="false"/><PARAMETER NAME="X-position measurement" NICKNAME="X-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Y-position measurement" NICKNAME="Y-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Z-position measurement" NICKNAME="Z-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="X-position" NICKNAME="X-position" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Y-position" NICKNAME="Y-position" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Z-position" NICKNAME="Z-position" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Render in all object slices" NICKNAME="Render in all object slices" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.ShowImage" DISABLEABLE="true" ENABLED="true" ID="1636962716078" NAME="Show image" NICKNAME="Show image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="true" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Display image" NICKNAME="Display image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Title mode" NICKNAME="Title mode" VALUE="Image name" VISIBLE="false"/><PARAMETER NAME="Quick normalisation" NICKNAME="Quick normalisation" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageSaver" DISABLEABLE="true" ENABLED="true" ID="1636962735245" NAME="Save image" NICKNAME="Save image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Save location" NICKNAME="Save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="File name (generic)" NICKNAME="File name (generic)" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Append series mode" NICKNAME="Append series mode" VALUE="Series number" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Add filename suffix" NICKNAME="Add filename suffix" VALUE="_overlay" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="File format" NICKNAME="File format" VALUE="TIF" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/><PARAMETER NAME="Save as RGB" NICKNAME="Save as RGB" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Compression mode" NICKNAME="Compression mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Quality (0-100)" NICKNAME="Quality (0-100)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Frame rate (fps)" NICKNAME="Frame rate (fps)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Flatten overlay" NICKNAME="Flatten overlay" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES></ROOT>
\ No newline at end of file
diff --git a/Ex1_NucleiSegmentation/ExampleResults/Ex1_3DStack1_S1_overlay.tif b/Ex1_NucleiSegmentation/ExampleResults/Ex1_3DStack1_S1_overlay.tif
index f100d32..085ffbe 100644
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diff --git a/Ex1_NucleiSegmentation/ExampleResults/Ex1_3DStack2_S1_overlay.tif b/Ex1_NucleiSegmentation/ExampleResults/Ex1_3DStack2_S1_overlay.tif
index 6dd09f7..1351ebb 100644
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diff --git a/Ex1_NucleiSegmentation/ExampleResults/Ex1_NucleiSegmentation.xlsx b/Ex1_NucleiSegmentation/ExampleResults/Ex1_NucleiSegmentation.xlsx
index acf58ea..63a4b20 100644
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diff --git a/Ex2_ObjectTracking/Ex2_ObjectTracking.mia b/Ex2_ObjectTracking/Ex2_ObjectTracking.mia
index 6b2d3bc..dbaaa2c 100644
--- a/Ex2_ObjectTracking/Ex2_ObjectTracking.mia
+++ b/Ex2_ObjectTracking/Ex2_ObjectTracking.mia
@@ -1 +1 @@
-<?xml version="1.0" encoding="UTF-8"?><ROOT MIA_VERSION="1.4.2"><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.InputControl" DISABLEABLE="false" ENABLED="true" ID="1681799582733" NAME="Input control" NICKNAME="Input control" NOTES="The file used here is called &quot;Ex2_Cell-Image-Library-11813.tif&quot;, which shows a timelapse of yolk syncytial layer (YSL) nuclei.&#10;&#10;The timeseries is from the Cell Image Library (http://cellimagelibrary.org/images/11813)  and has the DOI 10.7295/W9CIL11813.  This timeseries was made available by Mark Cooper through Zebrafish - The Living Laboratory and is released under a CC BY-NC-SA 3.0 license." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input path" NICKNAME="Input path" VALUE="F:\Java Projects\mia-examples\Ex2_ObjectTracking\Ex2_Cell-Image-Library-11813.tif" VISIBLE="true"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="All series" VISIBLE="false"/><PARAMETER NAME="Series list" NICKNAME="Series list" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Only load first file per folder" NICKNAME="Only load first file per folder" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only load first matching group" NICKNAME="Only load first matching group" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Pattern" NICKNAME="Pattern" VALUE="" VISIBLE="false"/><PARAMETER NAME="Spatial unit" NICKNAME="Spatial unit" VALUE="Micrometres" VISIBLE="false"/><PARAMETER NAME="Temporal unit" NICKNAME="Temporal unit" VALUE="Milliseconds" VISIBLE="false"/><PARAMETER NAME="Ignore case" NICKNAME="Ignore case" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add filter" NICKNAME="Add filter" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Simultaneous jobs" NICKNAME="Simultaneous jobs" VALUE="1" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Extension" NICKNAME="Extension"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="File" NICKNAME="File"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filename" NICKNAME="Filename"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Filepath" NICKNAME="Filepath"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series name" NICKNAME="Series name"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series number" NICKNAME="Series number"/></METADATA></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.OutputControl" DISABLEABLE="false" ENABLED="true" ID="1681799582753" NAME="Output control" NICKNAME="Output control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Add variable" NICKNAME="Add variable" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Run macro" NICKNAME="Run macro" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Macro mode" NICKNAME="Macro mode" VALUE="Macro text" VISIBLE="false"/><PARAMETER NAME="Macro text" NICKNAME="Macro text" VALUE="run(&quot;Enable MIA Extensions&quot;);&#10;&#10;// Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID)." VISIBLE="false"/><PARAMETER NAME="Macro file" NICKNAME="Macro file" VALUE="" VISIBLE="false"/><PARAMETER NAME="Export mode" NICKNAME="Export mode" VALUE="All together" VISIBLE="false"/><PARAMETER NAME="Individual save location" NICKNAME="Individual save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Group save location" NICKNAME="Group save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file/folder name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Metadata item for grouping" NICKNAME="Metadata item for grouping" VALUE="" VISIBLE="false"/><PARAMETER NAME="Continuous data export" NICKNAME="Continuous data export" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Save every n files" NICKNAME="Save every n files" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Export summary" NICKNAME="Export summary" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Summary mode" NICKNAME="Summary mode" VALUE="Per input file" VISIBLE="false"/><PARAMETER NAME="Metadata item for summary" NICKNAME="Metadata item for summary" VALUE="" VISIBLE="false"/><PARAMETER NAME="Show object counts" NICKNAME="Show object counts" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Export individual objects" NICKNAME="Export individual objects" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694380717694" NAME="GUI separator" NICKNAME="File loading" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1681799584382" NAME="Load image" NICKNAME="Load image" NOTES="The first step in this workflow loads the timeseries into MIA's workspace.  &#10;&#10;Here, this timeseries is simply named &quot;Timeseries&quot;.&#10;&#10;All parameters are left as their default values, which will load all frames.&#10;&#10;Something to note is that the timeseries isn't spatially or temporally calibrated, so calibrations of &quot;1&quot; will be applied.  As such, any &quot;spatially calibrated&quot; measurements will actually be in pixel units." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Timeseries" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="4" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="4" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694380732098" NAME="GUI separator" NICKNAME="Detection and tracking" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.SpotDetection" DISABLEABLE="false" ENABLED="true" ID="1694378043371" NAME="Spot detection" NICKNAME="Spot detection" NOTES="The &quot;Spot detection&quot; module uses TrackMate's Laplacian of Gaussian (LoG) detector.&#10;&#10;With this module, each frame of the input timeseries is filtered using a LoG filter with the defined radius (specific in pixel units).  This enhances spot-like features of that particular size.&#10;&#10;From the filtered image, any peaks above the specified threshold will be identified as &quot;Nuclei&quot; objects, which are then added to MIA's workspace for use in downstream modules.  Objects output by the &quot;Spot detection&quot; module contain a single coordinate closest to the detected centre of the spot.&#10;&#10;Although not used here, if dealing with 3D timeseries, &quot;spots&quot; can either be detected on a per-slice basis or in 3D using the &quot;Detection mode&quot; parameter.&#10;&#10;" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Timeseries" VISIBLE="false"/><PARAMETER NAME="Output spot objects" NICKNAME="Output spot objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Do sub-pixel localisation" NICKNAME="Do sub-pixel localisation" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Median filtering" NICKNAME="Median filtering" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Radius" NICKNAME="Radius" VALUE="3" VISIBLE="false"/><PARAMETER NAME="Threshold" NICKNAME="Threshold" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Estimate spot size" NICKNAME="Estimate spot size" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // QUALITY" NICKNAME="SPOT_DETECT // QUALITY" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // RADIUS_(PX)" NICKNAME="SPOT_DETECT // RADIUS_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // RADIUS_(µm)" NICKNAME="SPOT_DETECT // RADIUS_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // X_CENTROID_(PX)" NICKNAME="SPOT_DETECT // X_CENTROID_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // X_CENTROID_(µm)" NICKNAME="SPOT_DETECT // X_CENTROID_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Y_CENTROID_(PX)" NICKNAME="SPOT_DETECT // Y_CENTROID_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Y_CENTROID_(µm)" NICKNAME="SPOT_DETECT // Y_CENTROID_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Z_CENTROID_(SLICE)" NICKNAME="SPOT_DETECT // Z_CENTROID_(SLICE)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Z_CENTROID_(µm)" NICKNAME="SPOT_DETECT // Z_CENTROID_(µm)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.relate.TrackObjects" DISABLEABLE="false" ENABLED="true" ID="1681800188542" NAME="Track objects" NICKNAME="Track objects" NOTES="Also using TrackMate, the &quot;Track objects&quot; module takes any previously-detected objects and links them through time.  Tracked objects can have been detected by any upstream module, not just the &quot;Spot detection&quot; module.&#10;&#10;For each detected track, a &quot;Track&quot; object will be created.  This object contains no coordinate information, but rather acts as a parent object to all the associated &quot;Input objects&quot;.  As such, each &quot;Nuclei&quot; object in that track is a child of the track object.  Here, the track objects are simply called &quot;Tracks&quot;.&#10;&#10;By default, the &quot;Track objects&quot; module will optimse the links based on the distance between object centroids.  It's also possible to allow tracks to go undetected for a certain number of frames (the &quot;Maximum number of missing frames&quot; parameter).&#10;&#10;Beyond minimising the overall distance between object centroids, the &quot;Track objects&quot; module also allows minimising metrics such as difference in object volume and difference in track orientation.  In this example, these additional weights have been disabled.  To learn more, please see the module documentation." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Output track objects" NICKNAME="Output track objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Linking method" NICKNAME="Linking method" VALUE="Centroid" VISIBLE="false"/><PARAMETER NAME="Minimum overlap" NICKNAME="Minimum overlap" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Maximum linking distance (px)" NICKNAME="Maximum linking distance (px)" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Maximum number of missing frames" NICKNAME="Maximum number of missing frames" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Frame gap weighting" NICKNAME="Frame gap weighting" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Favour established tracks" NICKNAME="Favour established tracks" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Track length weighting" NICKNAME="Track length weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use volume (minimise volume change)" NICKNAME="Use volume (minimise volume change)" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Volume weighting" NICKNAME="Volume weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Maximum volume change (px^3)" NICKNAME="Maximum volume change (px^3)" VALUE="1000" VISIBLE="false"/><PARAMETER NAME="Direction weighting mode" NICKNAME="Direction weighting mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Orientation range mode" NICKNAME="Orientation range mode" VALUE="-180 to 180 degs" VISIBLE="false"/><PARAMETER NAME="Preferred direction" NICKNAME="Preferred direction" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Direction tolerance" NICKNAME="Direction tolerance" VALUE="180" VISIBLE="false"/><PARAMETER NAME="Direction weighting" NICKNAME="Direction weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use measurement (minimise change)" NICKNAME="Use measurement (minimise change)" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement" NICKNAME="Measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement weighting" NICKNAME="Measurement weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Maximum measurement change" NICKNAME="Maximum measurement change" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACKING // NEXT_OBJECT_IN_TRACK_ID" NICKNAME="TRACKING // NEXT_OBJECT_IN_TRACK_ID" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACKING // PREVIOUS_OBJECT_IN_TRACK_ID" NICKNAME="TRACKING // PREVIOUS_OBJECT_IN_TRACK_ID" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ChildObjectCount" DISABLEABLE="false" ENABLED="true" ID="1694380001145" NAME="Child object count" NICKNAME="Child object count" NOTES="Badly-detected tracks may only contain a few points.  We can filter these out by calculating the number of child &quot;Nuclei&quot; objects associated with each &quot;Track&quot; object.&#10;&#10;The &quot;Child object count&quot; module adds a measurement to each parent object (the &quot;Track&quot; objects in this case) reporting how many children there are.&#10;&#10;Unlike normal measurements, the object count measurements are dynamic; that is, they're calculated live, so will keep track if children are added or remove from parent objects." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Child objects" NICKNAME="Child objects" VALUE="Nuclei" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="COUNT // Nuclei" NICKNAME="COUNT // Nuclei" OBJECT_NAME="Tracks"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByMeasurement" DISABLEABLE="false" ENABLED="true" ID="1694380010110" NAME="Based on measurement" NICKNAME="Minimum number of timepoints" NOTES="With the number of child &quot;Nuclei&quot; objects calculated for each &quot;Track&quot; object, we can use the &quot;Based on measurement&quot; object filter module (renamed here to &quot;Minimum number of timepoints&quot;) to remove any tracks which weren't present in each timepoints." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Less than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="5" VISIBLE="true"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement to filter on" NICKNAME="Measurement to filter on" VALUE="COUNT // Nuclei" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterWithWithoutParent" DISABLEABLE="false" ENABLED="true" ID="1694380029264" NAME="With / without parent" NICKNAME="With / without parent" NOTES="The previous module (&quot;Based on measurement&quot;) has removed the &quot;Track&quot; objects detected in too few timepoints; however, the child &quot;Nuclei&quot; objects are still present in the workspace.  &#10;&#10;To remove any &quot;Nuclei&quot; objects which no longer have associated tracks, we use the &quot;With/without parent&quot; module." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Remove objects without parent" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Store filter results" NICKNAME="Store filter results" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694386967593" NAME="GUI separator" NICKNAME="Detection and tracking" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.spatial.MeasureTrackMotion" DISABLEABLE="false" ENABLED="true" ID="1694379447949" NAME="Measure track motion" NICKNAME="Measure track motion" NOTES="We've now got our final set of tracks, so can measure track motion metrics.  We will export some of the these to the Excel spreadsheet and also use them to colour-code the track overlay image.&#10;&#10;This module assigns measurements to both the track objects (metrics that summarise the overall track, like total path length) and also to the individual timepoint objects (instantaneous metrics, such as the velocity at that point in time)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input track objects" NICKNAME="Input track objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Input spot objects" NICKNAME="Input spot objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Subtract average motion" NICKNAME="Subtract average motion" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Identify leading point" NICKNAME="Identify leading point" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Orientation mode" NICKNAME="Orientation mode" VALUE="Relative to both points" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ANGULAR_PERSISTENCE" NICKNAME="TRACK_ANALYSIS // ANGULAR_PERSISTENCE" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(PX)" NICKNAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(µm)" NICKNAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // DETECTION_FRACTION" NICKNAME="TRACK_ANALYSIS // DETECTION_FRACTION" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // DIRECTIONALITY_RATIO" NICKNAME="TRACK_ANALYSIS // DIRECTIONALITY_RATIO" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // DURATION_(FRAMES)" NICKNAME="TRACK_ANALYSIS // DURATION_(FRAMES)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(PX)" NICKNAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(PX)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(µm)" NICKNAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(µm)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // FIRST_FRAME" NICKNAME="TRACK_ANALYSIS // FIRST_FRAME" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(PX/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(µm/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // LAST_FRAME" NICKNAME="TRACK_ANALYSIS // LAST_FRAME" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(PX/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(PX/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(PX/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(SLICES/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(SLICES/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // RELATIVE_FRAME" NICKNAME="TRACK_ANALYSIS // RELATIVE_FRAME" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ROLLING_DIRECTIONALITY_RATIO" NICKNAME="TRACK_ANALYSIS // ROLLING_DIRECTIONALITY_RATIO" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(PX)" NICKNAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(µm)" NICKNAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(PX)" NICKNAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(PX)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(µm)" NICKNAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(µm)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // X_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // X_VELOCITY_(PX/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // X_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // X_VELOCITY_(µm/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Y_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // Y_VELOCITY_(PX/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Y_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // Y_VELOCITY_(µm/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Z_VELOCITY_(SLICES/FRAME)" NICKNAME="TRACK_ANALYSIS // Z_VELOCITY_(SLICES/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Z_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // Z_VELOCITY_(µm/FRAME)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ObjectTimepoint" DISABLEABLE="false" ENABLED="true" ID="1694385111946" NAME="Object timepoint" NICKNAME="Object timepoint" NOTES="Another optional measurement we want to add to the results spreadsheet is the timepoint in which each &quot;Nuclei&quot; object exists.  This is added by the &quot;Object timepoint&quot; module." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TIMEPOINT" NICKNAME="TIMEPOINT" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ParentObjectID" DISABLEABLE="false" ENABLED="true" ID="1694386949013" NAME="Parent object ID" NICKNAME="Parent object ID" NOTES="One final measurement we may want is to add the parent &quot;Track&quot; ID number for each &quot;Nuclei&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Tracks" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="false" EXPORT_MIN="false" EXPORT_STD="false" EXPORT_SUM="false" NAME="PARENT_ID // Tracks" NICKNAME="PARENT_ID // Tracks" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694380715624" NAME="GUI separator" NICKNAME="Image output" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddTracks" DISABLEABLE="false" ENABLED="true" ID="1694379013734" NAME="Add tracks" NICKNAME="Add tracks" NOTES="Tracks can be rendered in 2D as lines in ImageJ overlays.&#10;&#10;The tracks can be coloured many different ways, but here we'll do it based on the instantaneous velocity of each track (a measurement associated with each &quot;Nuclei&quot; object).&#10;&#10;To prevent the overlay getting too crowded, the &quot;Limit track history&quot; option is enabled.  This only shows tracks from a specified number of most recent frames (here, 10 frames)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Instantaneous measurement value" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(µm/FRAME)" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Timeseries" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Spot objects" NICKNAME="Spot objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Limit track history" NICKNAME="Limit track history" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Track history (frames)" NICKNAME="Track history (frames)" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Line width" NICKNAME="Line width" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.ShowImage" DISABLEABLE="true" ENABLED="true" ID="1694380685577" NAME="Show image" NICKNAME="Show image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="true" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Display image" NICKNAME="Display image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Title mode" NICKNAME="Title mode" VALUE="Image name" VISIBLE="false"/><PARAMETER NAME="Quick normalisation" NICKNAME="Quick normalisation" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageSaver" DISABLEABLE="false" ENABLED="true" ID="1694380685577" NAME="Save image" NICKNAME="Save image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Save location" NICKNAME="Save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="File name (generic)" NICKNAME="File name (generic)" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Append series mode" NICKNAME="Append series mode" VALUE="Series number" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Add filename suffix" NICKNAME="Add filename suffix" VALUE="_overlay" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="File format" NICKNAME="File format" VALUE="TIF" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/><PARAMETER NAME="Save as RGB" NICKNAME="Save as RGB" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Compression mode" NICKNAME="Compression mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Quality (0-100)" NICKNAME="Quality (0-100)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Frame rate (fps)" NICKNAME="Frame rate (fps)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Flatten overlay" NICKNAME="Flatten overlay" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES></ROOT>
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8"?><ROOT MIA_VERSION="1.5.1"><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.InputControl" DISABLEABLE="false" ENABLED="true" ID="1681799582733" NAME="Input control" NICKNAME="Input control" NOTES="The file used here is called &quot;Ex2_Cell-Image-Library-11813.tif&quot;, which shows a timelapse of yolk syncytial layer (YSL) nuclei.&#10;&#10;The timeseries is from the Cell Image Library (http://cellimagelibrary.org/images/11813)  and has the DOI 10.7295/W9CIL11813.  This timeseries was made available by Mark Cooper through Zebrafish - The Living Laboratory and is released under a CC BY-NC-SA 3.0 license." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input path" NICKNAME="Input path" VALUE="/Users/sc13967/Documents/Programming/Java/mia-examples/Ex2_ObjectTracking/Ex2_Cell-Image-Library-11813.tif" VISIBLE="true"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="All series" VISIBLE="false"/><PARAMETER NAME="Series list" NICKNAME="Series list" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Only load first file per folder" NICKNAME="Only load first file per folder" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only load first matching group" NICKNAME="Only load first matching group" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Pattern" NICKNAME="Pattern" VALUE="" VISIBLE="false"/><PARAMETER NAME="Spatial unit" NICKNAME="Spatial unit" VALUE="Micrometres" VISIBLE="false"/><PARAMETER NAME="Temporal unit" NICKNAME="Temporal unit" VALUE="Milliseconds" VISIBLE="false"/><PARAMETER NAME="Ignore case" NICKNAME="Ignore case" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add filter" NICKNAME="Add filter" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Simultaneous jobs" NICKNAME="Simultaneous jobs" VALUE="1" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Extension" NICKNAME="Extension"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="File" NICKNAME="File"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filename" NICKNAME="Filename"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Filepath" NICKNAME="Filepath"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series name" NICKNAME="Series name"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series number" NICKNAME="Series number"/></METADATA></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.OutputControl" DISABLEABLE="false" ENABLED="true" ID="1681799582753" NAME="Output control" NICKNAME="Output control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Add variable" NICKNAME="Add variable" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Run macro" NICKNAME="Run macro" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Macro mode" NICKNAME="Macro mode" VALUE="Macro text" VISIBLE="false"/><PARAMETER NAME="Macro text" NICKNAME="Macro text" VALUE="run(&quot;Enable MIA Extensions&quot;);&#10;&#10;// Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID)." VISIBLE="false"/><PARAMETER NAME="Macro file" NICKNAME="Macro file" VALUE="" VISIBLE="false"/><PARAMETER NAME="Export mode" NICKNAME="Export mode" VALUE="All together" VISIBLE="false"/><PARAMETER NAME="Individual save location" NICKNAME="Individual save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Group save location" NICKNAME="Group save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file/folder name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Metadata item for grouping" NICKNAME="Metadata item for grouping" VALUE="" VISIBLE="false"/><PARAMETER NAME="Continuous data export" NICKNAME="Continuous data export" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Save every n files" NICKNAME="Save every n files" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Export summary" NICKNAME="Export summary" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Summary mode" NICKNAME="Summary mode" VALUE="Per input file" VISIBLE="false"/><PARAMETER NAME="Metadata item for summary" NICKNAME="Metadata item for summary" VALUE="" VISIBLE="false"/><PARAMETER NAME="Show object counts" NICKNAME="Show object counts" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Export individual objects" NICKNAME="Export individual objects" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694380717694" NAME="GUI separator" NICKNAME="File loading" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1681799584382" NAME="Load image" NICKNAME="Load image" NOTES="The first step in this workflow loads the timeseries into MIA's workspace.  &#10;&#10;Here, this timeseries is simply named &quot;Timeseries&quot;.&#10;&#10;All parameters are left as their default values, which will load all frames.&#10;&#10;Something to note is that the timeseries isn't spatially or temporally calibrated, so calibrations of &quot;1&quot; will be applied.  As such, any &quot;spatially calibrated&quot; measurements will actually be in pixel units." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Timeseries" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="512" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="4" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="4" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694380732098" NAME="GUI separator" NICKNAME="Detection and tracking" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.SpotDetection" DISABLEABLE="false" ENABLED="true" ID="1694378043371" NAME="Spot detection" NICKNAME="Spot detection" NOTES="The &quot;Spot detection&quot; module uses TrackMate's Laplacian of Gaussian (LoG) detector.&#10;&#10;With this module, each frame of the input timeseries is filtered using a LoG filter with the defined radius (specific in pixel units).  This enhances spot-like features of that particular size.&#10;&#10;From the filtered image, any peaks above the specified threshold will be identified as &quot;Nuclei&quot; objects, which are then added to MIA's workspace for use in downstream modules.  Objects output by the &quot;Spot detection&quot; module contain a single coordinate closest to the detected centre of the spot.&#10;&#10;Although not used here, if dealing with 3D timeseries, &quot;spots&quot; can either be detected on a per-slice basis or in 3D using the &quot;Detection mode&quot; parameter.&#10;&#10;" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Timeseries" VISIBLE="false"/><PARAMETER NAME="Output spot objects" NICKNAME="Output spot objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Do sub-pixel localisation" NICKNAME="Do sub-pixel localisation" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Median filtering" NICKNAME="Median filtering" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Radius" NICKNAME="Radius" VALUE="3" VISIBLE="false"/><PARAMETER NAME="Threshold" NICKNAME="Threshold" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Estimate spot size" NICKNAME="Estimate spot size" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // QUALITY" NICKNAME="SPOT_DETECT // QUALITY" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // RADIUS_(PX)" NICKNAME="SPOT_DETECT // RADIUS_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // RADIUS_(µm)" NICKNAME="SPOT_DETECT // RADIUS_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // X_CENTROID_(PX)" NICKNAME="SPOT_DETECT // X_CENTROID_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // X_CENTROID_(µm)" NICKNAME="SPOT_DETECT // X_CENTROID_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Y_CENTROID_(PX)" NICKNAME="SPOT_DETECT // Y_CENTROID_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Y_CENTROID_(µm)" NICKNAME="SPOT_DETECT // Y_CENTROID_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Z_CENTROID_(SLICE)" NICKNAME="SPOT_DETECT // Z_CENTROID_(SLICE)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SPOT_DETECT // Z_CENTROID_(µm)" NICKNAME="SPOT_DETECT // Z_CENTROID_(µm)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.relate.TrackObjects" DISABLEABLE="false" ENABLED="true" ID="1681800188542" NAME="Track objects" NICKNAME="Track objects" NOTES="Also using TrackMate, the &quot;Track objects&quot; module takes any previously-detected objects and links them through time.  Tracked objects can have been detected by any upstream module, not just the &quot;Spot detection&quot; module.&#10;&#10;For each detected track, a &quot;Track&quot; object will be created.  This object contains no coordinate information, but rather acts as a parent object to all the associated &quot;Input objects&quot;.  As such, each &quot;Nuclei&quot; object in that track is a child of the track object.  Here, the track objects are simply called &quot;Tracks&quot;.&#10;&#10;By default, the &quot;Track objects&quot; module will optimse the links based on the distance between object centroids.  It's also possible to allow tracks to go undetected for a certain number of frames (the &quot;Maximum number of missing frames&quot; parameter).&#10;&#10;Beyond minimising the overall distance between object centroids, the &quot;Track objects&quot; module also allows minimising metrics such as difference in object volume and difference in track orientation.  In this example, these additional weights have been disabled.  To learn more, please see the module documentation." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Output track objects" NICKNAME="Output track objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Linking method" NICKNAME="Linking method" VALUE="Centroid" VISIBLE="false"/><PARAMETER NAME="Minimum overlap" NICKNAME="Minimum overlap" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Maximum linking distance (px)" NICKNAME="Maximum linking distance (px)" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Maximum number of missing frames" NICKNAME="Maximum number of missing frames" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Frame gap weighting" NICKNAME="Frame gap weighting" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Favour established tracks" NICKNAME="Favour established tracks" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Track length weighting" NICKNAME="Track length weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use volume (minimise volume change)" NICKNAME="Use volume (minimise volume change)" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Volume weighting" NICKNAME="Volume weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Maximum volume change (px^3)" NICKNAME="Maximum volume change (px^3)" VALUE="1000" VISIBLE="false"/><PARAMETER NAME="Direction weighting mode" NICKNAME="Direction weighting mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Orientation range mode" NICKNAME="Orientation range mode" VALUE="-180 to 180 degs" VISIBLE="false"/><PARAMETER NAME="Preferred direction" NICKNAME="Preferred direction" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Direction tolerance" NICKNAME="Direction tolerance" VALUE="180" VISIBLE="false"/><PARAMETER NAME="Direction weighting" NICKNAME="Direction weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use measurement (minimise change)" NICKNAME="Use measurement (minimise change)" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement" NICKNAME="Measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement weighting" NICKNAME="Measurement weighting" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Maximum measurement change" NICKNAME="Maximum measurement change" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACKING // NEXT_OBJECT_IN_TRACK_ID" NICKNAME="TRACKING // NEXT_OBJECT_IN_TRACK_ID" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACKING // PREVIOUS_OBJECT_IN_TRACK_ID" NICKNAME="TRACKING // PREVIOUS_OBJECT_IN_TRACK_ID" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ChildObjectCount" DISABLEABLE="false" ENABLED="true" ID="1694380001145" NAME="Child object count" NICKNAME="Child object count" NOTES="Badly-detected tracks may only contain a few points.  We can filter these out by calculating the number of child &quot;Nuclei&quot; objects associated with each &quot;Track&quot; object.&#10;&#10;The &quot;Child object count&quot; module adds a measurement to each parent object (the &quot;Track&quot; objects in this case) reporting how many children there are.&#10;&#10;Unlike normal measurements, the object count measurements are dynamic; that is, they're calculated live, so will keep track if children are added or remove from parent objects." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Child objects" NICKNAME="Child objects" VALUE="Nuclei" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="COUNT // Nuclei" NICKNAME="COUNT // Nuclei" OBJECT_NAME="Tracks"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByMeasurement" DISABLEABLE="false" ENABLED="true" ID="1694380010110" NAME="Based on measurement" NICKNAME="Minimum number of timepoints" NOTES="With the number of child &quot;Nuclei&quot; objects calculated for each &quot;Track&quot; object, we can use the &quot;Based on measurement&quot; object filter module (renamed here to &quot;Minimum number of timepoints&quot;) to remove any tracks which weren't present in each timepoints." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Less than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="5" VISIBLE="true"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement to filter on" NICKNAME="Measurement to filter on" VALUE="COUNT // Nuclei" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterWithWithoutParent" DISABLEABLE="false" ENABLED="true" ID="1694380029264" NAME="With / without parent" NICKNAME="With / without parent" NOTES="The previous module (&quot;Based on measurement&quot;) has removed the &quot;Track&quot; objects detected in too few timepoints; however, the child &quot;Nuclei&quot; objects are still present in the workspace.  &#10;&#10;To remove any &quot;Nuclei&quot; objects which no longer have associated tracks, we use the &quot;With/without parent&quot; module." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Remove objects without parent" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Store filter results" NICKNAME="Store filter results" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694386967593" NAME="GUI separator" NICKNAME="Detection and tracking" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.spatial.MeasureTrackMotion" DISABLEABLE="false" ENABLED="true" ID="1694379447949" NAME="Measure track motion" NICKNAME="Measure track motion" NOTES="We've now got our final set of tracks, so can measure track motion metrics.  We will export some of the these to the Excel spreadsheet and also use them to colour-code the track overlay image.&#10;&#10;This module assigns measurements to both the track objects (metrics that summarise the overall track, like total path length) and also to the individual timepoint objects (instantaneous metrics, such as the velocity at that point in time)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input track objects" NICKNAME="Input track objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Input spot objects" NICKNAME="Input spot objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Position mode" NICKNAME="Position mode" VALUE="Object centroid" VISIBLE="false"/><PARAMETER NAME="X-position measurement" NICKNAME="X-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Y-position measurement" NICKNAME="Y-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Z-position measurement" NICKNAME="Z-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Subtract average motion" NICKNAME="Subtract average motion" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Identify leading point" NICKNAME="Identify leading point" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Orientation mode" NICKNAME="Orientation mode" VALUE="Relative to both points" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ANGULAR_PERSISTENCE" NICKNAME="TRACK_ANALYSIS // ANGULAR_PERSISTENCE" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(PX)" NICKNAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(µm)" NICKNAME="TRACK_ANALYSIS // CUMULATIVE_PATH_LENGTH_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // DETECTION_FRACTION" NICKNAME="TRACK_ANALYSIS // DETECTION_FRACTION" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // DIRECTIONALITY_RATIO" NICKNAME="TRACK_ANALYSIS // DIRECTIONALITY_RATIO" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // DURATION_(FRAMES)" NICKNAME="TRACK_ANALYSIS // DURATION_(FRAMES)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(PX)" NICKNAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(PX)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(µm)" NICKNAME="TRACK_ANALYSIS // EUCLIDEAN_DISTANCE_(µm)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // FIRST_FRAME" NICKNAME="TRACK_ANALYSIS // FIRST_FRAME" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(PX/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(µm/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // LAST_FRAME" NICKNAME="TRACK_ANALYSIS // LAST_FRAME" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(PX/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_INSTANTANEOUS_SPEED_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(PX/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_X_VELOCITY_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(PX/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Y_VELOCITY_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(SLICES/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(SLICES/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // MEAN_Z_VELOCITY_(µm/FRAME)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // RELATIVE_FRAME" NICKNAME="TRACK_ANALYSIS // RELATIVE_FRAME" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ROLLING_DIRECTIONALITY_RATIO" NICKNAME="TRACK_ANALYSIS // ROLLING_DIRECTIONALITY_RATIO" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(PX)" NICKNAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(PX)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(µm)" NICKNAME="TRACK_ANALYSIS // ROLLING_EUCLIDEAN_DISTANCE_(µm)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(PX)" NICKNAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(PX)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(µm)" NICKNAME="TRACK_ANALYSIS // TOTAL_PATH_LENGTH_(µm)" OBJECT_NAME="Tracks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // X_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // X_VELOCITY_(PX/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // X_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // X_VELOCITY_(µm/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Y_VELOCITY_(PX/FRAME)" NICKNAME="TRACK_ANALYSIS // Y_VELOCITY_(PX/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Y_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // Y_VELOCITY_(µm/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Z_VELOCITY_(SLICES/FRAME)" NICKNAME="TRACK_ANALYSIS // Z_VELOCITY_(SLICES/FRAME)" OBJECT_NAME="Nuclei"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TRACK_ANALYSIS // Z_VELOCITY_(µm/FRAME)" NICKNAME="TRACK_ANALYSIS // Z_VELOCITY_(µm/FRAME)" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ObjectTimepoint" DISABLEABLE="false" ENABLED="true" ID="1694385111946" NAME="Object timepoint" NICKNAME="Object timepoint" NOTES="Another optional measurement we want to add to the results spreadsheet is the timepoint in which each &quot;Nuclei&quot; object exists.  This is added by the &quot;Object timepoint&quot; module." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="TIMEPOINT" NICKNAME="TIMEPOINT" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ParentObjectID" DISABLEABLE="false" ENABLED="true" ID="1694386949013" NAME="Parent object ID" NICKNAME="Parent object ID" NOTES="One final measurement we may want is to add the parent &quot;Track&quot; ID number for each &quot;Nuclei&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Tracks" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="false" EXPORT_MIN="false" EXPORT_STD="false" EXPORT_SUM="false" NAME="PARENT_ID // Tracks" NICKNAME="PARENT_ID // Tracks" OBJECT_NAME="Nuclei"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694380715624" NAME="GUI separator" NICKNAME="Image output" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddTracks" DISABLEABLE="false" ENABLED="true" ID="1694379013734" NAME="Add tracks" NICKNAME="Add tracks" NOTES="Tracks can be rendered in 2D as lines in ImageJ overlays.&#10;&#10;The tracks can be coloured many different ways, but here we'll do it based on the instantaneous velocity of each track (a measurement associated with each &quot;Nuclei&quot; object).&#10;&#10;To prevent the overlay getting too crowded, the &quot;Limit track history&quot; option is enabled.  This only shows tracks from a specified number of most recent frames (here, 10 frames)." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Instantaneous measurement value" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="White" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="TRACK_ANALYSIS // INSTANTANEOUS_SPEED_(µm/FRAME)" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Timeseries" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Tracks" VISIBLE="false"/><PARAMETER NAME="Spot objects" NICKNAME="Spot objects" VALUE="Nuclei" VISIBLE="false"/><PARAMETER NAME="Position mode" NICKNAME="Position mode" VALUE="Object centroid" VISIBLE="false"/><PARAMETER NAME="X-position measurement" NICKNAME="X-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Y-position measurement" NICKNAME="Y-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Z-position measurement" NICKNAME="Z-position measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Limit track history" NICKNAME="Limit track history" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Track history (frames)" NICKNAME="Track history (frames)" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Line width" NICKNAME="Line width" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.ShowImage" DISABLEABLE="true" ENABLED="true" ID="1694380685577" NAME="Show image" NICKNAME="Show image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="true" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Display image" NICKNAME="Display image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Title mode" NICKNAME="Title mode" VALUE="Image name" VISIBLE="false"/><PARAMETER NAME="Quick normalisation" NICKNAME="Quick normalisation" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageSaver" DISABLEABLE="false" ENABLED="true" ID="1694380685577" NAME="Save image" NICKNAME="Save image" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Save location" NICKNAME="Save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="File name (generic)" NICKNAME="File name (generic)" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Append series mode" NICKNAME="Append series mode" VALUE="Series number" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Add filename suffix" NICKNAME="Add filename suffix" VALUE="_overlay" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="File format" NICKNAME="File format" VALUE="TIF" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/><PARAMETER NAME="Save as RGB" NICKNAME="Save as RGB" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Compression mode" NICKNAME="Compression mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Quality (0-100)" NICKNAME="Quality (0-100)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Frame rate (fps)" NICKNAME="Frame rate (fps)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Flatten overlay" NICKNAME="Flatten overlay" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES></ROOT>
\ No newline at end of file
diff --git a/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813.xlsx b/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813.xlsx
index c52f976..708ecd8 100644
Binary files a/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813.xlsx and b/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813.xlsx differ
diff --git a/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813_S1_overlay.tif b/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813_S1_overlay.tif
index 1c4cc3f..c1b8ab8 100644
Binary files a/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813_S1_overlay.tif and b/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813_S1_overlay.tif differ
diff --git a/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813_S1_tracks.avi b/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813_S1_tracks.avi
new file mode 100644
index 0000000..4965b09
Binary files /dev/null and b/Ex2_ObjectTracking/ExampleResults/Ex2_Cell-Image-Library-11813_S1_tracks.avi differ
diff --git a/Ex3_Skeletonisation/Ex3_Skeletonisation.mia b/Ex3_Skeletonisation/Ex3_Skeletonisation.mia
index a5acae3..73faa87 100644
--- a/Ex3_Skeletonisation/Ex3_Skeletonisation.mia
+++ b/Ex3_Skeletonisation/Ex3_Skeletonisation.mia
@@ -1 +1 @@
-<?xml version="1.0" encoding="UTF-8"?><ROOT MIA_VERSION="1.4.2"><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.InputControl" DISABLEABLE="false" ENABLED="true" ID="1638297565958" NAME="Input control" NICKNAME="Input control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input path" NICKNAME="Input path" VALUE="F:\Java Projects\mia-examples\Ex3_Skeletonisation\Ex3_Skeletonisation.tif" VISIBLE="true"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="All series" VISIBLE="false"/><PARAMETER NAME="Series list" NICKNAME="Series list" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Only load first file per folder" NICKNAME="Only load first file per folder" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only load first matching group" NICKNAME="Only load first matching group" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Pattern" NICKNAME="Pattern" VALUE="" VISIBLE="false"/><PARAMETER NAME="Spatial unit" NICKNAME="Spatial unit" VALUE="Micrometres" VISIBLE="false"/><PARAMETER NAME="Temporal unit" NICKNAME="Temporal unit" VALUE="Milliseconds" VISIBLE="false"/><PARAMETER NAME="Ignore case" NICKNAME="Ignore case" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add filter" NICKNAME="Add filter" VALUE="" VISIBLE="false"><COLLECTION><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Extension" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="tif" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (include)" VISIBLE="false"/></PARAMS><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Filename" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="_overlay" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (exclude)" VISIBLE="false"/></PARAMS></COLLECTION></PARAMETER><PARAMETER NAME="Simultaneous jobs" NICKNAME="Simultaneous jobs" VALUE="1" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Extension" NICKNAME="Extension"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="File" NICKNAME="File"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filename" NICKNAME="Filename"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filepath" NICKNAME="Filepath"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series name" NICKNAME="Series name"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series number" NICKNAME="Series number"/></METADATA></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.OutputControl" DISABLEABLE="false" ENABLED="true" ID="1638297565958" NAME="Output control" NICKNAME="Output control" NOTES="Configuring the exported Excel spreadsheet.  This will spreadsheet report the length of both the individual and network DNA ovjects. " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Add variable" NICKNAME="Add variable" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Run macro" NICKNAME="Run macro" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Macro mode" NICKNAME="Macro mode" VALUE="Macro text" VISIBLE="false"/><PARAMETER NAME="Macro text" NICKNAME="Macro text" VALUE="run(&quot;Enable MIA Extensions&quot;);&#10;&#10;// Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID)." VISIBLE="false"/><PARAMETER NAME="Macro file" NICKNAME="Macro file" VALUE="" VISIBLE="false"/><PARAMETER NAME="Export mode" NICKNAME="Export mode" VALUE="All together" VISIBLE="false"/><PARAMETER NAME="Individual save location" NICKNAME="Individual save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Group save location" NICKNAME="Group save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file/folder name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Metadata item for grouping" NICKNAME="Metadata item for grouping" VALUE="" VISIBLE="false"/><PARAMETER NAME="Continuous data export" NICKNAME="Continuous data export" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Save every n files" NICKNAME="Save every n files" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Export summary" NICKNAME="Export summary" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Summary mode" NICKNAME="Summary mode" VALUE="Per input file" VISIBLE="false"/><PARAMETER NAME="Metadata item for summary" NICKNAME="Metadata item for summary" VALUE="" VISIBLE="false"/><PARAMETER NAME="Show object counts" NICKNAME="Show object counts" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Export individual objects" NICKNAME="Export individual objects" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925729349" NAME="GUI separator" NICKNAME="File loading" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1638297567118" NAME="Load image" NICKNAME="Load image" NOTES="In this standard image loading module we're loading the AFM image of DNA to the MIA workspace with the name &quot;Image&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Image" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="384" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="287" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="640" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="640" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925848319" NAME="GUI separator" NICKNAME="Detect DNA" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.FilterImage" DISABLEABLE="false" ENABLED="true" ID="1694706310794" NAME="Filter image" NICKNAME="Filter image" NOTES="The first processing step is to remove some of the noise in the raw image.  To do this, we apply a 2D Gaussian filter with a sigma of 1px.  This reduces the noise, but retains the DNA features, which are of a similar width to the chosen sigma value.&#10;&#10;The filtered image is added to the workspace with the name &quot;Filtered&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Image" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Gaussian 2D" VISIBLE="false"/><PARAMETER NAME="Filter radius" NICKNAME="Filter radius" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Filter radius 2" NICKNAME="Filter radius 2" VALUE="3.0" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Rolling filter method" NICKNAME="Rolling filter method" VALUE="Average" VISIBLE="false"/><PARAMETER NAME="Window indices" NICKNAME="Window indices" VALUE="-1-1" VISIBLE="false"/><PARAMETER NAME="Contour contrast" NICKNAME="Contour contrast" VALUE="Dark line" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.script.RunSingleCommand" DISABLEABLE="false" ENABLED="true" ID="1638299323511" NAME="Run single command" NICKNAME="Run single command" NOTES="The mica substrate on which the DNA is deposited gives a variable background that we wish to remove prior to detection of DNA.  To achieve this, we apply rolling ball background subtraction with a ball radius of 5px.  We can use a relatively small radius as we know the DNA shouldn't be wider than approximately 2-3px.&#10;&#10;MIA doesn't have an explicit module to run the rolling ball subtraction.  Instead, we can run this as a single macro command using the &quot;Run single command&quot; module.  This module is compatible with any ImageJ commands which have a corresponding macro command in the form run(&quot;[command]&quot;, &quot;[arguments]&quot;) and which also update the input image.  To find out if a command is compatible, start ImageJ's macro recorder (Plugins &gt; Macros &gt; Record...) and run the operation manually from the ImageJ interface.&#10;&#10;Since we won't need the &quot;Filtered&quot; image in its original form again, we update this image in the workspace with the background-subtracted image.  This helps reduce unnecessary memory usage. " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Command" NICKNAME="Command" VALUE="Subtract Background..." VISIBLE="false"/><PARAMETER NAME="Parameters" NICKNAME="Parameters" VALUE="rolling=5" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.threshold.GlobalAutoThreshold" DISABLEABLE="false" ENABLED="true" ID="1695827300950" NAME="Global auto-threshold" NICKNAME="Global auto-threshold" NOTES="The next step is to binarise the image using the &quot;Global auto-threshold&quot; module.  Here, we use the Otsu method and store the output in the workspace with the name &quot;Binary&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Output mode" NICKNAME="Output mode" VALUE="Calculate and apply" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Algorithm" NICKNAME="Algorithm" VALUE="Otsu" VISIBLE="false"/><PARAMETER NAME="Threshold multiplier" NICKNAME="Threshold multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use lower threshold limit" NICKNAME="Use lower threshold limit" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Lower threshold limit" NICKNAME="Lower threshold limit" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Measure on objects" NICKNAME="Measure on objects" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" IMAGE_NAME="Binary" NAME="THRESHOLD // GLOBAL Otsu" NICKNAME="THRESHOLD // GLOBAL Otsu"/></IMAGE_MEASUREMENTS><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.IdentifyObjects" DISABLEABLE="false" ENABLED="true" ID="1694706262899" NAME="Identify objects" NICKNAME="Identify objects" NOTES="The individual DNA objects are detected from the binary image using connected components labelling.  This process is done using the &quot;Identify objects&quot; module, which takes a binary image and identifies each connected (or 'contiguous') region as a separate object.&#10;&#10;These objects are added to the MIA workspace with the name DNA.&#10;&#10;To perform connected components labelling, MIA uses the MorphoLibJ plugin." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output objects" NICKNAME="Output objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Identify as single object" NICKNAME="Identify as single object" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Volume type" NICKNAME="Volume type" VALUE="Quadtree" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum strip width (px)" NICKNAME="Minimum strip width (px)" VALUE="60" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterOnImageEdge" DISABLEABLE="false" ENABLED="true" ID="1694706063682" NAME="Remove on image edge" NICKNAME="Remove on image edge" NOTES="One of the aims of this workflow is to measure the length of each single DNA molecule (i.e. not those where multiple molecules are overlapping).  As such, we can't accurately measure any that are in contact with the image edge.  To remove these, we use the &quot;Remove on image edge&quot; module.&#10;&#10;If we were simply counting objects, we may wish to only discard objects touching a couple of image edges (e.g. top and left); however, in this instance we want to remove DNA molecules touching any of the image edges." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Maximum permitted contact" NICKNAME="Maximum permitted contact" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Remove on top" NICKNAME="Remove on top" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Remove on left" NICKNAME="Remove on left" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Remove on bottom" NICKNAME="Remove on bottom" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Remove on right" NICKNAME="Remove on right" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Include Z-position" NICKNAME="Include Z-position" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store filter results" NICKNAME="Store filter results" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.spatial.MeasureObjectShape" DISABLEABLE="false" ENABLED="true" ID="1694998855476" NAME="Measure object shape" NICKNAME="Measure object shape" NOTES="At the moment, the &quot;DNA&quot; object collection contains a lot of small round objects which likely correspond to salt crystals and other debris.  To remove these, we can set a minimum diameter.&#10;&#10;First, we make this measurement using the &quot;Measure object shape&quot; module.  Measurements in 2D are calculated on Z-projected objects; however, as our objects are in 2D already this will make no difference." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Measure volume" NICKNAME="Measure volume" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected area" NICKNAME="Measure projected area" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected diameter" NICKNAME="Measure projected diameter" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Measure projected perimeter" NICKNAME="Measure projected perimeter" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure 3D metrics" NICKNAME="Measure 3D metrics" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Surface area method" NICKNAME="Surface area method" VALUE="13 directions" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(PX)" NICKNAME="SHAPE // PROJ_DIA_(PX)" OBJECT_NAME="DNA"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(µm)" NICKNAME="SHAPE // PROJ_DIA_(µm)" OBJECT_NAME="DNA"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByMeasurement" DISABLEABLE="true" ENABLED="true" ID="1694998908258" NAME="Based on measurement" NICKNAME="Based on measurement" NOTES="With the diameter measurements calculated, we can remove any &quot;DNA&quot; objects smaller than a specific size using the &quot;Based on measurement&quot; filter module." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Less than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="20" VISIBLE="true"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement to filter on" NICKNAME="Measurement to filter on" VALUE="SHAPE // PROJ_DIA_(PX)" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925858241" NAME="GUI separator" NICKNAME="Measurements" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.process.CreateSkeleton" DISABLEABLE="false" ENABLED="true" ID="1694925436767" NAME="Create skeleton" NICKNAME="Create skeleton" NOTES="To measure length of our &quot;DNA&quot; objects, we can use the &quot;Measure skeleton&quot; module.  Skeletonisation involves reducing objects to a single pixel-wide line.  During this process, the length of the skeleton objects is measured and added to the associated DNA object.&#10;&#10;Skeletons themselves are formed from networks of &quot;Edges&quot; and &quot;Junctions&quot;, where edges are line segments between two junctions.  Junctions can in turn have one or more connected edges.&#10;&#10;MIA provides two object relationship types, both of which are in use when creating skeletons.  Parent-child relationships allow for one-to-many relationships between objects and here, the &quot;DNA&quot; objects are parents to the child &quot;Skeleton&quot; objects.  Likewise, the &quot;Edges&quot; and &quot;Junctions&quot; are children of the &quot;Skeleton&quot; objects.  Since MIA allows for extended relationships, this means the &quot;Edges&quot; and &quot;Junctions&quot; are therefore grandchildren of the &quot;DNA&quot; objects.&#10;&#10;Conversely, partner relationships allow for many-to-many relationships and here are present between &quot;Edges&quot; and &quot;Junctions&quot;.&#10;&#10;The &quot;Measure skeleton&quot; module  uses the &quot;Analyze Skeleton&quot; ImageJ plugin." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.1.0"><PARAMETERS><PARAMETER NAME="Input mode" NICKNAME="Input mode" VALUE="Objects" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Add skeletons to workspace" NICKNAME="Add skeletons to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output skeleton objects" NICKNAME="Output skeleton objects" VALUE="Skeletons" VISIBLE="false"/><PARAMETER NAME="Output edge objects" NICKNAME="Output edge objects" VALUE="Edges" VISIBLE="false"/><PARAMETER NAME="Output junction objects" NICKNAME="Output junction objects" VALUE="Junctions" VISIBLE="false"/><PARAMETER NAME="Export loop objects" NICKNAME="Export loop objects" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output loop objects" NICKNAME="Output loop objects" VALUE="Loops" VISIBLE="false"/><PARAMETER NAME="Export largest shortest path" NICKNAME="Export largest shortest path" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output largest shortest path" NICKNAME="Output largest shortest path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Minimum branch length" NICKNAME="Minimum branch length" VALUE="5" VISIBLE="true"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // LENGTH_(PX)" NICKNAME="SKELETON // LENGTH_(PX)" OBJECT_NAME="Edges"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="true" EXPORT_MIN="false" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // LENGTH_(µm)" NICKNAME="SKELETON // LENGTH_(µm)" OBJECT_NAME="Edges"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(PX)" NICKNAME="SKELETON // SUM_LENGTH_(PX)" OBJECT_NAME="DNA"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="true" EXPORT_MIN="false" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(µm)" NICKNAME="SKELETON // SUM_LENGTH_(µm)" OBJECT_NAME="DNA"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByPartners" DISABLEABLE="false" ENABLED="true" ID="1694706692780" NAME="Number of partners" NICKNAME="Number of partners" NOTES="For our analysis, we only want to measure the length of individual DNA molecules.  That means, we need a way of identifying any &quot;DNA&quot; objects formed from multiple overlapping molecules.&#10;&#10;One way to do this is to count the number of lose DNA ends there are, which we can do by counting the number of &quot;Junction&quot; objects which only have a single connected &quot;Edge&quot;.  For this, we use the &quot;Number of partners&quot; object filter.  With this filter we don't want to remove any junctions with a single connected edge; rather, we want to move them to a separate class which we call &quot;Ends&quot;.&#10;&#10;The &quot;Ends&quot; objects are added to the MIA workspace and automatically inherit any relationships that same object had when it was a &quot;Junction&quot;.  In this case these are direct relationships with &quot;Skeleton&quot; and &quot;Edge&quot; objects as well as the extended grandparent-grandchild relationship to &quot;DNA&quot; that arises as a result of being a child of an object (&quot;Skeletons&quot;) which itself is a child of a &quot;DNA&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Junctions" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Move filtered objects to new class" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="Ends" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Equal to" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Partner objects" NICKNAME="Partner objects" VALUE="Edges" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByChildren" DISABLEABLE="false" ENABLED="true" ID="1694706728197" NAME="Number of children" NICKNAME="Number of children" NOTES="We can now estimate which &quot;DNA&quot; objects are formed from multiple overlapping DNA molecules based on the number of grandchild &quot;Enda&quot; object relationships they have. &#10;&#10;Using the &quot;Number of children&quot; module, we can apply this filter and move any &quot;DNA&quot; objectw with more than 2 &quot;Ends&quot; grandchildren to a new object collection called &quot;Networks&quot;. As before, the objects moved to the new collection will retain all existing relationships and measurements, meaning we can export the length of each &quot;Network&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Move filtered objects to new class" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="Networks" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Greater than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="2" VISIBLE="false"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Child objects" NICKNAME="Child objects" VALUE="Skeletons // Ends" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(PX)" NICKNAME="SHAPE // PROJ_DIA_(PX)" OBJECT_NAME="Networks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(µm)" NICKNAME="SHAPE // PROJ_DIA_(µm)" OBJECT_NAME="Networks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(PX)" NICKNAME="SKELETON // SUM_LENGTH_(PX)" OBJECT_NAME="Networks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="true" EXPORT_MIN="false" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(µm)" NICKNAME="SKELETON // SUM_LENGTH_(µm)" OBJECT_NAME="Networks"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ParentObjectID" DISABLEABLE="false" ENABLED="true" ID="1696040403713" NAME="Parent object ID" NICKNAME="Parent object ID" NOTES="The &quot;Parent object ID&quot; module adds a measurement to the selected object, containing the ID (if any) of a particular parent class. This can be exported to the Excel spreadsheet. &#10;&#10;Here, for the &quot;Edges&quot; objects, we're adding the ID of the grandparent &quot;DNA&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Edges" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Skeletons // DNA" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="false" EXPORT_MIN="false" EXPORT_STD="false" EXPORT_SUM="false" NAME="PARENT_ID // Skeletons // DNA" NICKNAME="PARENT_ID // Skeletons // DNA" OBJECT_NAME="Edges"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ParentObjectID" DISABLEABLE="false" ENABLED="true" ID="1696460149571" NAME="Parent object ID" NICKNAME="Parent object ID" NOTES="As with the previous module, we're adding a measurement that reports the ID number of the grandparent &quot;Network&quot; ovjects." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Edges" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Skeletons // Networks" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="false" EXPORT_MIN="false" EXPORT_STD="false" EXPORT_SUM="false" NAME="PARENT_ID // Skeletons // Networks" NICKNAME="PARENT_ID // Skeletons // Networks" OBJECT_NAME="Edges"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925755615" NAME="GUI separator" NICKNAME="Image output" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.configure.SetDisplayRange" DISABLEABLE="false" ENABLED="true" ID="1694926127961" NAME="Set intensity display range" NICKNAME="Set intensity display range" NOTES="For the purpose of visualisation, the &quot;Filtered&quot; image is used. To make the DNA molecules easier to see, the intensity display range of the image is adjusted. This process doesnr affect the pixel information stored in the image, rather it chamges how the image is displayed on screen. &#10;&#10;The &quot;precise&quot; method hwre allows us to specify the fraction of pixels that will have clipped intensities at the top and bottom of the display range. &#10;&#10;This module adds a new &quot;Overlay&quot; image to the workspace. " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Calculation mode" NICKNAME="Calculation mode" VALUE="Precise" VISIBLE="false"/><PARAMETER NAME="Calculation source" NICKNAME="Calculation source" VALUE="Internal" VISIBLE="false"/><PARAMETER NAME="External source" NICKNAME="External source" VALUE="" VISIBLE="false"/><PARAMETER NAME="Clipping fraction (min)" NICKNAME="Clipping fraction (min)" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Clipping fraction (max)" NICKNAME="Clipping fraction (max)" VALUE="0.01" VISIBLE="false"/><PARAMETER NAME="Set minimum value" NICKNAME="Set minimum value" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Set maximum value" NICKNAME="Set maximum value" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum range value" NICKNAME="Minimum range value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum range value" NICKNAME="Maximum range value" VALUE="255.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectFill" DISABLEABLE="false" ENABLED="true" ID="1694705240541" NAME="Add object fill" NICKNAME="Add object fill" NOTES="In this example we'll display the DNA as a fill overlay, rather than an outline. a fill is an overlay thst goes over the top of the entire pixel. &#10;&#10;In order to see some of the pixel intensity, the opacity has been set to 50%. All single DNA molecules detected by this workflow are coloured cyan - this will contrast the overlapping molecules stored in the &quot;Networks&quot; collection, which we'll colour magenta in the next step." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="Cyan" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectFill" DISABLEABLE="false" ENABLED="true" ID="1694706046687" NAME="Add object fill" NICKNAME="Add object fill" NOTES="As with the &quot;DNA&quot; objects, we render the &quot;Networks&quot; objects with a fill overlay. The only difference ia that they're coloured magenta." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="Magenta" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Networks" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.ShowImage" DISABLEABLE="true" ENABLED="true" ID="1694925777350" NAME="Show image" NICKNAME="Show image" NOTES="Optionally displaying the image." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="true" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Display image" NICKNAME="Display image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Title mode" NICKNAME="Title mode" VALUE="Image name" VISIBLE="false"/><PARAMETER NAME="Quick normalisation" NICKNAME="Quick normalisation" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageSaver" DISABLEABLE="true" ENABLED="true" ID="1694925777350" NAME="Save image" NICKNAME="Save image" NOTES="Optionally saving the image to the same folder as the input image, but woth the suffix &quot;_overlay&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Save location" NICKNAME="Save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="File name (generic)" NICKNAME="File name (generic)" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Append series mode" NICKNAME="Append series mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Add filename suffix" NICKNAME="Add filename suffix" VALUE="_overlay" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="File format" NICKNAME="File format" VALUE="TIF" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/><PARAMETER NAME="Save as RGB" NICKNAME="Save as RGB" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Compression mode" NICKNAME="Compression mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Quality (0-100)" NICKNAME="Quality (0-100)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Frame rate (fps)" NICKNAME="Frame rate (fps)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Flatten overlay" NICKNAME="Flatten overlay" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES></ROOT>
\ No newline at end of file
+<?xml version="1.0" encoding="UTF-8"?><ROOT MIA_VERSION="1.5.1"><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.InputControl" DISABLEABLE="false" ENABLED="true" ID="1638297565958" NAME="Input control" NICKNAME="Input control" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input path" NICKNAME="Input path" VALUE="/Users/sc13967/Documents/Programming/Java/mia-examples/Ex3_Skeletonisation/Ex3_Skeletonisation.tif" VISIBLE="true"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="All series" VISIBLE="false"/><PARAMETER NAME="Series list" NICKNAME="Series list" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Only load first file per folder" NICKNAME="Only load first file per folder" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Only load first matching group" NICKNAME="Only load first matching group" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Pattern" NICKNAME="Pattern" VALUE="" VISIBLE="false"/><PARAMETER NAME="Spatial unit" NICKNAME="Spatial unit" VALUE="Micrometres" VISIBLE="false"/><PARAMETER NAME="Temporal unit" NICKNAME="Temporal unit" VALUE="Milliseconds" VISIBLE="false"/><PARAMETER NAME="Ignore case" NICKNAME="Ignore case" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Add filter" NICKNAME="Add filter" VALUE="" VISIBLE="false"><COLLECTION><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Extension" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="tif" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (include)" VISIBLE="false"/></PARAMS><PARAMS><PARAM NAME="Filter source" NICKNAME="Filter source" VALUE="Filename" VISIBLE="false"/><PARAM NAME="Filter value" NICKNAME="Filter value" VALUE="_overlay" VISIBLE="false"/><PARAM NAME="Filter type" NICKNAME="Filter type" VALUE="Matches partially (exclude)" VISIBLE="false"/></PARAMS></COLLECTION></PARAMETER><PARAMETER NAME="Simultaneous jobs" NICKNAME="Simultaneous jobs" VALUE="1" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Extension" NICKNAME="Extension"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="File" NICKNAME="File"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filename" NICKNAME="Filename"/><METADATUM EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" NAME="Filepath" NICKNAME="Filepath"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series name" NICKNAME="Series name"/><METADATUM EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" NAME="Series number" NICKNAME="Series number"/></METADATA></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.core.OutputControl" DISABLEABLE="false" ENABLED="true" ID="1638297565958" NAME="Output control" NICKNAME="Output control" NOTES="Configuring the exported Excel spreadsheet.  This will spreadsheet report the length of both the individual and network DNA ovjects. " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Add variable" NICKNAME="Add variable" VALUE="" VISIBLE="false"><COLLECTION/></PARAMETER><PARAMETER NAME="Run macro" NICKNAME="Run macro" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Macro mode" NICKNAME="Macro mode" VALUE="Macro text" VISIBLE="false"/><PARAMETER NAME="Macro text" NICKNAME="Macro text" VALUE="run(&quot;Enable MIA Extensions&quot;);&#10;&#10;// Get a list of Workspace IDs with Ext.MIA_GetListOfWorkspaceIDs() and set active workspace with Ext.MIA_SetActiveWorkspace(ID)." VISIBLE="false"/><PARAMETER NAME="Macro file" NICKNAME="Macro file" VALUE="" VISIBLE="false"/><PARAMETER NAME="Export mode" NICKNAME="Export mode" VALUE="All together" VISIBLE="false"/><PARAMETER NAME="Individual save location" NICKNAME="Individual save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Group save location" NICKNAME="Group save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file/folder name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Metadata item for grouping" NICKNAME="Metadata item for grouping" VALUE="" VISIBLE="false"/><PARAMETER NAME="Continuous data export" NICKNAME="Continuous data export" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Save every n files" NICKNAME="Save every n files" VALUE="10" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Export summary" NICKNAME="Export summary" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Summary mode" NICKNAME="Summary mode" VALUE="Per input file" VISIBLE="false"/><PARAMETER NAME="Metadata item for summary" NICKNAME="Metadata item for summary" VALUE="" VISIBLE="false"/><PARAMETER NAME="Show object counts" NICKNAME="Show object counts" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Export individual objects" NICKNAME="Export individual objects" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES><MODULES><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925729349" NAME="GUI separator" NICKNAME="File loading" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageLoader" DISABLEABLE="false" ENABLED="true" ID="1638297567118" NAME="Load image" NICKNAME="Load image" NOTES="In this standard image loading module we're loading the AFM image of DNA to the MIA workspace with the name &quot;Image&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Image" VISIBLE="false"/><PARAMETER NAME="Import mode" NICKNAME="Import mode" VALUE="Current file" VISIBLE="false"/><PARAMETER NAME="Reader" NICKNAME="Reader" VALUE="Bio-Formats" VISIBLE="false"/><PARAMETER NAME="Sequence root name" NICKNAME="Sequence root name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Name format" NICKNAME="Name format" VALUE="Generic (from metadata)" VISIBLE="false"/><PARAMETER NAME="Comment" NICKNAME="Comment" VALUE="" VISIBLE="false"/><PARAMETER NAME="Extension" NICKNAME="Extension" VALUE="" VISIBLE="false"/><PARAMETER NAME="Generic format" NICKNAME="Generic format" VALUE="" VISIBLE="false"/><PARAMETER NAME="Include series number" NICKNAME="Include series number" VALUE="true" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Series mode" NICKNAME="Series mode" VALUE="Current series" VISIBLE="false"/><PARAMETER NAME="Series number" NICKNAME="Series number" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Channels" NICKNAME="Channels" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Slices" NICKNAME="Slices" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Frames" NICKNAME="Frames" VALUE="1-end" VISIBLE="false"/><PARAMETER NAME="Channel" NICKNAME="Channel" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Crop mode" NICKNAME="Crop mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Reference image" NICKNAME="Reference image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Left coordinate" NICKNAME="Left coordinate" VALUE="384" VISIBLE="false"/><PARAMETER NAME="Top coordinate" NICKNAME="Top coordinate" VALUE="287" VISIBLE="false"/><PARAMETER NAME="Width" NICKNAME="Width" VALUE="640" VISIBLE="false"/><PARAMETER NAME="Height" NICKNAME="Height" VALUE="640" VISIBLE="false"/><PARAMETER NAME="Objects for limits" NICKNAME="Objects for limits" VALUE="" VISIBLE="false"/><PARAMETER NAME="Scale mode" NICKNAME="Scale mode" VALUE="No scaling" VISIBLE="false"/><PARAMETER NAME="X scale factor" NICKNAME="X scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Y scale factor" NICKNAME="Y scale factor" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Dimension mismatch mode" NICKNAME="Dimension mismatch mode" VALUE="Disallow (fail upon mismatch)" VISIBLE="false"/><PARAMETER NAME="Pad intensity mode" NICKNAME="Pad intensity mode" VALUE="Black (0)" VISIBLE="false"/><PARAMETER NAME="Set manual spatial calibration" NICKNAME="Set manual spatial calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="XY calibration (dist/px)" NICKNAME="XY calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Z calibration (dist/px)" NICKNAME="Z calibration (dist/px)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Set manual temporal calibration" NICKNAME="Set manual temporal calibration" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Frame interval (time/frame)" NICKNAME="Frame interval (time/frame)" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Force bit depth" NICKNAME="Force bit depth" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output bit depth" NICKNAME="Output bit depth" VALUE="8" VISIBLE="false"/><PARAMETER NAME="Minimum input intensity" NICKNAME="Minimum input intensity" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum input intensity" NICKNAME="Maximum input intensity" VALUE="1.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925848319" NAME="GUI separator" NICKNAME="Detect DNA" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.FilterImage" DISABLEABLE="false" ENABLED="true" ID="1694706310794" NAME="Filter image" NICKNAME="Filter image" NOTES="The first processing step is to remove some of the noise in the raw image.  To do this, we apply a 2D Gaussian filter with a sigma of 1px.  This reduces the noise, but retains the DNA features, which are of a similar width to the chosen sigma value.&#10;&#10;The filtered image is added to the workspace with the name &quot;Filtered&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Image" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Gaussian 2D" VISIBLE="false"/><PARAMETER NAME="Filter radius" NICKNAME="Filter radius" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Filter radius 2" NICKNAME="Filter radius 2" VALUE="3.0" VISIBLE="false"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Rolling filter method" NICKNAME="Rolling filter method" VALUE="Average" VISIBLE="false"/><PARAMETER NAME="Window indices" NICKNAME="Window indices" VALUE="-1-1" VISIBLE="false"/><PARAMETER NAME="Contour contrast" NICKNAME="Contour contrast" VALUE="Dark line" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.script.RunSingleCommand" DISABLEABLE="false" ENABLED="true" ID="1638299323511" NAME="Run single command" NICKNAME="Run single command" NOTES="The mica substrate on which the DNA is deposited gives a variable background that we wish to remove prior to detection of DNA.  To achieve this, we apply rolling ball background subtraction with a ball radius of 5px.  We can use a relatively small radius as we know the DNA shouldn't be wider than approximately 2-3px.&#10;&#10;MIA doesn't have an explicit module to run the rolling ball subtraction.  Instead, we can run this as a single macro command using the &quot;Run single command&quot; module.  This module is compatible with any ImageJ commands which have a corresponding macro command in the form run(&quot;[command]&quot;, &quot;[arguments]&quot;) and which also update the input image.  To find out if a command is compatible, start ImageJ's macro recorder (Plugins &gt; Macros &gt; Record...) and run the operation manually from the ImageJ interface.&#10;&#10;Since we won't need the &quot;Filtered&quot; image in its original form again, we update this image in the workspace with the background-subtracted image.  This helps reduce unnecessary memory usage. " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Command" NICKNAME="Command" VALUE="Subtract Background..." VISIBLE="false"/><PARAMETER NAME="Parameters" NICKNAME="Parameters" VALUE="rolling=5" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.process.threshold.GlobalAutoThreshold" DISABLEABLE="false" ENABLED="true" ID="1695827300950" NAME="Global auto-threshold" NICKNAME="Global auto-threshold" NOTES="The next step is to binarise the image using the &quot;Global auto-threshold&quot; module.  Here, we use the Otsu method and store the output in the workspace with the name &quot;Binary&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Output mode" NICKNAME="Output mode" VALUE="Calculate and apply" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Algorithm" NICKNAME="Algorithm" VALUE="Otsu" VISIBLE="false"/><PARAMETER NAME="Threshold multiplier" NICKNAME="Threshold multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Use lower threshold limit" NICKNAME="Use lower threshold limit" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Lower threshold limit" NICKNAME="Lower threshold limit" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Measure on objects" NICKNAME="Measure on objects" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" IMAGE_NAME="Binary" NAME="THRESHOLD // GLOBAL Otsu" NICKNAME="THRESHOLD // GLOBAL Otsu"/></IMAGE_MEASUREMENTS><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.detect.IdentifyObjects" DISABLEABLE="false" ENABLED="true" ID="1694706262899" NAME="Identify objects" NICKNAME="Identify objects" NOTES="The individual DNA objects are detected from the binary image using connected components labelling.  This process is done using the &quot;Identify objects&quot; module, which takes a binary image and identifies each connected (or 'contiguous') region as a separate object.&#10;&#10;These objects are added to the MIA workspace with the name DNA.&#10;&#10;To perform connected components labelling, MIA uses the MorphoLibJ plugin." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Binary" VISIBLE="false"/><PARAMETER NAME="Output objects" NICKNAME="Output objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Detection mode" NICKNAME="Detection mode" VALUE="3D" VISIBLE="false"/><PARAMETER NAME="Identify as single object" NICKNAME="Identify as single object" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Volume type" NICKNAME="Volume type" VALUE="Quadtree" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum strip width (px)" NICKNAME="Minimum strip width (px)" VALUE="60" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterOnImageEdge" DISABLEABLE="false" ENABLED="true" ID="1694706063682" NAME="Remove on image edge" NICKNAME="Remove on image edge" NOTES="One of the aims of this workflow is to measure the length of each single DNA molecule (i.e. not those where multiple molecules are overlapping).  As such, we can't accurately measure any that are in contact with the image edge.  To remove these, we use the &quot;Remove on image edge&quot; module.&#10;&#10;If we were simply counting objects, we may wish to only discard objects touching a couple of image edges (e.g. top and left); however, in this instance we want to remove DNA molecules touching any of the image edges." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Maximum permitted contact" NICKNAME="Maximum permitted contact" VALUE="0" VISIBLE="false"/><PARAMETER NAME="Remove on top" NICKNAME="Remove on top" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Remove on left" NICKNAME="Remove on left" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Remove on bottom" NICKNAME="Remove on bottom" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Remove on right" NICKNAME="Remove on right" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Include Z-position" NICKNAME="Include Z-position" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store filter results" NICKNAME="Store filter results" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.spatial.MeasureObjectShape" DISABLEABLE="false" ENABLED="true" ID="1694998855476" NAME="Measure object shape" NICKNAME="Measure object shape" NOTES="At the moment, the &quot;DNA&quot; object collection contains a lot of small round objects which likely correspond to salt crystals and other debris.  To remove these, we can set a minimum diameter.&#10;&#10;First, we make this measurement using the &quot;Measure object shape&quot; module.  Measurements in 2D are calculated on Z-projected objects; however, as our objects are in 2D already this will make no difference." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Measure volume" NICKNAME="Measure volume" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected area" NICKNAME="Measure projected area" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure projected diameter" NICKNAME="Measure projected diameter" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Measure projected perimeter" NICKNAME="Measure projected perimeter" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measure 3D metrics" NICKNAME="Measure 3D metrics" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Connectivity" NICKNAME="Connectivity" VALUE="26" VISIBLE="false"/><PARAMETER NAME="Surface area method" NICKNAME="Surface area method" VALUE="13 directions" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(PX)" NICKNAME="SHAPE // PROJ_DIA_(PX)" OBJECT_NAME="DNA"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(µm)" NICKNAME="SHAPE // PROJ_DIA_(µm)" OBJECT_NAME="DNA"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByMeasurement" DISABLEABLE="true" ENABLED="true" ID="1694998908258" NAME="Based on measurement" NICKNAME="Based on measurement" NOTES="With the diameter measurements calculated, we can remove any &quot;DNA&quot; objects smaller than a specific size using the &quot;Based on measurement&quot; filter module." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Remove filtered objects" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Less than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="20" VISIBLE="true"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Measurement to filter on" NICKNAME="Measurement to filter on" VALUE="SHAPE // PROJ_DIA_(PX)" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925858241" NAME="GUI separator" NICKNAME="Measurements" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.process.CreateSkeleton" DISABLEABLE="false" ENABLED="true" ID="1694925436767" NAME="Create skeleton" NICKNAME="Create skeleton" NOTES="To measure length of our &quot;DNA&quot; objects, we can use the &quot;Measure skeleton&quot; module.  Skeletonisation involves reducing objects to a single pixel-wide line.  During this process, the length of the skeleton objects is measured and added to the associated DNA object.&#10;&#10;Skeletons themselves are formed from networks of &quot;Edges&quot; and &quot;Junctions&quot;, where edges are line segments between two junctions.  Junctions can in turn have one or more connected edges.&#10;&#10;MIA provides two object relationship types, both of which are in use when creating skeletons.  Parent-child relationships allow for one-to-many relationships between objects and here, the &quot;DNA&quot; objects are parents to the child &quot;Skeleton&quot; objects.  Likewise, the &quot;Edges&quot; and &quot;Junctions&quot; are children of the &quot;Skeleton&quot; objects.  Since MIA allows for extended relationships, this means the &quot;Edges&quot; and &quot;Junctions&quot; are therefore grandchildren of the &quot;DNA&quot; objects.&#10;&#10;Conversely, partner relationships allow for many-to-many relationships and here are present between &quot;Edges&quot; and &quot;Junctions&quot;.&#10;&#10;The &quot;Measure skeleton&quot; module  uses the &quot;Analyze Skeleton&quot; ImageJ plugin." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.1.0"><PARAMETERS><PARAMETER NAME="Input mode" NICKNAME="Input mode" VALUE="Objects" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Binary logic" NICKNAME="Binary logic" VALUE="Black (0) background" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Add skeletons to workspace" NICKNAME="Add skeletons to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output skeleton objects" NICKNAME="Output skeleton objects" VALUE="Skeletons" VISIBLE="false"/><PARAMETER NAME="Output edge objects" NICKNAME="Output edge objects" VALUE="Edges" VISIBLE="false"/><PARAMETER NAME="Output junction objects" NICKNAME="Output junction objects" VALUE="Junctions" VISIBLE="false"/><PARAMETER NAME="Export loop objects" NICKNAME="Export loop objects" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output loop objects" NICKNAME="Output loop objects" VALUE="Loops" VISIBLE="false"/><PARAMETER NAME="Export largest shortest path" NICKNAME="Export largest shortest path" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output largest shortest path" NICKNAME="Output largest shortest path" VALUE="" VISIBLE="false"/><PARAMETER NAME="Minimum branch length" NICKNAME="Minimum branch length" VALUE="5" VISIBLE="true"/><PARAMETER NAME="Calibrated units" NICKNAME="Calibrated units" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // LENGTH_(PX)" NICKNAME="SKELETON // LENGTH_(PX)" OBJECT_NAME="Edges"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="true" EXPORT_MIN="false" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // LENGTH_(µm)" NICKNAME="SKELETON // LENGTH_(µm)" OBJECT_NAME="Edges"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(PX)" NICKNAME="SKELETON // SUM_LENGTH_(PX)" OBJECT_NAME="DNA"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="true" EXPORT_MIN="false" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(µm)" NICKNAME="SKELETON // SUM_LENGTH_(µm)" OBJECT_NAME="DNA"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByPartners" DISABLEABLE="false" ENABLED="true" ID="1694706692780" NAME="Number of partners" NICKNAME="Number of partners" NOTES="For our analysis, we only want to measure the length of individual DNA molecules.  That means, we need a way of identifying any &quot;DNA&quot; objects formed from multiple overlapping molecules.&#10;&#10;One way to do this is to count the number of lose DNA ends there are, which we can do by counting the number of &quot;Junction&quot; objects which only have a single connected &quot;Edge&quot;.  For this, we use the &quot;Number of partners&quot; object filter.  With this filter we don't want to remove any junctions with a single connected edge; rather, we want to move them to a separate class which we call &quot;Ends&quot;.&#10;&#10;The &quot;Ends&quot; objects are added to the MIA workspace and automatically inherit any relationships that same object had when it was a &quot;Junction&quot;.  In this case these are direct relationships with &quot;Skeleton&quot; and &quot;Edge&quot; objects as well as the extended grandparent-grandchild relationship to &quot;DNA&quot; that arises as a result of being a child of an object (&quot;Skeletons&quot;) which itself is a child of a &quot;DNA&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Junctions" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Move filtered objects to new class" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="Ends" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Equal to" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="1" VISIBLE="false"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Partner objects" NICKNAME="Partner objects" VALUE="Edges" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.filter.FilterByChildren" DISABLEABLE="false" ENABLED="true" ID="1694706728197" NAME="Number of children" NICKNAME="Number of children" NOTES="We can now estimate which &quot;DNA&quot; objects are formed from multiple overlapping DNA molecules based on the number of grandchild &quot;Enda&quot; object relationships they have. &#10;&#10;Using the &quot;Number of children&quot; module, we can apply this filter and move any &quot;DNA&quot; objectw with more than 2 &quot;Ends&quot; grandchildren to a new object collection called &quot;Networks&quot;. As before, the objects moved to the new collection will retain all existing relationships and measurements, meaning we can export the length of each &quot;Network&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Filter mode" NICKNAME="Filter mode" VALUE="Move filtered objects to new class" VISIBLE="false"/><PARAMETER NAME="Output (filtered) objects" NICKNAME="Output (filtered) objects" VALUE="Networks" VISIBLE="false"/><PARAMETER NAME="Method for filtering" NICKNAME="Method for filtering" VALUE="Greater than" VISIBLE="false"/><PARAMETER NAME="Reference mode" NICKNAME="Reference mode" VALUE="Fixed value" VISIBLE="false"/><PARAMETER NAME="Reference value" NICKNAME="Reference value" VALUE="2" VISIBLE="false"/><PARAMETER NAME="Reference value image" NICKNAME="Reference value image" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference image measurement" NICKNAME="Reference image measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value parent object" NICKNAME="Reference value parent object" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference object measurement" NICKNAME="Reference object measurement" VALUE="" VISIBLE="false"/><PARAMETER NAME="Reference value multiplier" NICKNAME="Reference value multiplier" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Store summary filter results" NICKNAME="Store summary filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Store individual filter results" NICKNAME="Store individual filter results" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Child objects" NICKNAME="Child objects" VALUE="Skeletons // Ends" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(PX)" NICKNAME="SHAPE // PROJ_DIA_(PX)" OBJECT_NAME="Networks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SHAPE // PROJ_DIA_(µm)" NICKNAME="SHAPE // PROJ_DIA_(µm)" OBJECT_NAME="Networks"/><MEASUREMENT EXPORT_GLOBAL="false" EXPORT_INDIVIDUAL="true" EXPORT_MAX="true" EXPORT_MEAN="true" EXPORT_MIN="true" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(PX)" NICKNAME="SKELETON // SUM_LENGTH_(PX)" OBJECT_NAME="Networks"/><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="true" EXPORT_MIN="false" EXPORT_STD="true" EXPORT_SUM="true" NAME="SKELETON // SUM_LENGTH_(µm)" NICKNAME="SKELETON // SUM_LENGTH_(µm)" OBJECT_NAME="Networks"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ParentObjectID" DISABLEABLE="false" ENABLED="true" ID="1696040403713" NAME="Parent object ID" NICKNAME="Parent object ID" NOTES="The &quot;Parent object ID&quot; module adds a measurement to the selected object, containing the ID (if any) of a particular parent class. This can be exported to the Excel spreadsheet. &#10;&#10;Here, for the &quot;Edges&quot; objects, we're adding the ID of the grandparent &quot;DNA&quot; object." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Edges" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Skeletons // DNA" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="false" EXPORT_MIN="false" EXPORT_STD="false" EXPORT_SUM="false" NAME="PARENT_ID // Skeletons // DNA" NICKNAME="PARENT_ID // Skeletons // DNA" OBJECT_NAME="Edges"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.objects.measure.miscellaneous.ParentObjectID" DISABLEABLE="false" ENABLED="true" ID="1696460149571" NAME="Parent object ID" NICKNAME="Parent object ID" NOTES="As with the previous module, we're adding a measurement that reports the ID number of the grandparent &quot;Network&quot; ovjects." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Edges" VISIBLE="false"/><PARAMETER NAME="Parent object" NICKNAME="Parent object" VALUE="Skeletons // Networks" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS><MEASUREMENT EXPORT_GLOBAL="true" EXPORT_INDIVIDUAL="true" EXPORT_MAX="false" EXPORT_MEAN="false" EXPORT_MIN="false" EXPORT_STD="false" EXPORT_SUM="false" NAME="PARENT_ID // Skeletons // Networks" NICKNAME="PARENT_ID // Skeletons // Networks" OBJECT_NAME="Edges"/></OBJECT_MEASUREMENTS><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.system.GUISeparator" DISABLEABLE="false" ENABLED="true" ID="1694925755615" NAME="GUI separator" NICKNAME="Image output" NOTES="" SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Show in processing view" NICKNAME="Show basic" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in processing view" NICKNAME="Expanded basic GUI" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Expanded in editing view" NICKNAME="Expanded editing GUI" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.images.configure.SetDisplayRange" DISABLEABLE="false" ENABLED="true" ID="1694926127961" NAME="Set intensity display range" NICKNAME="Set intensity display range" NOTES="For the purpose of visualisation, the &quot;Filtered&quot; image is used. To make the DNA molecules easier to see, the intensity display range of the image is adjusted. This process doesnr affect the pixel information stored in the image, rather it chamges how the image is displayed on screen. &#10;&#10;The &quot;precise&quot; method hwre allows us to specify the fraction of pixels that will have clipped intensities at the top and bottom of the display range. &#10;&#10;This module adds a new &quot;Overlay&quot; image to the workspace. " SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.1"><PARAMETERS><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Filtered" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Calculation mode" NICKNAME="Calculation mode" VALUE="Precise" VISIBLE="false"/><PARAMETER NAME="Calculation source" NICKNAME="Calculation source" VALUE="Internal" VISIBLE="false"/><PARAMETER NAME="External source" NICKNAME="External source" VALUE="" VISIBLE="false"/><PARAMETER NAME="Clipping fraction (min)" NICKNAME="Clipping fraction (min)" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Clipping fraction (max)" NICKNAME="Clipping fraction (max)" VALUE="0.01" VISIBLE="false"/><PARAMETER NAME="Set minimum value" NICKNAME="Set minimum value" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Set maximum value" NICKNAME="Set maximum value" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Minimum range value" NICKNAME="Minimum range value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Maximum range value" NICKNAME="Maximum range value" VALUE="255.0" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectFill" DISABLEABLE="false" ENABLED="true" ID="1694705240541" NAME="Add object fill" NICKNAME="Add object fill" NOTES="In this example we'll display the DNA as a fill overlay, rather than an outline. a fill is an overlay thst goes over the top of the entire pixel. &#10;&#10;In order to see some of the pixel intensity, the opacity has been set to 50%. All single DNA molecules detected by this workflow are coloured cyan - this will contrast the overlapping molecules stored in the &quot;Networks&quot; collection, which we'll colour magenta in the next step." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="Cyan" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="DNA" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.overlays.AddObjectFill" DISABLEABLE="false" ENABLED="true" ID="1694706046687" NAME="Add object fill" NICKNAME="Add object fill" NOTES="As with the &quot;DNA&quot; objects, we render the &quot;Networks&quot; objects with a fill overlay. The only difference ia that they're coloured magenta." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Colour mode" NICKNAME="Colour mode" VALUE="Single colour" VISIBLE="false"/><PARAMETER NAME="Colour map" NICKNAME="Colour map" VALUE="Spectrum" VISIBLE="false"/><PARAMETER NAME="Single colour" NICKNAME="Single colour" VALUE="Magenta" VISIBLE="false"/><PARAMETER NAME="Child objects for colour" NICKNAME="Child objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Measurement for colour" NICKNAME="Measurement for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Parent object for colour" NICKNAME="Parent object for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Partner objects for colour" NICKNAME="Partner objects for colour" VALUE="" VISIBLE="false"/><PARAMETER NAME="Opacity (%)" NICKNAME="Opacity (%)" VALUE="100.0" VISIBLE="false"/><PARAMETER NAME="Range minimum mode" NICKNAME="Range minimum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Minimum value" NICKNAME="Minimum value" VALUE="0.0" VISIBLE="false"/><PARAMETER NAME="Range maximum mode" NICKNAME="Range maximum mode" VALUE="Automatic" VISIBLE="false"/><PARAMETER NAME="Maximum value" NICKNAME="Maximum value" VALUE="1.0" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Input objects" NICKNAME="Input objects" VALUE="Networks" VISIBLE="false"/><PARAMETER NAME="Apply to input image" NICKNAME="Apply to input image" VALUE="true" VISIBLE="false"/><PARAMETER NAME="Add output image to workspace" NICKNAME="Add output image to workspace" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Output image" NICKNAME="Output image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Render in all frames" NICKNAME="Render in all frames" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Enable multithreading" NICKNAME="Enable multithreading" VALUE="true" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.visualise.ShowImage" DISABLEABLE="true" ENABLED="true" ID="1694925777350" NAME="Show image" NICKNAME="Show image" NOTES="Optionally displaying the image." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="true" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Display image" NICKNAME="Display image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="Title mode" NICKNAME="Title mode" VALUE="Image name" VISIBLE="false"/><PARAMETER NAME="Quick normalisation" NICKNAME="Quick normalisation" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE><MODULE CLASSNAME="io.github.mianalysis.mia.module.inputoutput.ImageSaver" DISABLEABLE="true" ENABLED="true" ID="1694925777350" NAME="Save image" NICKNAME="Save image" NOTES="Optionally saving the image to the same folder as the input image, but woth the suffix &quot;_overlay&quot;." SHOW_BASIC_TITLE="true" SHOW_OUTPUT="false" VERSION="1.0.0"><PARAMETERS><PARAMETER NAME="Save location" NICKNAME="Save location" VALUE="Save with input file" VISIBLE="false"/><PARAMETER NAME="Mirrored directory root" NICKNAME="Mirrored directory root" VALUE="" VISIBLE="false"/><PARAMETER NAME="File path" NICKNAME="File path" VALUE="" VISIBLE="false"/><PARAMETER NAME="File name (generic)" NICKNAME="File name (generic)" VALUE="" VISIBLE="false"/><PARAMETER NAME="Save name mode" NICKNAME="Save name mode" VALUE="Match input file name" VISIBLE="false"/><PARAMETER NAME="File name" NICKNAME="File name" VALUE="" VISIBLE="false"/><PARAMETER NAME="Append series mode" NICKNAME="Append series mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Append date/time mode" NICKNAME="Append date/time mode" VALUE="Never" VISIBLE="false"/><PARAMETER NAME="Add filename suffix" NICKNAME="Add filename suffix" VALUE="_overlay" VISIBLE="false"/><PARAMETER NAME="Input image" NICKNAME="Input image" VALUE="Overlay" VISIBLE="false"/><PARAMETER NAME="File format" NICKNAME="File format" VALUE="TIF" VISIBLE="false"/><PARAMETER NAME="Channel mode" NICKNAME="Channel mode" VALUE="Composite" VISIBLE="false"/><PARAMETER NAME="Save as RGB" NICKNAME="Save as RGB" VALUE="false" VISIBLE="false"/><PARAMETER NAME="Compression mode" NICKNAME="Compression mode" VALUE="None" VISIBLE="false"/><PARAMETER NAME="Quality (0-100)" NICKNAME="Quality (0-100)" VALUE="100" VISIBLE="false"/><PARAMETER NAME="Frame rate (fps)" NICKNAME="Frame rate (fps)" VALUE="25" VISIBLE="false"/><PARAMETER NAME="Flatten overlay" NICKNAME="Flatten overlay" VALUE="false" VISIBLE="false"/></PARAMETERS><IMAGE_MEASUREMENTS/><OBJECT_MEASUREMENTS/><METADATA/></MODULE></MODULES></ROOT>
\ No newline at end of file
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