I am currently recreating the workflow published in Bray et al. GigaScience 2017. I have decided to run the pipelines in CellProfiler 2.2 and combine the pipelines together to eliminate some previous issues I had. (Project is attached)
allpipelines.cpproj (1.1 MB)
To only analyse 6 image sets (30 image files), it ended up taking about an hour to analyse… There must be something wrong with my pipelines… There are only 6 workers running although I have the limit set at around 24. Is there anyway that more workers could speed things up?
Next, the ExportToSpreadsheet is saving all measurements in separate cvs files. Is there anyway to consolidate them into one on the module… I know I could combine the cvs files into a single text file using Command Prompt but I am looking for a more efficient way.
Any help is appreciated!