search

knime-ip / knip

KNIME Image Processing Extension
https://www.knime.com/community/image-processing
50 stars 11 forks source link

KNIP Nodes: Add Stain Separation Node #300

Open JohM3i opened 8 years ago

JohM3i commented 8 years ago

There should be a node, which does Stain Separation on Images.

There exists a ImageJ plugin which does Stain Separation on RGB Images with Color Deconvolution. The plugin can't be executed with the imageJ macro. In the Plugin, there are several predefinied Stain vectors to do Stain

like H&E, H DAB, H&E DAB, etc.

You can download the java files and class files here: http://www.mecourse.com/landinig/software/cdeconv/cdeconv.html

For further readings you can use the Paper: Ruifrok AC, Johnston DA. Quantification of histochemical staining by color deconvolution. Anal Quant Cytol Histol 23: 291-299, 2001.

imagejan commented 8 years ago

In the Plugin, there are several predefinied Stain vectors to do Stain

Note that these predefined vectors are meant as examples only, and there should be a method for users to provide their own vectors.

See Gabriel Landini's comments in a discussion about the Colour Deconvolution plugin:

That is crucial, the built-in vectors are there only as examples, I would expect everybody who is serious about their analyses to determine their own values according to the techniques and protocols they use