Edge lengths, vertex locations, etc. available to user?


I know we can find cell perimeters using CellProfiler, but is there any way to extract the following:

  1. individual edge lengths
  2. edge counts
  3. vertex locations
  4. vertex counts

I’ve done some looking through the modules with no luck, but perhaps I’m overlooking something? Thanks for any help you guys can provide!



The MeasureObjectAreaShape module in CellProfiler provides the basic morphological values for an identified object, such as perimeter, etc. However, CellProfiler doesn’t currently provide the measurements you mention as an explicit output. So, no, you weren’t overlooking anything :slight_smile:

However, if you used IdentifyPrimAutomatic (or a similar module) to pick out the cells, you might consider using ConvertToImage to convert the cell objects to a label matrix and then saving the label matrix to a file with SaveImages. A label matrix labels connected components (such as cells) in an image and might be further processed to get the additional parameters you need. If you are fluent in MATLAB , I suggest attempting to manually extract the parameters you want from the label matrix.

Hope this helps!