= Rationale =
In order to properly separate dyes in stained histological sections, it is necessary to establish the deconvolution stain vectors
(NOTE) These vectors should be assessed and determined** for a given stain combination and fixed imaging conditions**
== Samples ==
For each dye you use, you need a single-stained sample.
== Procedure in QuPath ==
=== Define Stain Names In Image ===
Load the image with the sample containing the first dye only
{nav Image Tab > Properties > Double click on Stain 1 and Stain 2 > name=Rename Stain Vectors, type=instructions}
{F7001633, float=left} {F7001625}
Before (Left) and After Renaming (Right)
===Estimate the First Stain Vector===
{nav Analyze > Preprocessing > Estimate stain vectors}
{F7001681}
Navigate the line on the graph that corresponds to the first stain vector. Do not move the other vector.
{nav click OK > name=Rename Vectors, type=instructions}
{F7001724}
== Repeat for second Stain Vector ==
{nav click OK > name=Rename Vectors, type=instructions}
== Save as a script ==
{nav Workflow Tab > Create Script> name=Delete all lines except the last one, type=instructions}
```
setColorDeconvolutionStains('{"Name" : "BIOP Sirius Red - Hematoxylin", "Stain 1" : "Sirius Red", "Values 1" : "0.26426 0.50354 0.82257 ", "Stain 2" : "Hematoxylin", "Values 2" : "0.75506 0.62505 0.19801 ", "Background" : " 222 222 222 "}');
```