auto-basket-detector-2D

ImageJ macro scripts for analyzing fluorescent microscopy images: segmenting cells, divide into quadrants, and quantify innervation

What is this repo for?

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
Automatic_cell_segmentation.ijm
Performs automatic segmentation of cells, specifically made with tiled images with uneven illumination in mind
ROI_manual_remover.ijm
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
Quad_basket_quant.ijm
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
Region_labeler.ijm
Creates user-defined region ROIs for subregions within an image (e.g. cortical layer, hippocampal subfields)
Region_analyzer.ijm
Will sort cell ROIs from a previous manual or automatic segmentation method into the region ROIs made with Region_labeler.ijm