Metadata-Version: 2.4
Name: lbm_suite2p_python
Version: 1.0.3
Summary: Light Beads Microscopy Pipeline using Suite2p
License-Expression: BSD-3-Clause
Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
Keywords: Pipeline,Numpy,Microscopy,ScanImage,Suite2p,tiff
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: <3.13,>=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: tifffile>=2025.3.30
Requires-Dist: zarr>=2.18.3
Requires-Dist: dask>=2025.3.0
Requires-Dist: mkl-fft>=1.3.13
Requires-Dist: imageio[ffmpeg]
Requires-Dist: matplotlib>=3.10.1
Requires-Dist: h5py
Requires-Dist: tqdm
Requires-Dist: mbo_utilities[all]
Requires-Dist: suite2p_mbo==1.0.4
Requires-Dist: pynwb>=3.0.0
Requires-Dist: icecream>=2.1.4
Provides-Extra: napari
Requires-Dist: napari; extra == "napari"
Provides-Extra: all
Requires-Dist: napari; extra == "all"
Dynamic: license-file

# Light Beads Microscopy (LBM) Pipeline: Suite2p

[![PyPI - Version](https://img.shields.io/pypi/v/lbm-suite2p-python)](https://pypi.org/project/lbm-suite2p-python/)

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

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

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)


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

---

## 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]"
```

---

## 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.
