Cellprofiler

- 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.

- 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

- 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

- 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

- 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.

- 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.