Installation Guide#
LBM-Suite2p-Python has been developed to be a pure pip install.
This makes the choice of virtual-environment less relevant, you can use venv, uv (recommended), conda, it does not matter.
Tip
While this pipeline is early in development, we recommend keeping a version of the codebase locally using git.
This will allow you to quickly pull changes and incorperate them into your environment without waiting for a pypi release.
git clone https://github.com/MillerBrainObservatory/LBM-Suite2p-Python.git
cd LBM-Suite2p-Python
pip install -e "."
# create a new project folder
mkdir my_project
cd my_project
# create our environment
uv venv --python 3.12.9
uv pip install lbm_suite2p_python
conda create -n lsp -c conda-forge python=3.12.9
conda activate lbm
git clone https://github.com/millerbrainobservatory/lbm_suite2p_python.git
cd lbm_suite2p_python
pip install -e .
GUI Dependencies#
sudo apt install libxcursor-dev libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev
You will need msvcc redistributable
Troubleshooting#
Git LFS Error: smudge filter lfs failed#
If you see:
error: external filter 'git-lfs filter-process' failed
fatal: docs/source/_static/guide_hello_world.png: smudge filter lfs failed
Disable smudge during sync:
GIT_LFS_SKIP_SMUDGE=1 uv sync --all-extras --active
To debug:
git lfs logs last
This avoids downloading large binary files (e.g. images, model checkpoints) managed by Git LFS.