Nucleus oversegmentation - plate9_2rep1_20200506_163349_413 - A02-0004

hci-unihd / antibodies-analysis-issues

Issue tracker for problems in the antibodies analysis workflow.

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Nucleus oversegmentation - plate9_2rep1_20200506_163349_413 - A02-0004 #78

Open tischi opened 4 years ago

tischi commented 4 years ago

{"plateName":"plate9_2rep1_20200506_163349_413","siteName":"A02-0004","pixelLocation":[4358.766681972538,1517.2305985654225,0.0],"analysisVersion":"06433667b2e6bbaa8118cc837e84abc6d0d5592a"}

@constantinpape

Some small stuff was detected as nuclei. Maybe also here a simple size filter could be an option...

Screenshot

constantinpape commented 4 years ago

Ok, we also have a better network for the nucleus segmentaton now, but I haven't tried it yet, will give it a go on this plate to see at some point.

constantinpape commented 4 years ago

@metavibor also suggested to do a max-threshold to filter out dirt in the dapi channel. I will do this later (it's closely related to the other QC based on intensities measured over the dilated nuclei anyways)