Published February 15, 2022
| Version 1.0.0
Software
Open
Gut Analysis Toolbox
Creators
- Sorensen, Luke
- Saito, Ayame
- Poon, Sabrina
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Noe Han, Myat
- Humenick, Adam
- Mutunduwe, Keith
- Glennan, Christie
- Mahdavian, Narges
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JH Brookes, Simon
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M McQuade, Rachel
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PP Foong, Jaime
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Sebastian K. King
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Gómez-de-Mariscal, Estibaliz
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Haase, Robert
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Carbone, Simona
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A. Veldhuis, Nicholas
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P. Poole, Daniel
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Rajasekhar, Pradeep
Description
Gut Analysis Toolbox or GAT allows the semi-automated analysis of the cells within the enteric nervous system of 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.
Link to the software: https://github.com/pr4deepr/GutAnalysisToolbox
To install the software in FIJI, follow instructions in the Wiki here.
The custom deep learning models are implemented in FIJI using StarDist and deepImagej. The training data, notebooks and details about models can be found here:
https://doi.org/10.5281/zenodo.6094887
Notes
If you use this software, please cite it as below.
Files
pr4deepr/GutAnalysisToolbox-zenodo.zip
Files
(221.1 MB)
| Name | Size | Download all |
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md5:f1abd3ba95a30d5219ad5158ae931407
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Additional details
Related works
- Is supplement to
- https://github.com/pr4deepr/GutAnalysisToolbox/tree/zenodo (URL)