LoadData Module for images from MetaXpress

cellprofiler

#1

Hello all,

I am trying to adapt the analysis pipeline used for Cell Painting to work for Distributed-CellProfiler. The biggest problem I’m having is getting a functional .csv file for the LoadData module, since Input module doesn’t work in Distributed ( :sob: ). Is there a quick way to generate this .csv file using images take with a MetaXpress since all the images have file names containing Well, Plate and Site information? I know the 3.0 wiki has a bit about it, but it only really allows you to easily separate path and filename and not much else.

Thank you!


#2

Hi,

My workaround here (because I’ve run into this exact problem before!) is to either

A) Rather than use LoadData, use CreateBatchFiles- DistributedCP DOES support batch files being passed instead of the pipeline file.

B) Have a “MakeImageSets” pipeline, which has the 4 input modules and nothing else- then use CellProfiler’s “ExportImageSetListing” option to get your nicely grouped image sets.