Simple ImageJ macro that lets you threshold an anatomy image to extract labeled structures. You can then divide the structures in two groups and quantify the differences in total labeling between those two groups.
If you believe there is a bias to one side in terms of labeling strength, this would allow you to quantify that by counting all labeled pixels without the backround and plotting a labeling profile.
Here an example of GFP labeled neurons to run the script on.
In the first step of the script the user can define two areas to compare. The labeling site was chosen to be compared by dividing it into left and right (see region 1 and 2). The calculated pixel count and ratio is written in the top left corner of the image.
In the second step the user can define areas across the site to bin and compare a bias in lateral innervation density. These are two user defined areas to be binned.
This is the pixel distribution across both of above defined bin areas.
Next a binned innervation map is calculated allowing to visualize any bias in innervation.
This image serves as a summary of all steps taken above.