Open constantinpape opened 4 years ago
Ok, I briefly discussed this with @wolny and for now, we think the best solution would be to determine the normalization parameters over the whole plate (excluding manual outliers!) in a first pass. For this, we should use robust estimators, so median and mad instead of mean and std or quantiles instead of min/max.
Currently both the network used for the nucleus segmentation as well as boundary and foreground prediction are not robust against localized image artifact. See https://github.com/hci-unihd/antibodies-analysis-issues/issues/82#issuecomment-629273517 for some examples.
I think this is because these artifacts alter the image statistics and mess up the normalization. We should use a more robust normalization procedure. Some ideas:
cc @wolny