orion-cirb / GFP_PV_PNN

GFP_PV_PNN

• Developed for: David
• Team: Prochiantz
• Date: November 2022
• Software: Fiji

Images description

3D images taken with a x60 objective

4 channels:

1. Alexa Fluor 647: PV cells
2. Alexa Fluor 546: PNN cells
3. EGFP: Gamma-H2AX
4. Hoechst 33342: nuclei

Plugin description

• Detect nuclei, PV and PNN cells with Cellpose
• Compute their colocalization
• Keep PV/PNN cells with a nucleus only
• Detect DAPI and Gamma-H2AX foci in each PV/PNN nucleus with Stardist

Dependencies

• 3DImageSuite Fiji plugin
• CLIJ Fiji plugin
• Cellpose conda environment + cyto2, cyto_PV1 (homemade) and livecell_PNN1 (homemade) models
• StarDist conda environment + pmls2.zip (homemade) model

Version history

Version 1 released on November 17, 2022.