v4.2.6

What's Changed

There are no changes to the functional CellProfiler codebase in this release compared to 4.2.5; the only changes are changes intended to make it easier to pip install CellProfiler by updating some pins that did not have wheels on some modern systems, and pinning at the top of their range packages whose updates break existing functionality. If you are using CellProfiler downloaded from our website, there is no need to update; these changes should only affect those installing via a local Python environment.

PRs

• Tighten some pins, loosen others by @bethac07 in #4801
• Recreate #4638 in 4.2.x by @bethac07 in #4803

Full Changelog: v4.2.5...v4.2.6

v4.2.5

What's Changed

• fix subsample values >1 overwriting input image by @callum-jpg in #4697
• Patch headless creation of properties files by @bethac07 in #4698
• Update resize.py by @bdiazroh in #4701
• Catch "no objects of any type" by @bethac07 in #4699

Also from Core

• Fix 3D object loading by @Mas515 in CellProfiler/core#135
• Don't break when loading with pipes in notes, 4.2.5 edition by @bethac07 in CellProfiler/core#137

Full Changelog: v4.2.4...v4.2.5

v4.2.4

What's Changed

• "Ignore errors" mode
• 3D CellProfiler Analyst support and better CellProfiler Analyst compatibility with fuzzy column matching
• Better deep learning compatibility with the SaveCroppedObjects module
• Lots of bug fixes, and some additional features

CellProfiler 4.2.4 differs from 4.2.3 only for users installing from PyPI, other users may use either version

New Contributors

@gnodar01, @Jihyeon-Je, @rsenft1, @LukeOZN, @callum-jpg, @ximion, @bdiazroh, @crisluengo, @vbruttin, @maldil, @ovesh

v4.2.3

• "Ignore errors" mode
• 3D CellProfiler Analyst support and better CellProfiler Analyst compatibility with fuzzy column matching
• Better deep learning compatibility with the SaveCroppedObjects module
• Lots of bug fixes, and some additional features

v4.2.3rc1

• Bump python-bioformats to 4.0.6
• Add widget_inspector option
• New way to make batch commands
• Allow users to run without stopping for errors in GUI and headless mode
• Add Numpy 1.23 support
• Add image ordering info to documentation
• Add additional save features to SaveCroppedObjects
• Add several customization options to DisplayDataOnImage
• Add z-dimension transform to resize
• Allow build with Python 3.9.x
• Add Z coordinates and 3D flag to exporttodatabase
• Add log transform settings to module help
• Add debug interpreter
• Revise workspace viewer default colors
• Add option to disable bit depth conversion in SaveImages
• Add convex hull mode to FillObjects
• Support display of text-based measurements
• Improve java detection in builds
• Add "FindMaxima" module
• Improve file list loader performance
• Other Bug Fixes

v4.2.1

• Fixed loading of pipelines containing older versions of the ClassifyObjects module.
• Fixed compatibility with some .model file types.
• Fixed loading of .cpproj files from older versions of CellProfiler.
• Improved error handling and display when entering test mode with images missing.
• Upgraded pipelines will now use the "faster" Costes method in MeasureColocalisation by default.
• In IdentifyPrimaryObjects, size of displayed local maxima is now configurable.
• Other bug fixes

v4.2.0

• ClassifyObjects can now assign classes using a model from CellProfiler Analyst 3.
• FilterObjects now supports models from CellProfiler Analyst 3.
• Objects removed by FilterObjects can now be retained as a second object set.
• ExportToDatabase now automatically detects image colours when generating CPA .properties files.
• Fixed CorrectIlluminationCalculate performance when using a median filter with a large window.
• Added 'advanced' mode to the Watershed module, based on the DeclumpObjects plugin.
• CombineObjects now supports 3D pipelines.
• Improved general performance of the CombineObjects module.
• Fixed a bug which prevented some pipelines made on MacOS from being loaded on Windows.
• On Windows, pipelines and projects should now load when starting CellProfiler with "Open With...".
• Fixed a bug which caused file lists to fail to save properly.
• Added tiff compression option to SaveImages.
• Other bug fixes.

v4.1.3

• New module: RunImageJMacro
• Fixed the 3D viewer
• Added "conserve memory" preference for machines with limited resources.
• ImageMath now properly respects the "ignore masks" option.
• Added standard deviation projection option to ImageMath.
• Fixed a bug where the Threshold module could hang.
• Added optional JSON pipeline format
• Other bug fixes

v4.0.7

• Added log normalisation option to thresholding. Replicates CP3's 3-class Otsu results.
• Added a faster Costes calculation method to MeasureColocalization.
• Fixes to pipeline loading.
• Fixed some startup issues.
• Other bug fixes

v4.0.6

• Fixed an issue with figure display in some modules.
• MeasureImageIntensity now supports calculation of custom percentiles.
• Fixed a bug with CombineObjects not saving object counts.
• Other bug fixes