# Gut Analysis ToolBox - Documentation

## Gut Analysis Toolbox Documentation

- [Home](https://gut-analysis-toolbox.gitbook.io/docs/home.md): Introduction to Gut Analysis ToolBox
- [1. Choosing the right parameters](https://gut-analysis-toolbox.gitbook.io/docs/1.-choosing-the-right-parameters.md)
- [2. Cell counts and ganglia analysis](https://gut-analysis-toolbox.gitbook.io/docs/2.-cell-counts-and-ganglia-analysis.md)
- [Batch Analysis](https://gut-analysis-toolbox.gitbook.io/docs/2.-cell-counts-and-ganglia-analysis/batch-analysis.md): Integrate GAT into your workflow!
- [3. Spatial Analysis](https://gut-analysis-toolbox.gitbook.io/docs/3.-spatial-analysis.md)
- [4. Analyzing the Results](https://gut-analysis-toolbox.gitbook.io/docs/4.-analyzing-the-results.md): How to deal with them spreadsheets!!
- [5. Segmentation options](https://gut-analysis-toolbox.gitbook.io/docs/5.-segmentation-options.md): What to do when segmentation in GAT doesn't work so well.
- [6. QuPath for analysing ENS](https://gut-analysis-toolbox.gitbook.io/docs/6.-qupath-for-analysing-ens.md): Using QuPath for analysing enteric neurons
- [7. Multiplex](https://gut-analysis-toolbox.gitbook.io/docs/7.-multiplex.md)
- [Multiplex image alignment](https://gut-analysis-toolbox.gitbook.io/docs/7.-multiplex/multiplex-image-alignment.md): Register images from multiplexed imaging round
- [Multiplex analysis](https://gut-analysis-toolbox.gitbook.io/docs/7.-multiplex/multiplex-analysis.md)
- [Other resources](https://gut-analysis-toolbox.gitbook.io/docs/7.-multiplex/other-resources.md)
- [8. Calcium Imaging Analysis](https://gut-analysis-toolbox.gitbook.io/docs/8.-calcium-imaging-analysis.md): Analyzing calcium imaging data of the ENS
- [Image alignment/registration](https://gut-analysis-toolbox.gitbook.io/docs/8.-calcium-imaging-analysis/image-alignment-registration.md): Correction of motion artefacts due to tissue contraction or other movement
- [Extracting calcium traces](https://gut-analysis-toolbox.gitbook.io/docs/8.-calcium-imaging-analysis/extracting-calcium-traces.md): Workflow to extract calcium responses from the aligned data
- [Other Resources](https://gut-analysis-toolbox.gitbook.io/docs/8.-calcium-imaging-analysis/other-resources.md)
- [9. GATv2](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2.md): Set up, launch and navigate GAT v2 — start here.
- [Analyse Neurons](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/analyse-neurons.md): Count neurons labelled with Hu, and optionally cells per ganglia.
- [Multichannel – No Hu](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/multichannel-no-hu.md): Analyse subtype markers without a pan-neuronal Hu label (experimental).
- [Multichannel – With Hu](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/multichannel-with-hu.md): Count neurons and their subtypes when you have a Hu channel.
- [Spatial Analysis](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/spatial-analysis.md): Measure how cells are distributed and related in space.
- [Calcium Imaging](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/calcium-imaging.md): Align calcium imaging movies and extract fluorescence traces.
- [Multiplex](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/multiplex.md): Align images from multiple rounds of multiplex staining.
- [Merge Analysis](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/merge-analysis.md): Combine results from many images into one table.
- [Tools](https://gut-analysis-toolbox.gitbook.io/docs/9.-gatv2/tools.md): Test and tune parameters before running a full analysis.
- [System Requirements](https://gut-analysis-toolbox.gitbook.io/docs/system-requirements.md): System requirements for running GAT
- [Analysis tools & workflows of interest](https://gut-analysis-toolbox.gitbook.io/docs/analysis-tools-and-workflows-of-interest.md): Collection of potentially interesting tools or approaches for image analysis in the ENS
- [Contributing to GAT](https://gut-analysis-toolbox.gitbook.io/docs/contributing-to-gat.md)
- [Troubleshooting](https://gut-analysis-toolbox.gitbook.io/docs/troubleshooting.md)
- [List of major bugs fixed](https://gut-analysis-toolbox.gitbook.io/docs/troubleshooting/list-of-major-bugs-fixed.md): This page is to document the issues we've encountered and fixed till date
- [Citing GAT](https://gut-analysis-toolbox.gitbook.io/docs/citing-gat.md): How to cite GAT!
- [Citations](https://gut-analysis-toolbox.gitbook.io/docs/citations.md): Papers that cite GAT
- [Features](https://gut-analysis-toolbox.gitbook.io/docs/features.md): Summary of features that are being added
- [Feedback](https://gut-analysis-toolbox.gitbook.io/docs/feedback.md): Use this google form for reporting errors or requesting features
- [Ganglia Models](https://gut-analysis-toolbox.gitbook.io/docs/benchmarks/ganglia-models.md): Ganglia model benchmark v3 vs v2