i have some questions regarding Batch_data.mat.
basically i will just write what i think is happening and it would be nice if you could confirm
my idea of this file is that it basically contains:
i) the cellprofiler pipeline
ii) the filenames and paths to all the images to be analysed
ad ii): this avoids that loadimages has to walk through all the directories and files to find the imagesets to be analysed (as specified by the -f and -l options)
in fact i am writing this, because we ran CellProfiler on the cluster without using the Batch_data.mat file (which works as well). But it got super slow. And we think the reason was that LoadImages had to retrieve the list of all images for each job that was started, thereby basically killing our filesystem.
we hope now that this is solved by using Batch_data.mat as a input pipeline instead of the .cp file, because Batch_data.mat already contains a list of the files to be analysed.
is this interpretation correct?
Thanks so much,