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imcflibs.imagej.objects3d.get_objects_within_intensity removed,
as it is now present in the Image3D suite.
The methodmcib3d.geom.Objects3DPopulation.getObjectsWithinIntensityRange performs the same function as the removed method from this package.
imcflibs.imagej.misc.save_script_parameters to record all user-defined Fiji script parameters for reproducibility.
Saves the values of all #@ script inputs to a defined text file. Automatically excludes runtime parameters and any inputs declared with style="password".
Adds support for passing a list of files (list_files) directly to the define_dataset_manual function, enabling the use of explicit file lists in "show_list" mode rather than relying solely on file patterns.
Refactors the imcflibs.image.bdv.fuse_dataset_bdvp function to allow specifying the number of resolution levels, LZW compression, and the fusion method, and updated its parameter names and documentation for clarity and flexibility.
Utility and code quality improvements:
Adds a new utility function imcflibs.image.pathtools.join_files_with_channel_suffix to generate lists of filenames with channel suffixes, facilitating workflows where each channel is stored in a separate file.
Updates the imcflibs.imagej.bdv.resave_as_h5 function to use the correct processing options object and changed the ImageJ command to "Resave as HDF5 (local)" for better accuracy.
Imports and minor cleanups:
Adds import for AlphaFusedResampledSource to support the new fusion method default, and made minor whitespace and code cleanups.
Activity
ehrenfeu commentedon Jan 14, 2026
From #105
python-imcflibs/src/imcflibs/imagej/bioformats.py
Lines 355 to 356 in a6efb3f
ehrenfeu commentedon Jan 14, 2026
From #107
python-imcflibs/src/imcflibs/imagej/bdv.py
Line 792 in 60d8756
💡 See adfb659 for the relevant change. 💡
ehrenfeu commentedon Jan 14, 2026
From #97
https://github.com/imcf/python-imcflibs/pull/97/files#diff-4081a780db4183b557296c24ba3ff525cd37229282906f57c8cefca2fa04000bL24-R30
ehrenfeu commentedon Jan 14, 2026
From #103
https://github.com/imcf/python-imcflibs/pull/103/files#diff-f359b77c3cf49a2f6f603fe816a4f19e3b335dd6a53a8f5aa01c87e36742fe38L526-R556
rohangirishrao commentedon Jan 15, 2026
From PR #123
Removed function in
imcflibs.imagej.objects3dimcflibs.imagej.objects3d.get_objects_within_intensityremoved,as it is now present in the Image3D suite.
The method
mcib3d.geom.Objects3DPopulation.getObjectsWithinIntensityRangeperforms the same function as the removed method from this package.rohangirishrao commentedon Jan 21, 2026
From PR #140
New function in
imcflibs.imagej.miscimcflibs.imagej.misc.save_script_parametersto record all user-defined Fiji script parameters for reproducibility.Saves the values of all
#@script inputs to a defined text file. Automatically excludes runtime parameters and any inputs declared withstyle="password".This was removed in a later PR!
17 remaining items
CellKai commentedon Jun 24, 2026
From PR #107
imcflibs.imagej.bdv.define_dataset_autodoes not split time points by default any more.lguerard commentedon Jun 24, 2026
From PR #118
Enhancements to dataset definition and export:
imcflibs.image.bdv.fuse_dataset_bdvpfunction to allow specifying the number of resolution levels, LZW compression, and the fusion method, and updated its parameter names and documentation for clarity and flexibility.Utility and code quality improvements:
imcflibs.image.pathtools.join_files_with_channel_suffixto generate lists of filenames with channel suffixes, facilitating workflows where each channel is stored in a separate file.imcflibs.imagej.bdv.resave_as_h5function to use the correct processing options object and changed the ImageJ command to "Resave as HDF5 (local)" for better accuracy.Imports and minor cleanups:
AlphaFusedResampledSourceto support the new fusion method default, and made minor whitespace and code cleanups.lguerard commentedon Jun 24, 2026
From PR #116
imcflibs.pathtools.listdir_matchingfunction to support recursive directory traversal.lguerard commentedon Jun 24, 2026
From #104
Fix issue with java path object in
imcflibs.misc.save_image_with_extensionrohangirishrao commentedon Jun 24, 2026
From PR #146
Changes for interactive test files in
tests/interactive-imagej.py, so that they can be dragged directly into a Fiji and run.CellKai commentedon Jun 24, 2026
From PR #108
imcflibs.imagej.bioformats.import_imagenow accepts importing a specified image region (=crop).lguerard commentedon Jun 24, 2026
From PR #91
Adds pixel calibration to the converted file in
imcflibs.imagej.misc.run_imarisconvertCellKai commentedon Jun 24, 2026
From PR #110
Add dependencies to installation instructions
rohangirishrao commentedon Jun 24, 2026
From PR #133
Enhance installation instructions in README.md
CellKai commentedon Jun 24, 2026
From PR #112
Add a function to set a TrackMate spot filter with specified filter key and values in
imcflibs.imagej.trackmate.set_spotfilterCellKai commentedon Jun 24, 2026
From PR #124
Fix Ruff linting errors in
imcflibs.imagej.trackmate.set_spotfilter