CellProfiler 4.2 Release

June 24, 2021

David R. Stirling

Hi all,

We’ve now released CellProfiler 4.2! You can download it from https://cellprofiler.org/releases

We have a few new features and improvements in this release. There have been numerous smaller bug fixes, but the key changes are as follows:

  • We’ve fixed an issue which was causing the CorrectIlluminationCalculate module to run extremely slowly when using a median filter with a large window. Results using this filter may be slightly different from previous versions of CP4, but should now be the same as results from CellProfiler 3.
  • We’ve expanded the ClassifyObjects module to allow the use of a classifier model (or rules list) generated by CellProfiler Analyst 3. Resulting measurements tables will contain a column with the assigned class name of each object, plus columns recording the probability of an object belonging to each class.

You also have the ability to capture specific classes as new object sets to use downstream in the CellProfiler pipeline. Using the interface below, you can generate as many object sets as desired based on the classes produced by your classifier.

Please note that to use model files, you’ll need to make sure that all measurements that were used to generate it in CPA are also available at the point in the pipeline where ClassifyObjects runs.

  • FilterObjects now also supports models from CellProfiler Analyst 3. This will now work for all classifier types, not just FastGentleBoosting.
  • Objects removed by FilterObjects can now be retained as a second object set. This means that you can carry forward objects which pass and fail your filter as two separate sets, without needing to run a second copy of the module.
  • ExportToDatabase now automatically detects image colours when generating CPA .properties files. Previously all images were assumed to be greyscale.
  • The Watershed module now has an “advanced” mode offering more options for segmenting touching objects. You may recognise these settings from the DeclumpObjects plugin, which was very powerful and so has been integrated into the main Watershed module.

  • The CombineObjects module has been upgraded to support 3D pipelines. We’ve also made some performance optimisations which should dramatically improve processing speed when working with large object sets. On top of that, we’ve also addressed a bug which made objects get incorrectly lost in some circumstances.
  • Windows users should no longer have trouble opening pipelines exported on MacOS. We’ve also fixed a bug which caused project files to sometimes save file lists incorrectly.
  • On Windows, you should now be able to open pipelines and projects by “Opening with” CellProfiler. Previously this would start the program but not load the file.
  • The SaveImages module now has a new option to save 2D .tif files with compression (3D tif files are always saved with compression). This should help to reduce the disk space needed when saving lots of files.

Special thanks to David Stirling, Beth Cimini, Pearl Ryder, Madison Bowden, Alice Lucas and Mark Hiner for contributing to this release!