- Developed for: Rania
- Team: Fuchs
- Date: October 2022
- Software: Fiji
3D images taken with a x60 objective
2 channels:
- CSU_405: DAPI nuclei
- CSU_488: ORF1p cells
- Detect DAPI nuclei and ORF1p cells with Cellpose
- Keep ORF1p cells with a nucleus only
- Detect ORF1p dots with Stardist
- Give various measurements in the nucleus, inner nucleus, inner ring, outer ring and cytoplasm
- 3DImageSuite Fiji plugin
- Cellpose conda environment + cyto2 model
- StarDist conda environment + pmls2.zip (homemade) model
Version 1 released on October 14, 2022.