Announcing CellProfiler 3.1.9

Hello all! It’s been a crazy last few months for the CellProfiler team, as we’ve been hiring some new members to the team and working hard on the transition to Python 3, which will bump us into CellProfiler version 4. Keep your eyes peeled for exciting content (and much more forum help) in the future!

We did want to bring you one last release in the 3.X series, though, especially for OSX 10.14 users who have been left without a useable build. This release also has some minor bugfixes in RelateObjects and IdentifySecondaryObjects.

As usual, you will find this new release (and links to all our old releases) on our releases page.

Thanks very much to Allen Goodman, Matthew Bowden, Anne Carpenter, Jan Eglinger, and GitHub user “cloudsforest” for their contributions on this release.


I can not wait to try it but AVAST says there is a Trojan … ???
Should I continue to install it ???
Best regards


It’s certainly not a Trojan, though I do have to say disappointingly we weren’t able to code sign it; I don’t know if that’s what AVAST is reacting to? Can you let me know OS version, AVAST version, etc?

ETA: Screenshot (or even better, copied-and-pasted-text) of the error message would definitely also help.

I’m pretty sure it’s not a real Trojan but more likely an Avast mistake. :grinning:
Here are some screenshots.
My config:
i7 8700/64 GB Ram / Win 10
avast.tif (749.5 KB) Win.tif (304.6 KB) Win2.tif (129.5 KB)

Just to let you know the manual for 3.1.9 seems to be down:

Attempted access was from the manuals page.

1 Like

Try now! The dumb person who uploaded it forgot to make it public.

(That dumb person is me).


Hello, does this version include the Viewer for the Test mode?
Thanks very much

Unfortunately no! We unfortunately had so much work to do on CellProfiler4 with just getting the rest of the wx functionality moved we weren’t able to re-incorporate the workspace viewer at this time; we haven’t forgotten about it though, and are hoping to bring it back for possibly CellProfiler 4.1.

Then, can I ask a big favour? Could you please add a way to save (either with the pipeline or separately) the viewer’s parameters (displayed images, objects, measurements, etc.)?
Pretty please…
For those of us who always have to tweak parameters for different cell lines the viewer is an extremely useful tool, so recalling a previous view setup would save a lot of time.
Thanks very much

Hi Carlos,

Neat idea, and we do have something similar in CPA- I have added it to the GitHub for things to think about when we resurrect the viewer.