Cell shape and counting


I’m still learning how to measure using CellProfiler. I wanted to quantify the number of muscle cells and measure/outline their shapes on different topographies. I also want to save a file with the outline on those cells for my research.

I also wanted to measure roundness of cells versus the ones with cytoplasmic extensions.

I am trying to run a modified version of shaping pipeline but it doesn’t seem to work with my images. DL_classify_shapes.cppipe (9.1 KB)

I am uploading an example image of my data, could you please assist how to move forward?

I noticed my .tif images are not visible on the forum so I’m uploading the jpeg counterparts.

Many thanks,


I’m afraid I’m not exactly sure what I’m looking at here- these are three different channels of the same image, yes? What’s marked in each channel?

I’m also not exactly sure what you mean by “not working”- can you clarify? Are you not able to run the pipeline at all, is it pulling out wrong channels, etc? Without more data it’s hard to help, other than to say if you want to save an image of your identified cells you need to add an “OverlayOutlines” and a “SaveImages” module to your pipeline.

PS TIFs don’t show nicely in the forum but they work fine for downloading.

Hi Beth,

Sorry for the confusion earlier.

I have figured out what I wanted to do, to measure shapes of my cells. But I would like to know what do each of these mean for my measurements?

Eccentricity, Form Factor, Compactness, Solidity.

Are they all for measuring the roundness of the cell OR each of them have any other significance?


Eccentricity is for roundness, the others are more for uneven-ness or holes; if you click the MeasureObjectSizeShape module in your list of analysis modules and then click the ‘?’ just below, you can get the help feature for that module which defines all of those terms.

Glad you got it figured out!