Cell Profiler new version


I’ve downloaded yesterday the new version of Cell Profiler that you recently released, and surprisingly, I get significantly different results using the same pipelines comparing to the previous version I had (I’ve been using CP for more than a year). I analyzed the same set of images with the previous and new versions of CP, and the results with the new version are less good. I haven’t changed any of the parameters, yet it seems to identify less spots in the images in the new version, and the colocalization isn’t as good.

I was wondering whether you have any comments about it. Also, can I delete this new version and download again the previous version that I had?

Thank you!


Hi Efrat,

That seems disturbing! It is possible this thread might help you. Essentially check the “Fill holes” option in your Identify modules.

If not, all of our changes are found here: github.com/CellProfiler/CellPro … by-version. We are certainly mindful that we don’t want major segmentation changes between versions and we haven’t added nor seen many in our experience. But we are more than happy to help you look! If this doesn’t answer your question, please post you old and new pipelines and an example set of images.