ImageJ macro scripts for analyzing fluorescent microscopy images: segmenting cells, divide into quadrants, and quantify innervation
- This repo contains a number of scripts used in my paper for quantifying the pericellular basket-type innervation of fluorescently-labeled target cell soma
- These scripts work on 2D multichannel fluorescent images. They require a cell soma/cell marker channel (you could also use DAPI) and a fluorescent marker of innervation
- Theoretically it could be brightfield, but it was made with fluorescence in mind.
All are .ijm files written in the ImageJ macro programming language. They can be dragged and dropped into Fiji or installed using the Plugins > Macros > Install... menu.
- Performs user-assisted segmentation of cells using a magic wand tool
- Performs automatic segmentation of cells, specifically made with tiled images with uneven illumination in mind
- Opens images and their associated ROIs from automatic or manual methods and allows the user to remove (or add, technically) ROIs
- Useful with the automatic method to correct for any inaccurate segmentation
- Divides cell ROIs generated from previous two macros into quadrants
- Removes the center (to prevent a single bouton from being counted in all quadrants)
- Segments the innervation/fiber channel
- Quantifies the fiber area in each quadrant per cell
- Creates user-defined region ROIs for subregions within an image (e.g. cortical layer, hippocampal subfields)
- Will sort cell ROIs from a previous manual or automatic segmentation method into the region ROIs made with Region_labeler.ijm