orion-cirb / Iba1

Iba1

• Developed for: Julie
• Team: Rouach
• Date: March 2024
• Software: Fiji

Images description

3D images taken with a x40 objective on a spinning-disk microscope

1 channel: Iba1 microglia

With each image can be provided a .roi or .zip file containing one or multiple ROI(s).

Plugin description

• Detect microglial somas with Cellpose
• Segment microglial cells with median filtering + thresholding
• Compute background noise of Iba1 channel
• Give microglial somas number + microglial cells volume + microglial cells background-corrected mean and integrated intensity
• If ROI(s) provided, remove from the analysis microglia that are inside

Dependencies

• 3DImageSuite Fiji plugin
• CLIJ2 Fiji plugin
• Cellpose conda environment + cyto2_Iba1_microglia (homemade) model

Version history

Version 1 released on March 26, 2024.