This is my first attempt at using cell profiler, so I do not know much about its use. I do lots of work with Fiji, so that is the paradigm I know.
I am now attempting to reproduce something which i wrote in FIji, using cell profiler.
I am using the speckle detection pipeline example, and have it working on my images.
However, my images (after some preprocessing done in Fiji) exist as mulit-TIFF image stacks. So I have a single TIFF file with 10 images (from 10 fields) of speckles, and a second multi-Image TIFF with 10 images of dapi stained nuclei.
My problem is that I want the speckle detection pipeline to run on all 10 image, and it only runs on the first image in the stack.
I suppose that I can rewrite the multi-image TIFFs as individually sequentially numbers images in a directory. I hope that there is a better way (like the imageJ stacks that I know and love).
I also want to know how to do flow control (loops, conditionals, etc) in a pipeline.
Thanks in advance – sorry if these beginner’s questions should have been obvious.