I’m using a BD Pathway to do my image acquisition. I tested a pipeline that does a merge of three dyes on many sets of images that I previously copied in a new folder (image only) without any problem.
When I tried this same pipeline on a folder created by the BD Pathway (with many folders, images and files containing experiment informations) I found out CellProfiler were always using the same image to do the merges. I tried File>Open Image with many images but CellProfiler were always opening the same image. I tried too look if some file made by the BD Pathway could be the cause of the problem and finally found a file, called Experiment.exp that is responsible for the problem. If I remove only this file, my pipeline works fine. But it seems there is more files affecting Cellprofiler because if I let only the Experiment.exp removing all other experiment information files I get an over-saturated image as output (cannot even identify what it is). Is this file is known to affect CellProfiler ?
I’m using version 9978 on Windows XP.