Transform to Threshold Image for Tissue

[bhashemian]

Is your feature request related to a problem? Please describe.
A transform that given a RGB image (a tile from histopathology image or a WSI at low resolution), apply thresholding algorithm to distinguish the tissue from the background, and outputs a binary mask and some statistics.

[JHancox]

A slightly different use-case is when you tile the input and the thresholded output is binary per tile. This results in the same low-res binary mask but is accomplished in a different way. Usually this is done at an intermediate resolution with the output being low res.

[bhashemian]

@JHancox Thanks for providing the use case. Could you please elaborate a bit?

• What is the purpose of that mask?
• Is threshold filter each pixel of the tile or the entire tile?

[JHancox]

The purpose of the binary mask (foreground/background) is the same as usual - to eliminate the background from any computation.
The way it might work is:

• Ingest the WSI at the lowest feasible resolution
• Split it into tiles
• Evaluate whether each tile is above or below some threshold using the pixel values and some function (e.g. variance, mean value, otsu etc)
• Return a binary image with each pixel representing a tile.
• Use the mask so that, say, inference is only done on foreground tissue