From af827a04d741fb1fba851643e1b04127606b8b5f Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Wed, 24 Jun 2026 16:28:10 +0200 Subject: [PATCH 1/4] Add all changes for major release 2.0.0 --- CHANGELOG.md | 115 ++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 114 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 892dbc51..7fef0688 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,10 +4,123 @@ ## 2.0.0 -### Changed +This major release brings a host of additions and breaking changes across +multiple modules. For detailed information, please refer to the +[API documentation][apidocs]. + +### Added โœจ + +#### 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 โ™ป๏ธ * 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.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.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`: + * Enhancement to support recursive directory traversal + * Adds `recursive` parameter to include files from subdirectories + +### Removed ๐Ÿ—‘๏ธ + +#### `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 ๐Ÿ“ + +* Update `README.md` installation instructions to install imcflibs into a + "vanilla" Fiji, including required dependencies. + +### Interactive Tests ๐Ÿงช + +* All interactive test files in `tests/interactive-imagej` are now `.py`, so + that they can be dragged directly into a Fiji and run. + ## 1.5.0 This release brings a lot of additions, not all changes and functions are From a28b505b43b0dc00a2691be119ea60c1cbe1bb7f Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Wed, 24 Jun 2026 16:36:17 +0200 Subject: [PATCH 2/4] Change listing indentation to make linter happy --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7fef0688..afc0a96d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -99,8 +99,8 @@ multiple modules. For detailed information, please refer to the #### `imcflibs.pathtools` * `imcflibs.pathtools.listdir_matching`: - * Enhancement to support recursive directory traversal - * Adds `recursive` parameter to include files from subdirectories + * Add support for recursive directory traversal. + * Add `recursive` parameter to include files from subdirectories. ### Removed ๐Ÿ—‘๏ธ From 5965eff225f74271ff5d0594bba6cd2a4825020b Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Thu, 25 Jun 2026 13:47:25 +0200 Subject: [PATCH 3/4] Add minor changes that were missed --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index afc0a96d..635faa40 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -63,6 +63,7 @@ multiple modules. For detailed information, please refer to the * `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` @@ -73,6 +74,7 @@ multiple modules. For detailed information, please refer to the 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 `suffix`to append custom text to output filenames. #### `imcflibs.imagej.objects3d` From 019cf51b2ad796dc5c70c6b85b574f1f51ad605a Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Thu, 25 Jun 2026 13:50:31 +0200 Subject: [PATCH 4/4] Shorten lines to pass linter check --- CHANGELOG.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 635faa40..9bfa2a33 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -61,9 +61,10 @@ multiple modules. For detailed information, please refer to the #### `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.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` @@ -74,7 +75,8 @@ multiple modules. For detailed information, please refer to the 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 `suffix`to append custom text to output filenames. +* `imcflibs.imagej.misc.save_image_in_format`: This method also accepts a new + optional parameter `suffix`to append custom text to output filenames. #### `imcflibs.imagej.objects3d`