Overlaying Coordinates On Image by Selecting Coordinates on Image

Hello! I am new to bioinformatics, and I was wondering what the best way to tackle this problem was. I am able to get coordinate data points out of my neuron mapping software. I want to overlay them/overlay a heat map of them on a representative coronal brain section. I can make the 2D heat map easily in both R or Python. However, I can’t figure out how to overlay this heat map over the section. Ideally, I would be able to select and set a few points on the image, and the coordinates would extrapolate themselves over them, and then I can make a heat map directly over the image. I have downloaded ImageJ (complete newbie to this) and have tried Landmark Correspondences, but it just warps the images. It looks like I may be able to do this in some image editing software, but I’m pretty out of my depth. Any suggestions would be appreciated!


Not sure you mean ImageJ or Fiji, in case there are a couple of registration solutions in Plugins>Registration in Fiji. Using the search bar of Fiji you should be able to find the related wiki documentation.

Otherwise in ICY there is also a registration solution that is well documented

If you want to go for manual registration with a image editing software, I used Paint.NET which is a simpler than Gimp but much better than the basic paint. You could give it a try.