I’m a grad student that is currently trying to (partly) automate the image analysis of our histological slides of atherosclerotic plaques as a side project. I’m very new to this and I’m a bit overwhelmed by all the different options that are available when it comes to software. I had a few questions regarding the image analysis of plaques in the aortic valve:
At the moment, I’m exploring with simple pipelines in Cellprofiler, would this also be the software you would recommend when looking at histological slides at this magnification?
I was currently thinking of outlining the valve itself and the plaque tissue of the valve as a whole and the three subvalves manually, as I couldn’t see a way this could be done automatically. Do you think there might be training software to do so automatically? And more generally, which software/training algorithm would you recommend using for histological slides when you’re not necessarily interested in every individual cell?
The white crystal-like structures, alot of them can be seen in the lower right corner of the plaque, are as white as the background but they are part of the plaque area. Is there a way to distinguish background from these cholesterol crystals?
The information I want to obtain in the end is the percentage of the area of each plaque that is stained, if possible per subvalve. As it may be important for training, I’d like to add that although the picture below was still taken manually with a microscope, we do have a slidescanner now that is able to make much more consistent and high res scans (.tiff).
Any help would be greatly appreciated!