267 - Processing whole slide images (as tiles)
Code generated in the video can be downloaded from here:
Demo using H&E normalization and H / E signal separation.
Here, we use openslide to read a whole slide image.
We will then extract a lower reolution version of the image to normalize it and then to extract H and E signals separately.
We will also perform the exact operation on the entire whole slide image by extracting tilee, processing them, and saving processed images separately.
Please note that this code will not cover putting tiles back into a whole slide image (image pyramid). You can explore pyvips or similar package to put together tiles into an image pyramid.
For an introduction to openslide, please watch video 266:
For details about H&E normalization, please watch my video 122:
Useful references:
A method for normalizing histology slides for quantitative analysis. M. Macenko et al., ISBI 2009
Efficient nucleus detector in histopathology images. J.P. Vink et al., J Microscopy, 2013
Other useful references:
