https://github.com/rsenft1/auto-basket-detector-2d
ImageJ macro scripts for analyzing fluorescent microscopy images: segmenting cells, divide into quadrants, and quantify innervation
https://github.com/rsenft1/auto-basket-detector-2d
ijm image-classification image-processing imagej-macro-scripts microscopy microscopy-images publication-code region-rois rois science-research segmenting-cells
Last synced: 4 months ago
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ImageJ macro scripts for analyzing fluorescent microscopy images: segmenting cells, divide into quadrants, and quantify innervation
- Host: GitHub
- URL: https://github.com/rsenft1/auto-basket-detector-2d
- Owner: rsenft1
- License: mit
- Created: 2020-12-31T04:43:25.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2020-12-31T05:22:48.000Z (over 5 years ago)
- Last Synced: 2023-12-16T16:11:06.322Z (over 2 years ago)
- Topics: ijm, image-classification, image-processing, imagej-macro-scripts, microscopy, microscopy-images, publication-code, region-rois, rois, science-research, segmenting-cells
- Homepage:
- Size: 18.6 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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.
# Macros/Code in this repo
### 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.
### Manual_cell_segmentation.ijm
* 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
# How to cite this repo:
### If you want to use these scripts in your own research, please do! If you publish, please cite the original publication: Senft et al., 2020 (in press, more details added soon)
## If you experience any issues... Please feel free to raise it to me using the Issues section