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Gut Analysis ToolBox - Documentation
  • Home
  • 🚀1. Choosing the right parameters
  • 🔢2. Cell counts and ganglia analysis
    • 📄Batch Analysis
  • 🗺️3. Spatial Analysis
  • 💻4. Analyzing the Results
  • 🌋5. Segmentation options
  • 🚅6. QuPath for analysing ENS
  • 🧮7. Multiplex
    • Multiplex image alignment
    • Multiplex analysis
    • Other resources
  • 🔬8. Calcium Imaging Analysis
    • Image alignment/registration
    • Extracting calcium traces
    • Other Resources
  • System Requirements
  • Analysis tools & workflows of interest
  • Contributing to GAT
  • Troubleshooting
    • List of major bugs fixed
  • Citing GAT
  • Citations
  • Features
  • Feedback
  • Benchmarks
    • Ganglia Models
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  • Mihir Pendse, Haley De Selle, Nguyen Vo, Gabriella Quinn, Chaitanya Dende, Yun Li, Cristine N Salinas, Tarun Srinivasan, Daniel C Propheter, Alexander A Crofts, Eugene Koo, Brian Hassell, Kelly A Ruhn, Prithvi Raj, Yuuki Obata, Lora V Hooper (2023) Macrophages regulate gastrointestinal motility through complement component 1q eLife 12:e78558; doi:

  • Hamilton, A.M., Blackmer-Raynolds, L., Li, Y. et al. Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury. npj Biofilms Microbiomes 10, 75 (2024). doi:

  • Barth, BB, Redington, ER, Gautam, N, Pelot, NA, Grill, WM. Calcium image analysis in the moving gut. Neurogastroenterology & Motility. 2023; 00:e14678. doi:

  • Han, M. N., Di Natale, M. R., Lei, E., Furness, J. B., Finkelstein, D. I., Hao, M. M., Diwakarla, S., & McQuade, R. M. (2025). Assessment of gastrointestinal function and enteric nervous system changes over time in the A53T mouse model of Parkinson's disease. Acta neuropathologica communications, 13(1), 58. doi:

doi.org/10.7554/eLife.78558
10.1038/s41522-024-00556-y
10.1111/nmo.14678
10.1186/s40478-025-01956-7