Stain Density Estimation

version 1.0.2 (20.4 MB) by Abhishek Selokar
Stain Deconvolution is used to determine Stain density Estimation in H&E microscopy images

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Updated 21 Nov 2021

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Stain Deconvolution results in separating the contributions of each of the applied stains present in the specimen.
Differential staining of cytoplasm, cell nuclei and other cell organelles, and specific proteins provide indicators of the distribution of the substance or structures to which a particular stain is specifically attached.
One of the most common examples is the Hematoxylin and Eosin (H&E) staining, with Hematoxylin (blue) mainly staining the cell nuclei, and Eosin (pink) acting as a cytoplasmic stain.
After applying the deconvolution function on H&E stained slides image we get separate images of Hematoxylin and Eosin which not only determines staining densities and overall absorption in areas with a specific color, but also determines densities of stains in each area.
This estimate of the stain uptake by the slide is important for understanding the density of cytoplasmic and nuclear proteins
Few input images and it's output have been provided in the file.
Step 1: Performing Stain deconvolution on an H&E stained image
Step 2: Reconstructing RGB image of different stain

Cite As

Abhishek Selokar (2022). Stain Density Estimation (https://www.mathworks.com/matlabcentral/fileexchange/102354-stain-density-estimation), MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2021b
Compatible with any release
Platform Compatibility
Windows macOS Linux
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