lbm_suite2p_python 2.0.3

Light Beads Microscopy Pipeline using Suite2p

Light Beads Microscopy (LBM) Pipeline: Suite2p

This package is still in a late-beta stage of development.

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

This pipeline uses the following open-source software:

• suite2p
• cellpose
• rastermap
• mbo_utilities
• scanreader

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Installation

This pipeline is installable with pip:

pip install lbm_suite2p_python
# with uv: uv pip install lbm_suite2p_python

We highly encourage the use of a virtual environment. If you are unfamiliar with virtual environments, see our documentation here.

You may also use git to clone and install locally for updates not yet released to pypi:

git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
cd LBM-Suite2p-Python

# make sure your virtual environment is active
pip install "." 

Features

2.0.0

• Process ScanImage multi-ROI as separate datasets
• Post-processing cell filters for area, exceptional events and eccentricity

1.0.0

• Suite2p planar segmentation
• DF/F, baseline calculation and documentation
• Aggregate planar outputs into volumetric dataset

Issues

Widgets may throw "Invalid Rect" errors. This can be safely ignored until it is resolved.

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Acknowledgements

This pipeline is mostly a volumetric wrapper around suite2p, cellpose and Suite3D. We thank the contributors to those projects.

Thank you to the developers of scanreader, which provides a clean interface to ScanImage metadata using only tifffile and numpy.