Version 1.6.5

New plugin features

• "MIA Headless" can now be run from an ImageJ macro without displaying any GUI elements. The parameters can be recorded using the ImageJ macro recorder. This functionality is still in development, so all parameters must be specified. Future development will aim to only require non-default values to be specified. When no "variables" are present, variables=\"\" must be included in the macro arguments (this isn't automatically added by the macro recorder).

New modules

• "Z interpolator" module can be used to reduce the spacing between Z-slices for objects. Coordinates for the added slices are generated using ImageJ's binary interpolation functionality. This works best for larger objects, with minimal shape change between slices.

Other

• Bugfixes for "Create distance bands", "Duplicate objects" and "Grow objects".
• Other general bugfixes.

Version 1.6.4

New modules

• "Adopt parent metadata" allows objects to add a new metadata item that mirrors that of a parent object. This is equivalent to the existing "Adopt parent measurement" module.
• "Duplicate objects" creates an exact replica of all objects in a collection. It can optionally also duplicate measurements, relationships and metadata associated with each object.
• "Resolve object overlap" removes overlapping object regions. The division between overlapping objects is set half way between the non-overlapping object edges.

New module features

• "Extract object edges" now allows users to specify weighting mode for distance transform.
• "Grow objects" can now update the input object as well as create totally new (child) objects.
• "Manually identify objects" has updated overlay rendering options. Overlays can be either semi-transparent "fills" or outlines. They can also be coloured according to ID number, assigned class (if present) or single colours. This module also gains an option to select contiguous regions of an image without any existing objects (accessed via new "Tools" menu from object selection window).

Other

• Improved memory handling for ImgLib2 images
• General bugfixes

Version 1.6.3

New plugin features

• Optimised when analysis tester (determines which modules can run) executes. This should now run less often, resulting in better plugin performance, especially with workflows containing large numbers of modules.

New modules

• "Save overlay as ROIs" creates a zipped ROI file containing all overlay items as ImageJ ROIs. This allows overlays to be saved and distributed without requiring the underlying image to be saved.

New module features

• "Adopt parent measurement", "Calculate statistics for children" and "Calculate statistics for partners" now allow multiple measurements to be selected within a single module instance. All measurements listed in a single module will have the same statistics (e.g. mean, minimum, etc.) applied. Also changed output measurement names to remove " in favour of [ and ].
• "Apply Weka object classification" now retains an instance of the classifier and only updates it when the classifier file path changes.
• Added minimum feet diameter to "Measure object shape".
• "Convert objects to image" can now use object metadata to colour objects.

Other

• Fixed lost module references when copying, pasting and performing undo/redo operations.
• General bugfixes

Version 1.6.2

New plugin features

• Workflows can be loaded directly from XLSX files that have previously been exported by MIA. These spreadsheets must retain the original "Configuration" sheet containing the "WORKFLOW CONFIGURATION (XML)" section.
• Module status updates are now shorter, so should fit more reliably into available space.

New modules

• "Create bounding boxes" creates a solid box around each object (up to the spatial limits in each direction) and assigns it as a child of the original object.
• "Export VOC annotations" creates Pascal VOC formal XML files for specified objects. Currently supports bounding boxes and object classes. These annotation files can be used for training deep learning models.
• "Filter with/without metadata" filters objects based on whether they have a specified metadata item associated with them. This is analogous to modules such as "Filter with/without measurement".

New module features

• "Manually identify objects" now has the option to assign classes to each object. These are specified as metadata items associated with those objects. For this, a new object classification window appears that displays all known classes as well as shorter lists for classes present in the image and also those recently used. Lists can be narrowed down using a class name search. New classes can be added. Class lists can be created from scratch or loaded from CSV files.
• "Manually identify objects" can also load pre-detected objects from another object collection. For example, these could be previously-detected objects that could be deleted, updated or assigned a new class.
• "Save objects as ROIs" can now optionally also save applied object classes.
• "Load objects from ROIs" can likewise load object classes where present in the input ROI files.

Other

• "Combine object sets" will now associate measurements, metadata and relationships with new objects created during merging.
• "Create distance bands" should be significantly faster when processing bands with a relatively small maximum distance (i.e. bands that only cover a small portion of the image).
• Other general bugfixes

Version 1.6.1

New modules

• "Plot track motility" module creates motility plots for tracks. These can either be rendered onto the same axes or created as one plot per axis (output as a stack of images). As with other plotting modules, these are output to the workspace as images. Each plot can be colour-coded according to the usual range of measurements and values.
  
• "Kalman tracking" module runs TrackMate's Kalman filter-based tracking. This performs best on objects moving in a near-linear manner. This module can handle track splitting and merging. When splitting and merging are enabled, tracks will be broken down into segments, which are regions of the track that contain no splits and merges. These track segment objects are children of the main track objects and are themselves parents to the indivudal timepoint objects. As such, they are inserted between the normal tracks and objects in "standard" tracks. Splitting and merging can be disabled.
• "Overlap tracking 3D" facilitates tracking based on 3D overlap of objects. As with the Kalman tracking module, it can handle track splitting and merging.

New module features

• The "Add tracks" overlay module can handle tracks with splitting and merging by selecting either the top-level track parent or the track segment parent.

Other

• Other general bug fixes and optimisations.

Version 1.6.0

New plugin features

• Insert dynamic parameters from the plugin GUI. Dynamic parameters, introduced in v1.1.0, are references to image and object measurements or metadata values that can be used in place of normal parameters. These values are evaluated at the time of use, so for example, an intensity threshold could be set as an image measurement (e.g. median image intensity) rather than needing to be fixed in advance. References to these dynamic parameters can now be added by right-clicking on the parameter name and selecting "Insert dynamic value".
  

• References to global variables can now also be added from the plugin GUI using the same method as described above.

• Convert buttons, tickboxes and drop-downs to text inputs. All parameter types can now be converted to accept plain text inputs by right-clicking their names. This allows global variables and dynamic parameters to be used for any parameter.

• Text metadata can now be associated with each object. These text metadata items are assigned by modules in a similar way to measurements and can be used in operations such as object filtering and as overlay text labels.

New modules

• Added ObjectSlicesTo3D module, which allows objects detected in individual slices to be combined into full 3D objects. Examples where this could be used are objects output by CellposeDetection and StarDistDetection.
• Added FilterByMetadata module, which allows object metadata items to be used to filter objects.

New module features

• ApplyWekaObjectClassification now adds an object metadata item reporting the assigned class.
• AddLabels can add object metadata items as an overlay.
• ImageCalculator can now perform pixel-wise comparative tests (e.g. equal to, greater than, etc.) to images.

Other

• Other general bug fixes and optimisations.

Version 1.5.2

• Added ability to measure location of brightest pixel in an image via MeasureObjectIntensity module.
• Enabled multithreading in Elastix image registration module
• Updated ConcatenateStacks2 to allow ImgLib2 images to be combined without duplication. This action removes the input images from the workspace. ConcatenateStacks2 module can be accessed by enabling deprecated modules via Edit > Preferences.
• General bug fixes and performance improvements

Version 1.5.1

• Changing any parameters in InputControl will now automatically cause the test file to be updated when clicking a module evaluation button (arrow to right of module name in "Editing mode"
• Bugfix for LostAndFoundItem items not being found. This should allow older workflows to be more reliably loaded again.

Version 1.5.0

• Moved from a single Maven artefact to multiple modules. These can be used to import only the relevant parts of MIA into another project. At the lowest level, there are coordinate handling and algorithm artefacts. Above these is the mia-core artefact, which defines most of MIA's functionality. Then, above these are artefacts dealing with MIA modules and macros. Finally, modules that require additional ImageJ update sites to be enabled are placed in their own artefacts (e.g. mia-deepimagej).
• Added modules implementing the PTBIOP wrappers for Cellpose and Elastix. These are in the Maven artefact mia-ptbiop and will only appear when the PTBIOP update site is enabled.
• General bugfixes and improvements.

Version 1.4.9

• Added "AdoptParentMeasurement" module, which allows children to copy a measurement from a parent object. This can be used in cases where a "Parent measurement" option has not been implemented (e.g. in the AddTracks module, where instantaneous colours based on a parent measurement are explicitly implemented).
• Added ability to use position measurements in AddTracks and MeasureTrackMotion modules rather than positions based on integer coordinates.