How to load a color image in CellProfiler?




I am comparing the object identification function with Cellomics’ results. I managed to save a copy of cellomics image with identified object outlined in blue color. Ideally, I’d like to read in that color image, and overlay nuclei outline identified by CellProfier on top of it. However, the cellomics images I read in using “loadimages” module were automatically converted to gray, which makes the cellomics outline too dark to be seen. Is there anyway to read it in as a color image, overlay another layer of outline (generated by cellprofiler) and save the image as a color image as well?

Thanks so much!


Hi Peng,

Are you sure that the original image is color? LoadImages keeps the original color values of an image; so if the input image is grayscale, it’s stored as gray intensity values, and if it’s color, it’s stored as an RGB color image.

Unless (1) the input image is actually gray and not color, or (2) there is a ColorToGray module after LoadImages that is inadvertently converting it to grayscale, it’s difficult to see how this would happen.

Have a look at the LoadImages window and confirm that the right color image is being input. But to address your original goal, yes, it should be straightforward to add another color outline on top of an image using OverlayOutlines.