- Developed for: Sandra
- Team: Fuchs
- Date: February 2023
- Software: Fiji
3D images taken with a x25 objective
3 channels:
- 405: Nuclei
- 488: Lamin (not mandatory)
- 561: ORF1P
- Detect nuclei with Cellpose
- Compute nuclei 3D shape descriptors
- In lamin channel (if provided), measure nuclei intensity
- In ORF1P channel, get cytoplasm using a Gaussian filter + Moments thresholding + nuclei subtraction
- In ORF1P channel, measure nuclei and cytoplasm intensity
- 3DImageSuite Fiji plugin
- CLIJ Fiji plugin
- Omnipose conda environment + cyto2 model
Version 1 released on February 16, 2023.