How do I save results from multiple image sets separately?


Hi all,

I’m currently using CP to apply DAPI nuclei masks onto GFP stained images, using DAPI nuclei as my objects and GFP as my image. For each run of my pipeline, I input two images: 1.) a DAPI image and 2.) the corresponding GFP image, and it works great. The problem is that I have hundreds of DAPI/GFP image sets that I have to analyze and I do not want to restart the pipeline for each set.

Is there a way (preferably via existing modules) to input all of my image sets and have CP run through them all sequentially, then save them all in separate files so none of them get overwritten?



Hi Daniel,
CellProfiler is designed exactly for such usage! Of course you can load all your images at once. Then you have to extract metadatas so that sets are correctly matched (which DAPI pict with which GFP pict). This is achieved using regex to extract informations either from name of your picts or from folder name…
Then in the pipeline you can save any “intermediate” pict for each image set (i.e. overlay of DAPI nuclei outlines on a multicolor image composed of your DAPI and GFP pictures) with a different name (so nothing is overwritten) constructed using the metadata information from each set…
If you’re lost, just give more information about how your source pictures are organized and what you excatly want as an analysis and we’ll help you with starting a proper CP pipeline :wink:
Good luck,