Prep for new looptrace

CHANGELOG.md

@@ -4,7 +4,21 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.3.0] - 2024-11-20
+This is compatible with the 0.11.x line of `looptrace`.
+
+### Changed
+* Updated expected column and file names of input to match those emitted by `looptrace` processing; 
+in particular, the file previously represented by `*_rois.proximity_accepted.nuclei_labeled.csv` is replaced by `*_rois.with_trace_ids.csv`.
+
+### Added
+* Now the joint tracing structure of ROIs from different regional barcodes / imaging timepoints can be visualised.
+
+### Changed
+* Adapted to new `looptrace` column names
+
 ## [v0.2.0] - 2024-10-21
+* This is compatible with the 0.10.x line line of `looptrace`.
 
 ### Changed
 * Patterns expected for input files:

docs/using-the-plugin.md

@@ -31,15 +31,17 @@ The spots are color-coded:
 
 Spot shape differs by $z$-slice; the $z$-slice closest to the truncated $z$-coordinate of the spot's centroid will be square while everywhere else will be circular. We do not add $z$ slices for spots for which the bounding box extends below $0$, but there can be $z$ slices "beyond" the true images, if a spot was detected close to the max $z$ depth. This may also change in a future release.
 
-For the ROIs/spots _resulting from_ a merger, you should see the ID of the ROI itself and the IDs of those which were merged to create it. 
-For the ROIs/spots _contributing to_ a merger, you should see the ID of the ROI itself and the ID(s) of the ROI(s) to which it contributed.
+Some spots are labeled:
+* For the ROIs/spots _resulting from_ a merger, you should see the ID of the ROI itself (`i=<merge ID>`).
+* For the ROIs/spots _contributing to_ a merger, you should see the ID of the resulting merger ROI (`i=<merge ID>`).
+* For the ROIs which participate in a larger tracing structure, you should see the ID (`t=<trace ID>`).
 
 ### Necessary data files
 1. 1 ZARR per field of view you wish to view, named like `P0001.zarr`
 1. 0 or 1 files of each of the following types, per field of view, organized into a folder that has the same field of view name as the ZARR, e.g. `P0001`. There must be at least 1 of these 3 files present:
     - A `*_rois.csv` file: unfiltered regional spots
     - A `*_rois.proximity_accepted.csv` file: regional spots after discarding those which are too close together
-    - A `*_rois.proximity_accepted.nuclei_labeled.csv` file: regional spots after proximity-based filtration and filtration for inclusion in nuclei
+    - A `*_rois.with_trace_ids.csv` file: regional spots after proximity-based filtration and labeling attribution of ROIs/spots to nuclei
 
 ### File format notes
 * For each spot, the following must be parsed:
@@ -51,4 +53,9 @@ For the ROIs/spots _contributing to_ a merger, you should see the ID of the ROI
 * The bounding box is defined by columns suffixed `Min` and `Max` for each axis, e.g. `zMin`, `zMax`, etc.
 * The timepoint is read from column `timepoint`.
 * The channel is read from the `channel` column.
-* For the `*_rois.proximity_accepted.nuclei_labeled.csv` file, `mergeRois` and `nucleusNumber` columns are parsed.
+* For the merge contributors file, the `mergeOutput` column is parsed to get the ID of the merge result.
+* For the `*_rois.with_trace_ids.csv` file, the following additional columns are parsed:
+    * `mergePartners` (to tell singleton ROIs from merger output ROIs)
+    * `nucleusNumber` (to tell nuclear from non-nuclear ROIs)
+    * `traceId` (to label ROIs which participate in a multi-ROI trace)
+    * `tracePartners` (to determine whether a ROI participates in a multi-rOI trace)

looptrace_regionals_vis/__init__.py

@@ -10,7 +10,7 @@
 
 from numpydoc_decorator import doc  # type: ignore[import-untyped]
 
-__version__ = "0.2.0"
+__version__ = "0.3"
 
 _PACKAGE_NAME = package = Path(__file__).parent.name
 

looptrace_regionals_vis/examples/P0001_rois.merge_contributors.csv

@@ -1,10 +1,10 @@
-index,fieldOfView,timepoint,spotChannel,zc,yc,xc,intensityMean,zMin,zMax,yMin,yMax,xMin,xMax,mergeIndices
+index,fieldOfView,timepoint,spotChannel,zc,yc,xc,intensityMean,zMin,zMax,yMin,yMax,xMin,xMax,mergeOutput
 0,P0001.zarr,79,0,3.907628987532479,231.9874778925304,871.9833511648726,118.26726920593931,-2.092371012467521,9.90762898753248,219.9874778925304,243.9874778925304,859.9833511648726,883.9833511648726,101
-1,P0001.zarr,79,0,17.994259347453493,24.042015416774795,1360.0069098862991,117.1394688491732,11.994259347453491,23.994259347453493,12.042015416774795,36.0420154167748,1348.0069098862991,1372.0069098862991,102;103
+1,P0001.zarr,79,0,17.994259347453493,24.042015416774795,1360.0069098862991,117.1394688491732,11.994259347453491,23.994259347453493,12.042015416774795,36.0420154167748,1348.0069098862991,1372.0069098862991,103
 2,P0001.zarr,79,0,23.00910242218976,231.98008711401275,871.9596645390719,116.14075915047448,17.009102422189756,29.00910242218976,219.98008711401275,243.98008711401275,859.9596645390719,883.9596645390719,101
-3,P0001.zarr,79,0,16.527137137619988,422.5165732477932,667.2129969610728,157.0530303030303,10.527137137619988,22.527137137619988,410.5165732477932,434.5165732477932,655.2129969610728,679.2129969610728,102;103
-4,P0001.zarr,79,0,16.950424004488077,118.88259896330818,349.6540530977019,161.81065410400436,10.950424004488076,22.95042400448808,106.88259896330818,130.88259896330817,337.6540530977019,361.6540530977019,102;103
+3,P0001.zarr,79,0,16.527137137619988,422.5165732477932,667.2129969610728,157.0530303030303,10.527137137619988,22.527137137619988,410.5165732477932,434.5165732477932,655.2129969610728,679.2129969610728,102
+4,P0001.zarr,79,0,16.950424004488077,118.88259896330818,349.6540530977019,161.81065410400436,10.950424004488076,22.95042400448808,106.88259896330818,130.88259896330817,337.6540530977019,361.6540530977019,103
 5,P0001.zarr,79,0,18.177805530982404,445.4564669785048,607.9657421380375,160.33961681087763,12.177805530982404,24.177805530982404,433.4564669785048,457.4564669785048,595.9657421380375,619.9657421380375,100
-6,P0001.zarr,79,0,17.83959674876146,1006.0753359579252,306.5263466292306,160.1254275940707,11.839596748761458,23.83959674876146,994.0753359579252,1018.0753359579252,294.5263466292306,318.5263466292306,100
+6,P0001.zarr,79,0,17.83959674876146,1006.0753359579252,306.5263466292306,160.1254275940707,11.839596748761458,23.83959674876146,994.0753359579252,1018.0753359579252,294.5263466292306,318.5263466292306,102
 7,P0001.zarr,79,0,17.70877472362621,1040.482813665982,290.6567022086824,163.12094117647058,11.70877472362621,23.70877472362621,1028.482813665982,1052.482813665982,278.6567022086824,302.6567022086824,100
 8,P0001.zarr,79,0,17.294947508199503,1701.3423124347908,1665.0076588607058,152.65736930345983,11.294947508199504,23.294947508199503,1689.3423124347908,1713.3423124347908,1653.0076588607058,1677.0076588607058,101

looptrace_regionals_vis/examples/P0001_rois.proximity_accepted.nuclei_labeled.csv → looptrace_regionals_vis/examples/P0001_rois.with_trace_ids.csv

@@ -1,10 +1,10 @@
-index,fieldOfView,timepoint,spotChannel,zc,yc,xc,intensityMean,zMin,zMax,yMin,yMax,xMin,xMax,mergeRois,nucleusNumber
-3,P0001.zarr,79,0,16.527137137619988,422.5165732477932,667.2129969610728,157.0530303030303,10.527137137619988,22.527137137619988,410.5165732477932,434.5165732477932,655.2129969610728,679.2129969610728,100;101,3
-4,P0001.zarr,79,0,16.950424004488077,118.88259896330818,349.6540530977019,161.81065410400436,10.950424004488076,22.95042400448808,106.88259896330818,130.88259896330817,337.6540530977019,361.6540530977019,,2
-5,P0001.zarr,79,0,18.177805530982404,445.4564669785048,607.9657421380375,160.33961681087763,12.177805530982404,24.177805530982404,433.4564669785048,457.4564669785048,595.9657421380375,619.9657421380375,,3
-6,P0001.zarr,79,0,17.83959674876146,1006.0753359579252,306.5263466292306,160.1254275940707,11.839596748761458,23.83959674876146,994.0753359579252,1018.0753359579252,294.5263466292306,318.5263466292306,102;110,7
-7,P0001.zarr,79,0,17.70877472362621,1040.482813665982,290.6567022086824,163.12094117647058,11.70877472362621,23.70877472362621,1028.482813665982,1052.482813665982,278.6567022086824,302.6567022086824,,7
-8,P0001.zarr,79,0,17.294947508199503,1701.3423124347908,1665.0076588607058,152.65736930345983,11.294947508199504,23.294947508199503,1689.3423124347908,1713.3423124347908,1653.0076588607058,1677.0076588607058,,4
-10,P0001.zarr,79,0,18.5289337545209,28.24453371789589,1634.215648033695,149.63521150882,12.5289337545209,24.5289337545209,16.244533717895894,40.24453371789589,1622.215648033695,1646.215648033695,,0
-11,P0001.zarr,79,0,18.266489401564822,533.7770489058973,1747.1225533182217,159.3707150612688,12.266489401564826,24.266489401564822,521.7770489058973,545.7770489058973,1735.1225533182217,1759.1225533182217,121;131,4
-12,P0001.zarr,79,0,18.09858176406764,863.1257478224696,984.5327240679828,146.90628445424477,12.09858176406764,24.09858176406764,851.1257478224696,875.1257478224696,972.5327240679828,996.5327240679828,,5
+index,fieldOfView,timepoint,spotChannel,zc,yc,xc,intensityMean,zMin,zMax,yMin,yMax,xMin,xMax,mergePartners,nucleusNumber,traceId,tracePartners
+3,P0001.zarr,79,0,16.527137137619988,422.5165732477932,667.2129969610728,157.0530303030303,10.527137137619988,22.527137137619988,410.5165732477932,434.5165732477932,655.2129969610728,679.2129969610728,100;101,3,13,5
+4,P0001.zarr,79,0,16.950424004488077,118.88259896330818,349.6540530977019,161.81065410400436,10.950424004488076,22.95042400448808,106.88259896330818,130.88259896330817,337.6540530977019,361.6540530977019,,2,14,
+5,P0001.zarr,79,0,18.177805530982404,445.4564669785048,607.9657421380375,160.33961681087763,12.177805530982404,24.177805530982404,433.4564669785048,457.4564669785048,595.9657421380375,619.9657421380375,,3,13,3
+6,P0001.zarr,79,0,17.83959674876146,1006.0753359579252,306.5263466292306,160.1254275940707,11.839596748761458,23.83959674876146,994.0753359579252,1018.0753359579252,294.5263466292306,318.5263466292306,102;110,7,16,7;12
+7,P0001.zarr,79,0,17.70877472362621,1040.482813665982,290.6567022086824,163.12094117647058,11.70877472362621,23.70877472362621,1028.482813665982,1052.482813665982,278.6567022086824,302.6567022086824,,7,16,6;12
+8,P0001.zarr,79,0,17.294947508199503,1701.3423124347908,1665.0076588607058,152.65736930345983,11.294947508199504,23.294947508199503,1689.3423124347908,1713.3423124347908,1653.0076588607058,1677.0076588607058,,4,17,
+10,P0001.zarr,79,0,18.5289337545209,28.24453371789589,1634.215648033695,149.63521150882,12.5289337545209,24.5289337545209,16.244533717895894,40.24453371789589,1622.215648033695,1646.215648033695,,0,18,
+11,P0001.zarr,79,0,18.266489401564822,533.7770489058973,1747.1225533182217,159.3707150612688,12.266489401564826,24.266489401564822,521.7770489058973,545.7770489058973,1735.1225533182217,1759.1225533182217,121;131,4,19,
+12,P0001.zarr,79,0,18.09858176406764,863.1257478224696,984.5327240679828,146.90628445424477,12.09858176406764,24.09858176406764,851.1257478224696,875.1257478224696,972.5327240679828,996.5327240679828,,5,16,6;7

looptrace_regionals_vis/napari.yaml

@@ -9,5 +9,5 @@ contributions:
     filename_patterns:
     - '*_rois.merge_contributors.csv'
     - '*_rois.proximity_rejected.csv'
-    - '*_rois.proximity_accepted.nuclei_labeled.csv'
+    - '*_rois.with_trace_ids.csv'
     accepts_directories: true