Hi Kevin,

For the background, without looking at your images, I can only give some general ideas. You can use adaptive thresholding (rolling ball) to separate foreground and background signals. If you are interested in some fancy algorithms, you can train a model to classify your image's pixels into foreground and background.

The "bleaching" problem, you can try some image enhancement methods to normalize the image contrast. However, most researchers try to enhance the label effect from biological aspect. I am not sure why you still have this issue. I would suggest you try improving your imaging instead of post processing.

Hope this will help.

Best,
Yang