Running Cell Profiler Analyst on a folder full of images using Python

I am looking to use Cell Profiler on my yeast assays. I already have every cell segmented out and want to perform measurements on a folder full of single cells. What is the easiest way to use Cell Profiler Analyst in Python to get a measurement vector per cell for downstream analysis?

Can you clarify- you have segmentations, and now you want to make measurements? For that, you need CellProfiler, not CellProfiler-Analyst; depending on the form your segmentations are in (label matrices, binary mask of all cells, binary mask of each cell individually), there are a couple different ways to set up a pipeline to recognize your segmentations and measure your objects, but it’s definitely doable!

Hi @bcimini,

Thanks a lot for your response. Yes, what I have is a folder full of tif file pairs - every cell and its binary mask. I will be very grateful if you can let me know how to setup the pipeline.


@bcimini just checking if you had a chance to check on this question for me. Happy to reach out to you via email if it will be easier.

Do you mind posting a pair of images? You just need to load the binary images in as objects. Then you can add a zillion measure modules!

@AnneCarpenter Please find attached 2 images and their corresponding binary masks after having already run them through an object detection pipeline. I have a folder full of such images and am interested in extracting the CellProfiler features for this stain given the object masks. Please advise.



You can load your binary images as objects (as mentioned by @AnneCarpenter) and compute the measurements you want to. As mentioned there are lots of measurements you could use from CellProfiler. You could also refer the example piplelines here to build a pipeline for your measurements. The change you might have to do is, load your images and their corresponding binary image/mask as objects. So that in case of intensity measurements you could use your images.
Hope this helps!

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