lbm-caiman-python

Name	lbm-caiman-python JSON
Version	0.7.0 JSON
	download
home_page	https://github.com/millerbrainobservatory/LBM-CaImAn-Python
Summary	Python implementation of the Light Beads Microscopy (LBM) computational pipeline.
upload_time	2024-09-27 15:47:14
maintainer	None
docs_url	None
author	Flynn OConnell
requires_python	>=3.9
license	None
keywords	pipeline numpy microscopy scanimage multiroi tiff
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # LBM-CaImAn-Python

[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh) [![Documentation](https://img.shields.io/badge/%20Docs-1f425f.svg)](https://millerbrainobservatory.github.io/LBM-CaImAn-Python/)

Python implementation of the Light Beads Microscopy (LBM) computational pipeline.

For the `MATLAB` implementation, see [here](https://github.com/MillerBrainObservatory/LBM-CaImAn-MATLAB/)

## Pipeline Steps:

1. Extraction
    - De-interleave zT
    - Scan Phase-Correlation
2. Registration
    - Template creation
    - Rigid registration
    - Piecewise-rigid registration
3. Segmentation
    - Iterative CNMF segmentation
    - Deconvolution
    - Refinement

# Requirements

- caiman
- numpy
- scipy

```{note}
See the `environment.yml` file at the root of this project for a complete list of package dependencies.
```

            

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