orion-cirb / Sox9_PV_CFos

Sox9_PV_CFos

• Developed for: Rachel
• Team: Prochiantz
• Date: January 2024
• Software: Fiji

Images description

3D images taken with a x25 objective on the Zeiss W1 spinning-disk microscope

4 channels:

1. CSU_405: DAPI
2. CSU_488: Sox9
3. CSU_561: CFos
4. CSU_642: PV

Plugin description

• Detect Sox9 and PV cells with Stardist
• For each channel, compute background noise as median intensity value of Z projection over min intensity
• For each cell, compute its volume and background-corrected intensity in its respective channel and in the CFos channel

Dependencies

• 3DImageSuite Fiji plugin
• Stardist "StandardFluo.zip" model

Version history

Version 1 released on January 24, 2024.