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hci-unihd / antibodies-analysis-issues

Issue tracker for problems in the antibodies analysis workflow.
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Too many cells but few in table - plate9_2rep1_20200506_163349_413 - A01-0004 #63

Open tischi opened 4 years ago

tischi commented 4 years ago

{"plateName":"plate9_2rep1_20200506_163349_413","siteName":"A01-0004","pixelLocation":[1431.4666666666667,1538.1333333333332,0.0],"analysisVersion":"7277791ce281aeba9b2dc9241d9dfb2cf84613fc"}

@metavibor this is one of the plates that "failed". The reason our current QC marked images as failed is because we put an upper limit on the number of cells per image and those images have too many cells (i.e. are overgrown). I actually think I would agree, however, we can, for now also disable this QC and add it back later once we know better what a good value for maximal number of cells per image is. What do you think?

@imagirom @constantinpape The value for n_cells in the table is very low for this image: 12. Could you please check why that is?

Screenshot

constantinpape commented 4 years ago

Ok, this is probably due to the cell level qc (I assume that these cells are smaller then our size criterion because they are so crowded). I will have a look once I updated the column names in the default tables as we just discussed.