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Gut Analysis ToolBox - Documentation
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  • 🚀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
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  • Benchmarks
    • Ganglia Models
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  1. 8. Calcium Imaging Analysis

Other Resources

PreviousExtracting calcium tracesNextSystem Requirements

Last updated 16 days ago

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  • ENS specific: Barth et al., 2022; and

  • : Python-based toolbox for analysing calcium imaging data. Comprehensive, but can be a bit hard to use as it doesn't really have a user interface. CaImAn is made accessible by the mesmerize package mentioned next.

  • Mesmerize: Python-based and one of my favourites due to its modularity and how it makes CaImAn accessible.

    • is the main application that can be used in Jupyter notebooks

    • provide a user interface so you don't have to enter commands

    There is a learning curve, but if you do a lot of calcium imaging, its worth persevering. The developers are extremely helpful too!

Extra coding effort:

  • Kornia:

🔬
Paper
MATLAB code/data
CaImAn
mesmerize-core
mesmerize-viz
https://kornia.readthedocs.io/en/latest/tracking.html