Selecting a circular ROI

I am using the Object counter/tracker pipelines to quantify mucus tethered to epithelial cells in the center of a circular well. The pipeline is working very well, however I would like to be able to identify a circular area for CellProfiler to quantify. Until now, I’ve been using a rectangular region of interest, however because my well is circular, is it possible to identify a circular ROI using CellProfiler?
Here’s an image to help explain what I mean. I would like to include only the area inside the red circle. The blue rectangle denotes my current ROI.

Yes, you could create a circular binary ROI mask in ImageJ or Photoshop or some other program (make sure it’s the same size as the rest of your images) and then load it as a single image, allowing you to use it for masking and/or measurement. Is that similar to what you’re doing now?

I’m actually not doing any masking. I crop the original image to exclude the background. I don’t have much experience with CellProfiler or ImageJ. Is there a pipeline for generating a mask that I can use?

Not to my knowledge, CP is more for analyzing images than creating ones de novo. You could do it in Illustrator or Photoshop or even something super simple like MSPaint- create an image the same dimensions as your original images, fill it with black; create a circle that’s the size and location of the area you want to mask, then fill it with white; save as .bmp, .tif, or .png.

Thank you so much! How do I apply the mask and then identify primary objects from the unmasked portions of the image?

Use the MaskImage module on your channel of interest, then run IdentifyPrimaryObjects on that.