orion-cirb / NeuN_CFos

NeuN_CFos

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

Images description

3D images taken with a x20 objective

2 channels:

1. CSU_488: NeuN cells
2. CSU_642: CFos cells

Plugin description

• Detect NeuN and CFos cells with Stardist
• Colocalize NeuN and CFos cells
• For each channel, compute background noise as median intensity value of Z projection over min intensity
• For each cell, compute its volume and intensity/background-corrected intensity in each channel in which it appears

Dependencies

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

Version history

Version 1 released on September 13, 2023.