Thank you for your prompt reply @ctrueden. I am specifically trying to deal with the problem I’ve already described here on StackOverflow. I am going to develop a software for a hair transplant company which allows them count the number of hairs they transplant for each patient. I may ask specifically about this on a separate question, but that’s all I am trying to achieve.
I am trying to count the number of white dots in that scalp picture using a combination of several methods and filters including: “Subtract Background”, “FFT > Bandpass Filter” (to correct uneven illumination), “Adjust > Threshold”, Posterizing (which seems not to be available in ImageJ), “Binary > Fill Holes”, “Filters > Median”, “Process > Binary > Erode, Dilate, Open, Close, Watershed”, “Analyze > Analyze Particles” and finally use the “ROI Manager” to show the found dots and count them. I may also need to use some filters from “Plugins > Fast Morphology > Morphological Filters”.
That’s all the features I think I need to use of ImageJ library behind the scenes in the application I am developing.
I also came across Cell Profiler which seems very promising. Do you think I can use it for my purpose?
And thank you for pointing out ImageJ2 APIs. Currently I am using the libraries shipped with ImageJ 1.49. Is it fine if I download https://github.com/imagej/imagej to work with ImageJ2 API? What about testing its functionality before using the API? Should I use Fiji instead of ImageJ?