I’m trying to use ImageJ’s analyze particles tool to count cells in images with cells and background tissue stained in different colors (red, magenta, green, and blue).
I have got the program to count cells for each image, one at a time. However, since I’m working with different filters/colors, I have to account for overlapping cells so that cells are not counted twice. I was wondering if there is an existing tool that detects and outputs overlapping cells or if there is a feature that outputs the x and y coordinates of the counted cells. With the coordinate values, I could write a program that outputs which cells were counted more than once with the different filters.
If not, are there alternative programs that I can use other than ImageJ? Thank you in advance for your help!