pyHiM

What's Changed

• Remove deprecated projectsBarcodes, refitBarcodes, localDriftCorrection modules in https://github.com/marcnol/pyHiM/pull/100
• added feature analyze_localizations in https://github.com/marcnol/pyHiM/pull/105
• Update pyHiM args parsing to use 2D and 3D shortcuts in https://github.com/marcnol/pyHiM/pull/108
• Feature/compare matrices in https://github.com/marcnol/pyHiM/pull/114
• Export to apiFISH functions from makeProjections in https://github.com/marcnol/pyHiM/pull/110
• segmentMasks3D outputs 2D and 3D labeled images in https://github.com/marcnol/pyHiM/pull/121
• added anisotropic tolerance drift in https://github.com/marcnol/pyHiM/pull/123
• Fix issues to run with pip installation in https://github.com/marcnol/pyHiM/pull/124
• Feature/plot trace 3d in https://github.com/marcnol/pyHiM/pull/136
• Remove useless generated files in https://github.com/marcnol/pyHiM/pull/118
• Feature/polygon trace in https://github.com/marcnol/pyHiM/pull/140
• 3D tracing enabled in https://github.com/marcnol/pyHiM/pull/146
• added distance threshold in https://github.com/marcnol/pyHiM/pull/148
• changed how matrix is converted into vector in https://github.com/marcnol/pyHiM/pull/153
• Refactor - makeProjections, Pipeline, Dask in https://github.com/marcnol/pyHiM/pull/159
• Doc (dev) - Describe no python files & build doc in https://github.com/marcnol/pyHiM/pull/160
• added filter for max distance in https://github.com/marcnol/pyHiM/pull/164
• Refactor parameters in https://github.com/marcnol/pyHiM/pull/167
• Ensures ROI uniqueness in https://github.com/marcnol/pyHiM/pull/181
• Clean deprecated outputs in https://github.com/marcnol/pyHiM/pull/182
• Rename parameter filename from "infoList.json" to "parameters.json" in https://github.com/marcnol/pyHiM/pull/183
• Update routine names in https://github.com/marcnol/pyHiM/pull/184
• Split outputs between data and human readable PNG in https://github.com/marcnol/pyHiM/pull/186
• bootstrapping in https://github.com/marcnol/pyHiM/pull/188
• added cellpose segmentation in https://github.com/marcnol/pyHiM/pull/191
• Refactor/align images to RegisterGlobal Feature in https://github.com/marcnol/pyHiM/pull/193
• Feature/mask cellpose in https://github.com/marcnol/pyHiM/pull/194
• Refactor/folders in https://github.com/marcnol/pyHiM/pull/204
• Refactor/parameters in https://github.com/marcnol/pyHiM/pull/207
• Integrate stardist in https://github.com/marcnol/pyHiM/pull/209
• Remove cv2 in https://github.com/marcnol/pyHiM/pull/221
• Fix (trace_filter) - Missing case 'label is None' in https://github.com/marcnol/pyHiM/pull/230
• Update environment yaml in https://github.com/marcnol/pyHiM/pull/232
• Tuto cellpose in https://github.com/marcnol/pyHiM/pull/233

Full Changelog: https://github.com/marcnol/pyHiM/compare/v0.7.0...v0.9.1

• Documentation refactoring
• Documentation available on ReadTheDocs
• Publication of pyHiM on the Python Package Index
• Remove deprecated files
• Graphical interface to configure pyHiM parameters

Full Changelog: https://github.com/marcnol/pyHiM/compare/v0.6.0...v0.7.0

Major changes

• created script to run SLURM jobs
• added mask segmentation in 3D using stardist
• updated AI network for 3D barcode segmentation
• compatibility with scikit-image 0.19
• generalized masks (not only based on DAPI)
• barcode localization filtering
• fully refactored buildPWDmatrix into: filter_localizations, register_localizations, build_traces, build_matrix
• use apiFISH instead of bigFISH for barcode gaussian fitting
• routine to analyze trace table files
• routine to filter trace table files

What's Changed

• Development by @marcnol in https://github.com/marcnol/pyHiM/pull/11

Full Changelog: https://github.com/marcnol/pyHiM/compare/v0.2.0...v0.3.0

Full Changelog: https://github.com/marcnol/pyHiM/commits/v0.2.0

• Fixed several bugs regarding segmentation of barcodes by stardist.
• Added 3D segmentation of nuclei masks using stardist.
• rewrote runHiM_cluster to use it in supercomputer center (mesoLR) and in lab cluster.
• fixed issues with compatibility with scikit image 0.19

Major changes:

• 3D local re-alignment using block decomposition
• 3D direct fitting using bigFISH
• Re-organization of infoList.json into a single parameter file.

What's Changed

• detect oldRT automatically in changeRT_infoList.py by @mg42 in https://github.com/marcnol/pyHiM/pull/13

Full Changelog: https://github.com/marcnol/pyHiM/compare/v0.3.0...v0.4.0