imcf/python-imcflibs: python-imcflibs-2.0.0

This major release brings a host of additions and breaking changes across multiple modules. For detailed information, please refer to the API documentation.

Added ✨

New functions in imcflibs.imagej.bioformats

• imcflibs.imagej.bioformats.get_reader gets the reader used for opening a file, allowing support for multi series files, and gets the highest pyramid level for infos.

New functions in imcflibs.imagej.bdv

• imcflibs.imagej.bdv.read_metadata_from_xml allows reading metadata back from the xml of a H5/XML couple.

New functions in imcflibs.imagej.misc

• imcflibs.imagej.misc.bytes_to_human_readable converts size from bytes to a more readable format.

New functions in imcflibs.imagej.trackmate

• imcflibs.imagej.trackmate.set_spotfilter to set a TrackMate spot filter with specified filter key and values.

New functions in imcflibs.imagej.pathtools

• imcflibs.imagej.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.

Changed ♻️

• Minimum required version for [python-micrometa] increased to 15.2.3.

imcflibs.imagej.bdv

• imcflibs.imagej.bdv.define_dataset_auto does not split time points by default any more.
• imcflibs.imagej.bdv.define_dataset_manual now supports passing a list of files (list_files) directly, enabling the use of explicit file lists in "show_list" mode rather than relying solely on file patterns.
• imcflibs.imagej.bdv.fuse_dataset_bdvp:
  • Fix a bug and expose additional parameters.
  • Allow specifying the number of resolution levels, LZW compression, and the fusion method; update parameter names and documentation for clarity and flexibility.
• imcflibs.imagej.bdv.interest_points_registration: Fix typo and add missing options.
• imcflibs.imagej.bdv.resave_as_h5: use the correct processing options object and change the ImageJ command to "Resave as HDF5 (local)" for better accuracy.

imcflibs.imagej.bioformats

• imcflibs.imagej.bioformats.import_image now accepts importing a specified image region (crop). Also fix a spelling mistake.
• imcflibs.imagej.bioformats.get_stage_coords returns the filename instead of full path.

imcflibs.imagej.misc

• imcflibs.imagej.misc.run_imarisconvert:
  • Now allows to select an output folder.
  • Adds pixel calibration to the converted file.
• imcflibs.imagej.misc.subtract_images now validates the slice count is equal for both images.
• imcflibs.imagej.misc.save_image_with_extension: fix issue with java path object.
• imcflibs.imagej.misc.save_image_in_format: This method also accepts a new optional parameter suffixto append custom text to output filenames.

imcflibs.imagej.objects3d

• imcflibs.imagej.objects3d.segment_3d_image: add option to filter out 3D objects touching the image borders when creating a label image.

imcflibs.imagej.resultstable

• imcflibs.imagej.resultstable.add_results_to_resultstable:
  • Add support for writing values to specific rows in a results table.
  • Raise an error when provided values don't match target rows.
  • Update docstring description and examples.

imcflibs.imagej.trackmate

• Improve support for 3D data and fix an issue for diameter of objects to be found using TrackMate.

imcflibs.omerotools

• imcflibs.omerotools.parse_url: safely handle empty input strings, and strip the link to ignore trailing white spaces.

imcflibs.pathtools

• imcflibs.pathtools.listdir_matching:
  • Add support for recursive directory traversal.
  • Add recursive parameter to include files from subdirectories.

Removed 🗑️

imcflibs.imagej.objects3d

• imcflibs.imagej.objects3d.get_objects_within_intensity has been removed as it is now present in the Image3D suite. The method mcib3d.geom.Objects3DPopulation.getObjectsWithinIntensityRange performs the same function as the removed method from this package.

Documentation 📝

• Update README.md installation instructions to install imcflibs into a "vanilla" Fiji, including required dependencies.

Interactive Tests 🧪

• All interactive test files in tests/interactive-imagej are now .py, so that they can be dragged directly into a Fiji and run.