Option to combine images of different channels of different fields into one output for one well

Hi everyone,

I analysed my images and used the ExportToSpreadsheet function. I was wondering if it is possible to condense the information in CellProfiler 3.0 so that I have one fill containing all information for each well?

I tried to use the MegreOutputFiles but for some reason cannot add the module to my pipeline.

Another issue I am having is that just to analyse 6 datasets its taking 1-3h. I have already adjusted the workers to its max but its still only using 6 of the 24 it could use. I also tried to use ExportToDatabase but am always getting errors…

Project_with_all_pipelines_version3.cpproj (189.5 KB)

Hello Celcile,

In ExportToSpreadsheet module, you could try to select and export specific measurements that you would like:

For your pipeline, there are no images attached, so I can’t test your pipeline.
In general, It would be best to separate Illumination correction from your analysis pipeline. Try moving all the CorrectIlluminationCalculate and Save those files modules to a separate pipeline and then bring those files into your analysis pipeline. In your analysis pipeline drag and drop the illum files in similar way that you bring your images into the pipeline. You would need to adjust the Metadata extraction and NamesAndTypes modules.