Improve background subtraction

adamjtaylor / miniature

Use dimensionality reduction to create thumnails for high-dimensional imaging

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Improve background subtraction #3

Open adamjtaylor opened 3 years ago

adamjtaylor commented 3 years ago

Options

Auto detection on if background is strongly separated from tissue in histogram method
K-means clustering
2 round dimensionality reduction

adamjtaylor commented 3 years ago

K-means clustering tested but is not robust and requires working out which cluster is tissue. Smoothing or an erode-dilate step might help fill in some of the holes in the tissue mask

adamjtaylor commented 3 years ago

For stitched images run the threshold only on values above true 0