Metadata-Version: 2.1
Name: lbm-caiman-python
Version: 0.7.0
Summary: Python implementation of the Light Beads Microscopy (LBM) computational pipeline.
Home-page: https://github.com/millerbrainobservatory/LBM-CaImAn-Python
Author: Flynn OConnell
Author-email: foconnell@rockefeller.edu
Project-URL: homepage, https://github.com/MillerBrainObservatory/
Project-URL: documentation, https://millerbrainobservatory.github.io/LBM-CaImAn-Python/index.html
Project-URL: source, https://github.com/MillerBrainObservatory/LBM-CaImAn-Python/
Keywords: Pipeline Numpy Microscopy ScanImage multiROI tiff
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Requires-Dist: tifffile
Requires-Dist: numpy>=1.24.3
Requires-Dist: numba>=0.57.0
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Requires-Dist: dask
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# 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.
```
