Gut Analysis Toolbox enables semi-automated analysis of the neuronal and glial distribution within the gut wall (enteric nervous system). It uses a combination of FIJI macros, StarDist, CLIJ
and deepImageJ for segmentation and analysis.
Click here to access the WIKI detailed instructions on how to use GAT.
You can also watch tutorials for GAT on Youtube.
What you can do with GAT:
- Semi-automated analysis of number of enteric neurons: Uses pan-neuronal marker Hu or anything with similar labelling
- Normalise counts to the number of ganglia.
- Count number of neuronal subtypes, such as ChAT, nNOS etc..
- Spatial analysis using number of neighboring cells.
- Calcium imaging analysis: Alignment of images and extraction of normalised traces
Reference
To cite GAT:
Sorensen, L., A. Humenick, S. S. B. Poon, M. N. Han, N. S. Mahdavian, R. Hamnett, E. Gómez-de-Mariscal, P. H. Neckel, A. Saito, K. Mutunduwe, C. Glennan, R. Haase, R. M. McQuade, J. P. P. Foong, S. J. H. Brookes, J. A. Kaltschmidt, A. Muñoz-Barrutia, S. K. King, N. A. Veldhuis, S. E. Carbone, D. P. Poole and P. Rajasekhar (2024). “Gut Analysis Toolbox: Automating quantitative analysis of enteric neurons.” bioRxiv: 2024.2001.2017.576140.
To download the training data, notebooks and associated models please go to the following Zenodo link:
