lbm_suite2p_python 1.0.5

Light Beads Microscopy Pipeline using Suite2p

Light Beads Microscopy (LBM) Pipeline: Suite2p

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
• cellpose
• rastermap
• mbo_utilities
• scanreader

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Installation

See the installation documentation 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]"

Issues

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

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Acknowledgements

Thank you to the developers of 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.