Hi everyone,
I am working with time series images taken by the Incucyte S3 in Dilution Cloning/Whole well imaging mode. What it means that I get images with the well in the middle but a perfect black background around it( https://imperialcollegelondon.box.com/shared/static/5v0349lyx39laxpeiujjzvt3qr0jwnyh.tif ).
When I do correction using BaSiC it seems to work okay except for the fact that florescence at the wall border is enhanced which makes the downstream analysis using trackmate a bit tricky.
Has anyone had a similar problem before and knows how to deal with such images best? Ideally using jython as I have hundreds of stacks to process 
One thing which adds to the problem is that the well border is not always lying in the same spot of the picture making automated cropping a bit tricky.
Thanks,
Jonas