- Developed for: Tom
- Team: Fuchs
- Date: March 2022
- Software: QuPath
2D images of mouse brain sections taken with the Axioscan
4 channels:
- DAPI: nuclei
- EGFP: microglia (?)
- Cy3: ORF1p cells
- Cy5: NeuN cells
Version 1:
- Detect nuclei, microglia and ORF1p and NeuN cells with Stardist
- Compute their colocalization
Version 2:
- Ignore EGFP channel
- Detect nuclei with Stardist and ORF1p and NeuN cells with Cellpose
- Compute their colocalization
- Compute background noise automatically in each annotation by taking into account every pixel that is not belonging to a cell (after Stardist/Cellpose detection)
- Handle hierarchy by skipping the analysis of parents regions
- Stardist QuPath extension + dsb2018_heavy_augment.pb model
- Cellpose QuPath extension and conda environment + cyto2 model
Version 1 (getnuclei.groovy) released on September 1, 2022.
Version 2 (getnuclei_improved.groovy) released on March 28, 2022.