orion-cirb / Th_Nucleus_Cytoplasm

Th_Nucleus_Cytoplasm

• Developed for: Olivia
• Team: Fuchs
• Date: February 2023
• Software: Fiji

Images description

3D images taken with a x20 objective

4 channels:

1. CSU_405: DAPI nuclei
2. CSU_488: Th cells
3. CSU_561: ORF1p
4. CSU_642: NeuN

Plugin description

• Detect DAPI nuclei with Cellpose
• Detect Th cells with Cellpose
• Detect NeuN cells with Cellpose
• Colocalize nuclei with Th and NeuN cells and tag each nucleus as being NeuN+/NeuN- and Th+/Th-
• Measure intensity of nuclei, cytoplasms and cells in ORF1p channel

Dependencies

• 3DImageSuite Fiji plugin
• Cellpose conda environment + cyto and cyto2 models

Version history

Version 2 released on February 22, 2023.