lbm_suite2p_python 2.2.0

Light Beads Microscopy Pipeline using Suite2p

LBM-Suite2p-Python

Status: Late-beta stage of development

A volumetric 2-photon calcium imaging processing pipeline for Light Beads Microscopy (LBM) datasets, built on Suite2p.

A GUI is available via mbo_utilities (GUI functionality will lag behind this pipeline).

Quick Start

See the installation documentation for GUI dependencies and troubleshooting.

uv pip install lbm_suite2p_python

Basic Usage

import lbm_suite2p_python as lsp

ops = {"two_step_registration": 1}
files = [
    r"D://demo//plane05_stitched.zarr",
    r"D://demo//plane06_stitched.zarr",
]

# Process entire volume
output_ops = lsp.run_volume(
    input_files=files,
    save_path=None,     # save next to tiffs
    ops=ops,
    keep_reg=True,      # Keep registered binaries
    force_reg=False,    # Skip if already registered
    force_detect=False  # Skip if stat.npy exists
)

Process a single plane:

ops_file = lsp.run_plane(
    input_path=files[0],
    save_path=None,
    ops=ops,
    keep_raw=False,  # Delete data_raw.bin after processing
    keep_reg=True    # Keep data.bin (registered binary)
)

Documentation

• Installation Guide
• User Guide - Complete usage examples
• API Reference

Built With

This pipeline integrates several open-source tools:

• Suite2p - Core registration and segmentation
• Cellpose - Anatomical segmentation (optional)
• Rastermap - Activity clustering (optional)
• mbo_utilities - ScanImage I/O and metadata
• scanreader - ScanImage metadata parsing

Issues & Support

• Bug reports: GitHub Issues
• Questions: See Suite2p documentation for Suite2p-specific questions
• Known issues: Widgets may throw "Invalid Rect" errors (upstream issue)

Contributing

Contributions are welcome! This project follows Suite2p's conventions and uses:

• Ruff for linting and formatting (line length: 88, numpy docstring style)
• pytest for testing
• Sphinx for documentation