> For the complete documentation index, see [llms.txt](https://gut-analysis-toolbox.gitbook.io/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://gut-analysis-toolbox.gitbook.io/docs/8.-calcium-imaging-analysis/other-resources.md).

# Other Resources

* ENS specific: Barth et al., 2022; [Paper ](https://onlinelibrary.wiley.com/doi/abs/10.1111/nmo.14678)and [`MATLAB` code/data](https://research.repository.duke.edu/concern/datasets/p8418p27q?locale=en)
* [**CaImAn**](https://github.com/flatironinstitute/CaImAn): `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.

  * [mesmerize-core ](https://github.com/nel-lab/mesmerize-core)is the main application that can be used in Jupyter notebooks
  * [mesmerize-viz ](https://github.com/kushalkolar/mesmerize-viz)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: <https://kornia.readthedocs.io/en/latest/tracking.html>