QuPath_ORF1P

• Developed for: Tom
• Team: Fuchs
• Date: March 2022
• Software: QuPath

Images description

2D images of mouse brain sections taken with the Axioscan

4 channels:

1. DAPI: nuclei
2. EGFP: microglia (?)
3. Cy3: ORF1p cells
4. Cy5: NeuN cells

Plugin description

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

Dependencies

• Stardist QuPath extension + dsb2018_heavy_augment.pb model
• Cellpose QuPath extension and conda environment + cyto2 model

Version history

Version 1 (getnuclei.groovy) released on September 1, 2022.

Version 2 (getnuclei_improved.groovy) released on March 28, 2022.