orion-cirb / RNA_Scope_DAPI

RNA_Scope_DAPI

• Developed for: Rachel
• Team: Prochiantz
• Date: March 2023
• Software: Fiji

Images description

3D images taken with a x25 objective

3 channels:

1. 405: DNA
2. 642: Foci X
3. 561: Foci Y

Plugin description

• Detect nuclei with Cellpose
• Detect foci X and foci Y with Stardist
• Compute foci number in each nucleus

Dependencies

• 3DImageSuite Fiji plugin
• CLIJ Fiji plugin
• Cellpose conda environment + cyto2 model
• Stardist conda environment + fociRNA-1.2.zip (homemade) model

Version history

Version 1 released on March 3, 2023