I am very new to CellProfiler, and I started using it to segment cells based on membrane fluorescence and nuclei. For that, I previously generate labelled nuclei images in FIJI (which I can manually correct easily), and I import them as objects into CellProfiler. I use these as “primary objects” to identify “secondary objects” in the membrane fluorescence image. Then, I can use the “SaveCroppedObjects” and save the individual masks as separate files in an output folder. I can later import these masks altogether into FIJI as image sequence, erode them, Z-project them, and I end up with a binary mask of the cells that I can add to the ROI manager. I like this strategy since I can easily manually correct a ROI if it is not OK. This has worked wonderfully for pairs of images (nuclei+membrane):
The problem is when I want to analyze multiple pairs of images at the same time. The pair of images share a numbering scheme, which seems automatically detected by CellProfiler:
I would like to have the individual masks of each pair of input images stored in a separate folder. However, in the SaveCroppedObjects window I can only specify one location, and the individual masks, which are named, for example, “Celula 1”, “Celula 2”, etc, get overwritten between the pair of images. At the end, I end up only with the individual masks of the last pair of images analyzed. Thus, currently I have to run CellProfiler for each image pair individually, which is very inefficient and time consuming.
If anyone could advice me on how to solve this, I would be very much greatful!