Otherwise CP chokes up: is this ~5Mb/well a limitation of our processing workstation or is a CP limitation?
5MB per well shouldn't max out your system, my guess is that it's a limit of your processing computer. Best way to test though would be to try the bigger ones on a more powerful computer.
Do you know of fast stitching tools that can be used in a high-processing computer (no windows or OS operating system?
I'm assuming you mean some sort of Linux cluster? If you need something that interfaces with a point-and-click program, FijiArchipelago apparently allows use of ImageJ (which has good fast stitching algorithms) on clusters (though I've not personally tried it); alternately if you've got someone code-savvy you could just use something like sci-kit image on a cluster installation of python.
When we start processing with CP we normally need to transfer back images to processing computer, this generates CP databases whose paths are linked to that computer so sharing results of the analysis is challenging.
You can change the paths in the database pretty easily with a simple SQL call like the one below (I do this all the time to send collaborators data or after I move images):
SET Image_PathName_Chan1 = REPLACE(Image_PathName_Chan1,'/path/from/processing' , '\\central\server' )
WHERE Image_PathName_Chan1 LIKE '%/path/from/processing%'
Keeping track of all this processing and transfer of data is difficult and we fear that as we increase the volume we will start losing data or losing track of the data.
So, do you have suggestions or tools on how to improve the workflow?
We haven't "officially-officially" launched this yet (likely by the end of the year), but we've been working on a tool called Distributed CellProfiler which allows you to easily run CellProfiler on Amazon Web Services; the advantage would be that the images are centrally located and any member of the lab could run the analysis and/or pull the results from their own personal computer. Take a look at the wiki for it, and let us know if you have questions/comments.