I am using a HCS machine but unfortunately, the plate layouts are not always perfectly aligned to the objectives. As a result, my wells can sometimes be shifted in the entire field of view of the image.
I need to crop the images (using circular ROI).
Is there a way to detect the region of the image where my signal is? knowing that I don’t have white pixel everywhere on the periphery of the well.
Do I have to write myself a script detecting the min and max X and Y positions of the white pixels, or is there a built-in function in ImageJ ?
I would recommend including the format and an image of one of your wells. Otherwise it would be hard to help.