Hi all, I’m doing several experiments that require analysis of hundreds of individual cell plates for total area of cells. Doing this by hand has been rather tedious, so I was hoping to automate the whole process using batch processing. I was ultimately able to automate everything, except the part where I clear out the area of the plate that does not contain the cells. I was wondering if there was any specific plugin within or outside of Fiji I could use to do this, or if it was possible to potentially code a macro or at least python script to do this process. I’m very new to Image-J, Fiji, macros, and coding in general, so any insight would be a lot of help!
Here are a few pictures to help elucidate my problem.
Final Image Before Analysis:
So essentially I was wondering how to automatically white out the background area without having to manually do it for each area. I assumed this would be done in the binary image but if anyone has any idea for how to do it earlier that could also be great.
Thank you all so much !