Use CellProfiler to re-shape objects in an image

Hello! I am unable to post an image do to certain restrictions around proprietary information, but I am trying to use CellProfiler to measure the dimensions of a cross-sectional scan or a wire braid (exciting that biology tools can be used for inorganics as well!). The metal wires are braided in a specific way and when scanned, producing ellipses in the cross-sectional image with dimensions that indicate the angle of the wires. The shape is very important to the measurements since eccentricity, major and minor axis are of concern, but the resulting image that measurements are taken from seems to be grainy and more “blobular” than actual ellipses.

Are there any tools to reshape the ellipses after the objects have been distinguished? I should mention that the ellipses touch each other and I’ve been using a modified version of the Colocalization example pipeline to separate the individual objects. I’m open to different methods for separating objects while keeping the integrity of the shape and/or using plugins.

Thanks in advance for the help!

Hi @szouela,

I think this depends on what you mean by “re-shape”. You can use the ErodeObjects or DilateObjects modules to do simple adjustments, and perhaps the Morph module for some other filters, but if you’re looking to ‘touch-up’ the segmentation it might be worth looking at the EditObjectsManually module?


I’ve used the dilate and erode functions to separate my objects and get them back to size but it compromises the shape of the objects and the resolution of the edges. I was wondering if there is something that will take those individual objects I’ve processed and mold them back into true ellipses. Let me know if you’re aware of anything that can do this! Thanks

Have you tried approaching this with watershed segmentation instead of erode/dilate steps?

I have, but it gives me the same problem.