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Colocalization cellmap tweak#161

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completementgaga wants to merge 44 commits intoClearAnatomics:v3.0.xClearAnatomics/ClearMap:v3.0.xfrom completementgaga:colocalization-cellmap-tweakcompletementgaga/ClearMap2:colocalization-cellmap-tweakCopy head branch name to clipboard

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Commits on Feb 26, 2025

• added the function label_representatives to maxima_detection.py, for example it allows to select a unique representative in each connect component of maxima.

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• Modified detect_cells_block using label_representatives, to avoid double detection of cells.

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• added detect_shape_mask to shape detection

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• added the option to specify dtype in the (if save:) clause of run_step

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• removed debug print calls

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• added the option save_as_binary_mask in run_cell_detection

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• removed wrong warning comment.

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• made detect_shape more versatile and removed its binary version.

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• added the forgotten watershed_line option

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• added sanity binarization in run_step

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• allow dtype specification from cell_detection_parameter in initialize_sinks

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• allow dtype specification from cell_detection_parameter in initialize_sinks

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• fixed forgotten case in the new shape_detection

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• Added the presave_parser option to parse result before saving in run_step.

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• fixed shape detection step using the presave_parser option orf run_step

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• removed old commented out code

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• Added RuntimeError exception in case watershedding would behave unexpectedly.

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• removed debug print call

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• edited the maxima representative extraction lines

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• added the case of mask=None in RuntimeError

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• removed some print calls

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• Added simple histo transfo when possible and added exception in shape_detection, to avoid buggy use of watershedding.

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• added a method to label pixels from their coords, nd version available in comments for python >= 3.11

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• fixed detect_shape with new computation of peaks, before that, the call to voxelize could yield nonseparated peaks and cause bugs

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• removed debug prints and added a comment

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• added the option to pass directly the initialized basins for watershedding in shape detection

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Commits on Feb 27, 2025

• erase any prior existing file at shape_path to prevent confusion of sink with source in IO.initialize

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• fixed merging error

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• replaced undue expectation of None output from AssetCollection.__getitem__ by "key in .." check.

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• DOC:docstring enhancement

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• made colocalization tests suitable for distribution

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Commits on Mar 3, 2025

• Update parallelism_test.py

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• Update parallelism_test.py

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• Update utils.py

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• Update cell_map.py

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• Update utils.py

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• Update Cells.py

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• Update Cells.py

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• Update Cells.py

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• Update workspace2.py

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Commits on Mar 5, 2025

• Update utils.py

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• Update parallelism_test.py

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• Update shape_detection.py

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• Update shape_detection.py

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