How should I do with counting muscle fibers(fibres)stained with HE?

Sample image and/or code

This is a large photo of several photos stitched together in an MIA way, it is a panoramic view of the muscle after being stained with HE, I would like to calculate its full number of muscle fibers (the ones in red circles) but it is almost impossible to count them manually because the number is so huge (I have about 50 of these photos!)

Hello everyone,

Hi all, I’m new to cell profiler. I want to use it to calculate the total number of myofibers after HE staining, but I don’t know how I should go about writing it? I found some pipelines, but they all seem to be out of date. If anyone knows and can answer, I’d appreciate it!!!

Thanks again!


I think starting from one of the pipelines you found is a great idea! Otherwise, you can start wtih some of our example pipelines, which may be slightly less tailored to your exact needs but should be up to date. If you need general CellProfiler help getting underway, you can check out our YouTube channel ; we’re happy to help you solve specific questions here (ie “my pipeline works great on X image but has problem A on Y image, can you help me figure out why?”) if you get stuck along the way!

Welcome to the CellProfiler user community!