semvec/pypi-packages huggingface dataset:
lbm-suite2p-python 1.0.0
Light Beads Microscopy Pipeline using Suite2p
License: BSD-3-Clause
Requires Python: <3.13,>=3.11
Keywords: Pipeline, Numpy, Microscopy, ScanImage, Suite2p, tiff

# Light Beads Microscopy (LBM) Pipeline: Suite2p

This package is still in a *beta* stage of development.

[![Documentation](https://img.shields.io/badge/Documentation-black?style=for-the-badge&logo=readthedocs&logoColor=white)](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/index.html)

A pipeline for processing 2-photon Light Beads Microscopy (LBM) datasets.

This pipeline uses the following software:

- [suite2p](https://github.com/MouseLand/suite2p)
- [cellpose](https://github.com/MouseLand/cellpose)
- [rastermap](https://github.com/MouseLand/rastermap)
- [mbo_utilities](https://github.com/MillerBrainObservatory/mbo_utilities)
- [scanreader](https://github.com/atlab/scanreader)

The LBM technlology described in the Nature Methods publication:

[![DOI](https://zenodo.org/badge/DOI/10.1007/978-3-319-76207-4_15.svg)](https://doi.org/10.1038/s41592-021-01239-8)

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## Installation

See the [installation documentation](https://millerbrainobservatory.github.io/LBM-Suite2p-Python/install.html) for more details.

This pipeline is fully installable with `pip`.

`conda` can still be used for the virual environment, but be mindful to only install packages with `conda install` when absolutely necessary.

We recommend cloning the repository, until a more established workflow is available to upload to PyPi.

```
git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
git clone https://github.com/Suite3D # TODO
cd LBM-Suite2p-Python

# make sure your virtual environment is active
pip install ".[all]"  # optional, contains ".[gui, notebook]"
```

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## Acknowledgements

Thank you to the developers of [scanreader](https://github.com/atlab/scanreader), which provides a clean interface to ScanImage metadata using only tifffile and numpy.

We vendor this repository because it is not published to an indexable Python package registry like PyPI.