I am trying to automate point counting on kidney slices. What we do now is take the image of the slice overlay a grid and if there is a cell at the intersection of the lines of the grid it is counted as positive, if the intersection lays on something other than our cell of interest, then it's negative. We only do this for points that fall in the section.

I think there has to be some way to define an area with a drawn line, and then get a pixel intensity value at every grid point within that area. I just need an output of the number of high-intensity points (+) vs low-intensity points (-) in the grid. but I don't know how to go about doing something like that. Does anyone have a way of doing this or know how to code something like for imageJ?

Even if it's not entirely accurate based on pixel value, I could review the output faster than if I had to just count all of them manually.