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.

• 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