Recent Releases of cellprofiler
cellprofiler - v4.2.8
What's Changed
- fix label assignment when different objects are neighbors by @bethac07 in https://github.com/CellProfiler/CellProfiler/pull/4929
- Bump to core 4.2.8 by @gnodar01 in https://github.com/CellProfiler/core/releases/tag/v4.2.8
Full Changelog: https://github.com/CellProfiler/CellProfiler/compare/v4.2.7...v4.2.8
- Python
Published by github-actions[bot] almost 2 years ago
cellprofiler - v4.2.7
Addresses issues CellProfiler/CellProfiler#4875, CellProfiler/CellProfiler#4873, CellProfiler/CellProfiler#4888, CellProfiler/CellProfiler#4890, CellProfiler/CellProfiler#4858, CellProfiler/CellProfiler#4833, CellProfiler/CellProfiler#4817, CellProfiler/CellProfiler#4862, CellProfiler/CellProfiler#4906
This release tackles a few minor issues, and most importantly is a working build of centrosome.
- Python
Published by github-actions[bot] almost 2 years ago
cellprofiler - 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 https://github.com/CellProfiler/CellProfiler/pull/4801
- Recreate #4638 in 4.2.x by @bethac07 in https://github.com/CellProfiler/CellProfiler/pull/4803
Full Changelog: https://github.com/CellProfiler/CellProfiler/compare/v4.2.5...v4.2.6
- Python
Published by github-actions[bot] almost 3 years ago
cellprofiler - v4.2.6rc1
What's Changed
- Tighten some pins, loosen others by @bethac07 in https://github.com/CellProfiler/CellProfiler/pull/4801
Full Changelog: https://github.com/CellProfiler/CellProfiler/compare/v4.2.5...v4.2.6rc1
- Python
Published by bethac07 almost 3 years ago
cellprofiler - v4.2.5
What's Changed
- fix subsample values >1 overwriting input image by @callum-jpg in https://github.com/CellProfiler/CellProfiler/pull/4697
- Patch headless creation of properties files by @bethac07 in https://github.com/CellProfiler/CellProfiler/pull/4698
- Update resize.py by @bdiazroh in https://github.com/CellProfiler/CellProfiler/pull/4701
- Catch "no objects of any type" by @bethac07 in https://github.com/CellProfiler/CellProfiler/pull/4699 ## Also from Core
- Fix 3D object loading by @mas515 in https://github.com/CellProfiler/core/pull/135
- Don't break when loading with pipes in notes, 4.2.5 edition by @bethac07 in https://github.com/CellProfiler/core/pull/137
Full Changelog: https://github.com/CellProfiler/CellProfiler/compare/v4.2.4...v4.2.5
- Python
Published by github-actions[bot] over 3 years ago
cellprofiler - 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
- Python
Published by github-actions[bot] almost 4 years ago
cellprofiler - 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
- Python
Published by github-actions[bot] almost 4 years ago
cellprofiler - 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
- Python
Published by github-actions[bot] almost 4 years ago
cellprofiler - 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
- Python
Published by github-actions[bot] almost 5 years ago
cellprofiler - 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.
- Python
Published by github-actions[bot] about 5 years ago
cellprofiler - 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
- Python
Published by github-actions[bot] over 5 years ago
cellprofiler - 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
- Python
Published by github-actions[bot] over 5 years ago
cellprofiler - 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
- Python
Published by github-actions[bot] over 5 years ago
cellprofiler - v4.0.5
- Fixed a crash when starting CellProfiler on non-English Windows versions.
- Added "trace module inputs/outputs" function.
- Brightness adjustment now works on colour plots.
- Assorted bug fixes.
- Python
Published by github-actions[bot] almost 6 years ago
cellprofiler - v4.0.4
- Fixed a bug where CellProfiler would fail to start on certain international versions of Windows.
- Moved the 3D viewer plane controls up to the toolbar, instead of them being part of the plot. This should improve performance.
- Added a "Check for updates" option to the "Help" menu. CellProfiler will now automatically notify users of new releases. This can be disabled in the preferences window.
- Assorted bug fixes.
- Python
Published by github-actions[bot] almost 6 years ago
cellprofiler - v3.1.9
- Minor bug fixes to RelateObjects and IdentifySecondaryObjects
This will be the final release in the CellProfiler 3.X series.
- Python
Published by bethac07 almost 7 years ago
cellprofiler - v3.1.8
Bug fixes in: * The nasty 'object index' bug in MeasureObjectIntensity/MeasureColocalization and a few more * The Circular Average Filter in Smooth * Writing in ExportToSpreadsheet when some objects have been filtered * The Median filter in CorrectIlluminationCalculate * Hitting 'Cancel' after a bug now actually cancels the run
- You can now pick-and-choose which measurements to run in MeasureColocalization
- Python
Published by bethac07 over 7 years ago
cellprofiler - v3.1.4
- Fix for rescaling bug in 3D
- Number of dependency updates
- Updated documentation for 3D modules
- Python
Published by bethac07 about 8 years ago
cellprofiler - 3.1.3
Fix for headless/GUI config differences.
- Python
Published by AetherUnbound over 8 years ago
cellprofiler - 3.1.2
Ensure backwards compatibility of watershed module and enable saving 5+ channel tiffs
- Python
Published by AetherUnbound over 8 years ago
cellprofiler - 3.1.1
Minor change to the watershed module for backwards compatibility.
- Python
Published by AetherUnbound over 8 years ago
cellprofiler - 2.3.1
Fixes bug preventing users to download .mat files from s3.
- Python
Published by mcquin over 8 years ago
cellprofiler - 2.3.0
Support s3 URLs, via boto3. See instructions for setup.
- Python
Published by mcquin over 8 years ago
cellprofiler - 2.2.2
Motivation: Users were unable to install CP2.2.1 correctly in pure pip.
Changes: * New dependency pinning (per #3488) ensure CP2.2.2 can be installed in pure pip * wx < 3 has been yanked, new installations will can only run in headless * Numerous compatibility changes and backported fixes (per #3455 & @chris-allan)
- Python
Published by AetherUnbound over 8 years ago
cellprofiler - 2.1.1
CellProfiler 2.1.1 is a scheduled patch release whose primary purpose is to address any issues in 2.1.0. Significant improvements: - Many bug fixes (detailed here ). - Improvements to the code behind the input modules to address issues with color image stacks. - Adding a caching layer to image file handling which should improve performance for image stacks. - Improving the compositing of overlays on images.
We have fixed a bug in the “fill holes” algorithm which will likely result in slightly different (and we feel, better) segmentations for IdentifyPrimaryObjects and IdentifySecondaryObjects modules with the “fill holes” option enabled. This will not affect most assays, but you may want to confirm this and continue to use 2.1.0 if reproducibility is a concern.
- Python
Published by ljosa almost 12 years ago