After some weeks playing with CellProfiler in order to find a pipeline adapted to analyze my histology samples, I hit a wall.
I am conducting a research project to understand skeletal muscle growth regulation in fish. For this project, I have a large quantity of histology slides to analyze (Hematoxylin and Eosin stain). I would like to record the number of muscle fibers and record their area/volume/diameter for each pictures in order to see if treated fish have developed an hyperplasia (increase in the number of muscle fibers) or/and an hypertrophy (increase in size) of the muscle fibers.
To do that, I used and mixed different pipelines and comments that I found in the forum and try to improve it for my pictures, however, it is not a success yet.
1- Removing the cells that are not full around the edge
2- Improve the detection of the cells and fill the inside of cells to retrieve the true volume of each fiber
3- Classify the cells and determine how many cells per range of sizes (i.e # of small, # of medium and # of large fibers)
I linked to this post some pictures and my current pipeline.
Thank you in advance for any help and feedback
Pipeline_Histology_MuscleF.cpproj (392 KB)