Announcing CellProfiler 3.1

Originally published at:

I’m excited to announce the release of CellProfiler 3.1.

Our focus for CellProfiler 3.1 was polishing features and squashing bugs introduced in CellProfiler 3.0. We also started laying down the foundation for our next release, CellProfiler 4.0, that will transition CellProfiler from Python 2 to Python 3, improve multiprocessing, and overhaul the interface.

There’re a few noteworthy changes that some users might enjoy like UTF-8 pipeline encoding, a simpler application bundle (that won’t require installing Java), and a variety of documentation improvements.

You can download CellProfiler 3.1 from the website. If you have feedback or questions, please let us know on the CellProfiler Forum message one of us on Twitter.

Of course this would not have been possible without the hard work of our software engineers and all our contributors- Allen Goodman, Claire McQuin, Matthew Bowden, Vasiliy Chernyshev, Kyle Karhohs, Jane Hung, Chris Allan, Vito Zanotelli, Carla Iriberri, and Christoph Moehl, take a bow!


Are there detailed release notes somewhere?

In particular, has the Test Mode Viewer been implemented yet?

We’re working on detailed release notes, sorry- we’ll try to have them up and ready soon.

The Workspace Viewer is unfortunately not implemented in the CP3 series yet- we urgently need to get CellProfiler updated to Python 3 before the end of Python 2 support, which means we need to make major changes to the main interface to upgrade that. Once we’ve done so, we can upgrade the Workspace Viewer interface as well- it’s high on our to-do list, we promise, we love it too!