Announcing CellProfiler 4.0

Hello to all of you and thank you so much for all your hard work.

I have the same error

Thanks, this is actually being triggered by a different image asset than what was previously reported, so the change we applied to the other image did work. That means that we hopefully do have a fix for this, although we might be able to find a more global solution.

It seems like CP4 shares the same Preferences settings as CP3. This is a problem since you need different settings for e.g. CellProfiler plugins directory. (See also Converting CellProfiler3 plugins to CellProfiler4)

It seems like CP4 shares the same Preferences settings as CP3. This is a problem since you need different settings for e.g. CellProfiler plugins directory. (See also Converting CellProfiler3 plugins to CellProfiler4 )

Hey Petter,

Nice to hear from you!

Outside of the small community of super-users (like you, and us!), in general we don’t suspect most CellProfiler users switch back-and-forth between versions of CellProfiler too frequently, and therefore having one set of preferences that follows the user when they upgrade is, for most folks, a feature not a bug.

We definitely will think about though that for some users it IS a hassle, and will try to think if we can come up with a solution that pleases everyone.

I agree that it is not a big issue, but it would still be nice to be able to run both versions at the same time - at least for a period where we need to convert pipelines and plugins from CP3 to CP4.

Totally agree, we’ll see if we can figure something clever out!

Hi @DStirling,

I have encountered an error message again. Still CP has not launched.


Yup, sorry about that. It’s a different image this time.

I was able to replicate the issue this morning, and have now prepared a more robust fix which should be in the next minor release. Thanks!

Thanks for the hard work! @DStirling

@AliNassar Ok, would you be able to try v4.0.4, which is currently available on the website? Please let me know if you still encounter issues!

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An update for you - as of release 4.0.4 CellProfiler will now use a different settings key for the plugins directory in CP4. It should copy over the CP3 setting to start with, but if you change it in CP4 it will no longer impact older installations.

Great! Thanks for the update.

I had the same error message as @AliNassar and v4.0.4. is working for me now. Thanks - Looking forward to trying it out!

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For those of you who use plugins for CellProfiler, we’ve now moved all CellProfiler 3 plugins to their own folder in the main CellProfiler-plugins repository, to make more clear that they shouldn’t be used with CellProfiler 4, and added a conversion guide.

To the degree that we have bandwidth and/or that they are used by the main CellProfiler team, we will be upgrading some of the existing CellProfiler3 plugins to CellProfiler 4; ultimately, though, we don’t guarantee maintenance of these, that is the responsibility of the contributing author. If you need a plugin and we haven’t gotten to it yet, we encourage you to upgrade it and then contribute the upgraded version back to the repository! We’re happy to help if you get stuck along the way.

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@DStirling Thanks for the hard work. It’s working!

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4 posts were split to a new topic: CellProfiler-Analyst Questions

Thank you for this fantastic new version of CellProfiler! Do you have a timeline on when the Linux instructions will be updated? Or do you have any guidance for the installation on a CentOS 7.2 cluster in the meantime? Thanks.

5 posts were split to a new topic: Upgrading plugins to CellProfiler 4

Hey @DStirling , first i would like to thank you for all your help so far. Second I would like to address some errors that I have been facing with CP 4 while running a pipieline on it for the first time (It was running well with CP3) and the run fails to complete and takes alot of time. I will attatch screen shots maybe you would be able to help !
Thanks in advance.

Hi @AliNassar,

Those errors are all related to your system running out of RAM (memory). It might help if you check the Windows Task Manager to see where it’s all going. It does look like you have several other applications open at the same time, which is likely to contribute to this problem. Otherwise if it’s all CellProfiler it might help if you could upload a copy of the pipeline.