New version of CellProfiler



A new version of CellProfiler has now been released! (1.0.5811)
Lots of bug fixes and additions - see the Version Notes for details.

Download it here:




Just a query, was the MCR installer file ever needed for Intel macs, for the previous version? Can’t remember.
I can’t get the new compiled version to run on leopard, whereas the previous works a treat.


Edit: My bad, it works now - had to install the MCR.

One more question: is there a list bug fixes?



The version notes ( … n.5811.txt) contain a list of bugfixes, new modules, etc.



What do I have to do, to get rid of the warnings upon loading old pipelines?
I clicked them away and reset all the parameters. I saved. Then I restarted CP and loaded the pipeline, but the old entries where partially there again (meaning no entries in some modules). I had to reset everything again.

Anyone else had this problem?



The procedure you’re describing is the correct one for loading old pipelines. However, remember CellProfiler is not intelligent enough to adjust all downstream modules to incorporate the changes in your parameters. For example, if you fix your RescaleIntensity module because it has changed in this new version, remember that all downstream modules have to be re-told the name of your rescaled image- otherwise they will fill in the default. If you forgot this, that could be why even after saving and reopening, it appeared as if some modules had reset (ie, SaveImages might show RescaledBlue, despite the fact that your rescaled image is named something else, and you already changed and saved this!).

I would double check this first, because typically adjusting the parameters, saving, and reopening is the correct procedure. If that doesn’t work, something else might be going on.

Let me know!


And Tim, if you want an even more detailed list of bug fixes, improvements, etc. we’re planning on opening up read-access to our svn repository sometime soon, so that you can read all of our edits. We’ll announce it on the website.



And no, the MCRinstaller was not needed for macs previously, since we used to supply the MCR folder for you. Since 2007b, Mathworks has changed the deployment process, such that each architecture needs to be supplied its own MCRInstaller file to be installed by the end user.



Hi David,

Sounds good!