first of all I am new to the field of automated image analysis and this community, so please excuse my limited expertise and “dumb” questions arising from this.
Those of you who I have been lucky enough to meet in Bordeaux have probably already heard of my current project. For those of you who have not I would like to give a quick summary:
I have a bunch of super-resolved images coming from consecutive imaging rounds each containing an individual set of proteins that need to be registered onto each other for correlation analyses. To aid this registration I am simultaneously imaging a set of fiducials in a separate color channel. Sadly (presumably because of non-chromatic aberrations) I can not use a simple rigid transformation to correct for the ROI displacement between imaging rounds. During the Bordeaux training school @christian_tischer therefore suggested to use BigWarp instead and it works like a charm as long as I do the registration manually. The obvious next step now is to automate that process for high-throughput analysis and that is where I am stuck at the moment.
My actual problem goes as follows:
I already managed the easy task of automatically extracting the fiducial coordinates from the respective images and saving them as .csv files. However I now need a way to combine those coordinate tables from the target and the moving image into one file to feed it into BigWarp or come up with a way to already acquire that table containing the coordinate pairs in the right format.
To add to that problem I also need to make sure that each pair of coordinates really originates from the same fiducial which could be done by only allowing pairs to be matched within a certain radius around the target fiducial, but again I have not found a way to do that so far.
Since I am using the current home-office situation to improve my coding skills I am happy to figure out the actual macro myself as far as I can (of course I am open for suggestions nevertheless), but I definitely need help coming up with a strategy to solve my problems from above.
So thanks in advance for any suggestions and stay safe (at home)!
P.S.: if you need any additional information or example images, I am happy to provide it.