- Developed for: Julie
- Team: Rouach
- Date: March 2024
- Software: Fiji
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).
- 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
- 3DImageSuite Fiji plugin
- CLIJ2 Fiji plugin
- Cellpose conda environment + cyto2_Iba1_microglia (homemade) model
Version 1 released on March 26, 2024.