Analysis scripts utilised for mouse connectivity paper
This package of ImageJ/Fiji macros is designed to allow the user to quantify fluorescent tracing photomicrographs and compare the connectivity between multiple regions in the brain
Lines in the startupmacro_addendum.txt should be added to the local startup macro file in your ImageJ/Fiji macro folder .ijm files numbered 1-5 should be copied into that folder as well
Workflow should proceed with:
- Preprocessing/Preprocessing batch-Grayscales colour images and filters for acquisition artefacts
- Background Subtraction- Preforms average background luminance subtraction based on user input ROI and thresholds image
- Quantification- Run either anterograde (which measures fibre percentage area coverage) or retrograde (measures cell counts per ROI) with thresholded images and counterstained images with ROIs for the demarcated brain regions
- Modulation index-Place quantification results for each region into array and run this matlab script to get a modulation index for preference between two regions (To Do)
For any more information regarding other macros and building your own macro scripts for ImageJ/Fiji visit: http://rsb.info.nih.gov/ij/developer/macro/macros.html
Any questions regarding this code can be directed to [email protected]