I’ve been trying to find a way to pre-process my images, but to no avail… Maybe someone here has any suggestion?
I have a large amount of microfluidics chip images where I am tracking flowing cells. I have used TrackMate successfully to do the tracking, but the characteristics of the chip required me to create a mask in order to constrain the analysis only to what is inside the channels. At the moment, I’m doing the cropping and masking individually per file, but it’s a time consuming process. The location (and sometimes orientation) of the chip changes slightly per image, making cropping macros useless.
This is a typical, direct from the microscope image:
And this is the type of cropping that I would like to do:
Is there anything I could use that would recognize the boundaries of the region I want to crop per image, so that I could then use the same mask and image calculation for all of the images?