I’m using flag image module to flag and stop downstream processing of low/quality images. I measure quality parameters and define these qualities parameters in flag image module and ask module to stop downstream processing if image fails QC test in the module. Unfortunately, it defines the relevent image as QC fail but doesn’t stop downstream processing and I get these images processing in my output csv files. PLZ help.
It would help us if you attached your pipeline so we can check things like:
- What version of CellProfiler are you running? Some bugs have been fixed in CP re: FlagImage and so you might be helped with a trunk build
- Do you have “Skip image set if flagged” checked Yes?
Give the trunk build a try and let us know!
Couldn’t really understand trunk version but seems like I can remove flagged images later from data files on the basis of flag score and this is actually better.
OK glad it works for you. Thanks for writing back.