orion-cirb / Nuclei_ORF1P

Nuclei_ORF1P

• Developed for: Rania
• Team: Fuchs
• Date: October 2022
• Software: Fiji

Images description

3D images taken with a x60 objective

2 channels:

1. CSU_405: DAPI nuclei
2. CSU_488: ORF1p cells

Plugin description

• 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

Dependencies

• 3DImageSuite Fiji plugin
• Cellpose conda environment + cyto2 model
• StarDist conda environment + pmls2.zip (homemade) model

Version history

Version 1 released on October 14, 2022.