Installation · Documentation · User Guide · Issues
A volumetric 2-photon calcium imaging processing pipeline for Light Beads Microscopy (LBM) datasets, built on Suite2p.
- Process volumetric calcium imaging data - motion correction, cell detection, and signal extraction across z-planes
- Automated quality diagnostics - ROI quality metrics, ΔF/F traces, and correlation maps
- Scalable architecture - process single planes or entire volumes with consistent parameters
Planar Suite2p outputs combined into a 3D representation of neural activity
Note:
lbm_suite2p_pythonis in late-beta stage of active development. File an issue for bugs or feature requests.
Installation
lbm_suite2p_python is available on PyPI:
We recommend using a virtual environment. For help setting up a virtual environment, see the MBO guide on virtual environments.
# create a new project folder
mkdir my_project && cd my_project
# create environment and install (uv recommended)
uv venv --python 3.12.9
uv pip install lbm_suite2p_python
# or with pip
pip install lbm_suite2p_python
Optional Dependencies
# With rastermap for activity clustering visualization
uv pip install "lbm_suite2p_python[rastermap]"
# With cellpose for anatomical cell detection (includes PyTorch)
uv pip install "lbm_suite2p_python[cellpose]"
# All optional dependencies
uv pip install "lbm_suite2p_python[all]"
Development Installation
git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
cd LBM-Suite2p-Python
uv pip install -e ".[dev]"
Quick Start
import lbm_suite2p_python as lsp
results = lsp.pipeline(
input_data="D:/data/raw", # path to file, directory, or list of files
save_path=None, # default: save next to input
ops=None, # default: use MBO-optimized parameters
planes=None, # default: process all planes (1-indexed)
roi_mode=None, # default: stitch multi-ROI data
keep_reg=True, # default: keep data.bin (registered binary)
keep_raw=False, # default: delete data_raw.bin after processing
force_reg=False, # default: skip if already registered
force_detect=False, # default: skip if stat.npy exists
dff_window_size=None, # default: auto-calculate from tau and framerate
dff_percentile=20, # default: 20th percentile for baseline
dff_smooth_window=None, # default: auto-calculate from tau and framerate
)
User Guide for full API reference and examples
Output Gallery
Planar Results
Each z-plane produces diagnostic images automatically saved during processing.
correlation image with ROI overlay |
mean image with ROI overlay |
ROI quality metrics |
ΔF/F traces sorted by quality |
Volumetric Results
Volume-level visualizations combine data across all z-planes.
XZ/YZ orthogonal projections |
activity sorted by similarity (rastermap) |
GUI
A graphical interface is available via mbo_utilities:
pip install mbo_utilities
mbo # launch GUI
mbo /path/to/data # open file directly
Note: GUI functionality may lag behind the latest pipeline features.
Troubleshooting
Git LFS Download Errors
If you see smudge filter lfs failed when installing from GitHub:
GIT_LFS_SKIP_SMUDGE=1 uv pip install git+https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
Or set it permanently:
# Windows
[System.Environment]::SetEnvironmentVariable('GIT_LFS_SKIP_SMUDGE', '1', 'User')
# Linux/macOS
echo 'export GIT_LFS_SKIP_SMUDGE=1' >> ~/.bashrc
source ~/.bashrc
GUI Dependencies
Linux / macOS:
sudo apt install libxcursor-dev libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev
Windows: Install Microsoft Visual C++ Redistributable
Built With
- Suite2p - Core registration and segmentation
- Cellpose - Anatomical segmentation (optional)
- Rastermap - Activity clustering (optional)
- mbo_utilities - ScanImage I/O and metadata
Issues & Support
- Bug reports: GitHub Issues
- Questions: See documentation or Suite2p docs
Contributing
Contributions are welcome! This project uses:
- Ruff for linting and formatting (line length: 88, numpy docstring style)
- pytest for testing
- Sphinx for documentation
2 maintainers
Metadata
2 maintainers
Release files for lbm_suite2p_python 3.3.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| lbm_suite2p_python-3.3.2.tar.gz | 198.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| lbm_suite2p_python-3.3.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 388.5 kB
Release files / lbm_suite2p_python-3.3.2.tar.gz
| Download URL | lbm_suite2p_python-3.3.2.tar.gz |
|---|---|
| Size | 198.7 kB |
| Tags | Source |
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Release files / lbm_suite2p_python-3.3.2-py3-none-any.whl
| Download URL | lbm_suite2p_python-3.3.2-py3-none-any.whl |
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| Size | 189.9 kB |
| Tags | Python 3 |
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