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Semi-automated analysis of cells of the enteric nervous system within the gastrointestinal tract.

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Gut Analysis Toolbox

Gut Analysis Toolbox or GAT allows the Semi-automated analysis of the enteric nervous system within the gastrointestinal tract. GAT enables quantification of enteric neurons and their subtypes. It runs in FIJI, a popular image analysis software in microscopy and uses deep learning models to segment cells of interest.

To get started, please go to the Wiki page.

You can also watch tutorials for GAT on Youtube.

If you have any difficulties, suggestions or find any bugs, create a post under Issues or you could use the Imagesc forum. Feel free to use the discussions if you'd like input on your analysis or would like to discuss relevant topics.

Installing and configuring GAT

Click on this video to watch how to install and configure FIJI and GAT

Youtube

GAT requires the following update sites:

  • BIG-EPFL
  • CSBDeep
  • clij
  • clij2
  • DeepImageJ
  • IJBP-Plugins (MorphoLibJ)
  • StarDist

GAT update site: https://sites.imagej.net/GutAnalysisToolbox/

Download model files

The model files are zipped and ready to download here:

Click to Download GAT FIJI model folders

Click here to see how to configure models after GAT installation in FIJI.

Click to Download QuPath model and scripts

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