Editing CellProfiler batch file

Dear all,

I’m new to CellProfiler and currently trying to set up pipeline for processing of images using cluster. The problem I run into is setting path to images in batch file. In particular my problem is that when I create batch file I use windows OS, while Linux is run on the cluster. Thus my image paths in batch file would look like D:/Images while I need to have /home/user/images for batch to access images on cluster.

Is there a way to solve that? Would I have to create batch file using the cluster version of CellProfiler?


The CreateBatchFiles module (name might be slightly different, this is from memory) has some input fields for path translation.

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Thanks! Totally missed the option. This seem to do exactly what I wanted.