sciai-lab / batchlib

Batch procesing for high-throughput screening data
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Make networks more robust against localized artifacts #131

Open constantinpape opened 4 years ago

constantinpape commented 4 years ago

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

constantinpape commented 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.