Setup a workflow for detecting nuclei in P1_H_C3H_M004_17.czi - P1_H_C3H_M004_17.czi #1.tif (available online, courtesy of Theresa Suckert, OncoRay, University Hospital Carl Gustav Carus, TU Dresden, license CC-BY 4.0)
Use operations such as
- Crop 2D
- Extract Channel
- Detect Maxima 2D?
- Threshold Otsu 2D?
- Binary Weka Pixel Classifier?
Export a Groovy script for QuPath using CluPath. You have to edit this script to make it work in QuPath: You need to remove the crop-step as cropping is done by QuPath. Replace the copy step by a copy slice step to extract a slice in QuPath, which correspond to the channel.
Before opening the Groovy script in QuPath, check that CluPath is installed.
