lbm-caiman-python 1.0.0

Light Beads Microscopy 2P Calcium Imaging Pipeline.

LBM-CaImAn-Python

Installation | Notebooks

Python implementation of the Light Beads Microscopy (LBM) computational pipeline.

For the MATLAB implementation, see here

Installation

Installation requires an active conda installation.

Note: Sometimes conda or mamba will get stuck at a step, such as creating an environment or installing a package. Pressing Enter on your keyboard can sometimes help it continue when it pauses.

1. Install mamba into your base environment:

• :exclamation: This step may take 10 minutes and display several messages like "Solving environment: failed with..." but it should eventually install mamba.

conda activate base 
conda install -c conda-forge mamba

2. Create a new environment and install mesmerize-core

• Here, we use the -n flag to name the environment lbm , but you can name it whatever you'd like.
• This step will install Python, mesmerize-core, CaImAn, and all required dependencies for those packages.

conda create -n lbm -c conda-forge mesmerize-core

If you already have CaImAn installed:

conda install -n name-of-env-with-caiman mesmerize-core

Activate the environment and install caimanmanager:

• if you used a name other than lbm, be sure to match the name you use here.

conda activate lbm
caimanmanager install

3. pip install lbm_caiman_python

Install the minimal lbm_caiman_python:

pip install lbm_caiman_python

# or, to get fastplotlib + jupyter lab
pip install "lbm_caiman_python[all]"

The example notebooks include visualizations using fastplotlib, install with:

For Developers

To get the newest version of this package:

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

cd LBM-CaImAn-Python

pip install ".[all]"

Troubleshooting

Conda Issues

if conda is behaving slow, clean the conda installation and update conda-forge:

conda clean -a

conda update -c conda-forge --all

Recommended Conda Distribution

The recommended conda installer is miniforge.

This is a community-driven conda/mamba installer with pre-configured packages specific to conda-forge.

This helps avoid conda-channel conflicts and avoids any issues with the Anaconda TOS.

You can install the installer from a unix command line:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

bash Miniforge3-$(uname)-$(uname -m).sh

Or download the installer for your operating system here.

Graphics Driver Issues

If you opted into installing fastplotlib and receive errors about graphics drivers, see the fastplotlib driver documentation.

Pipeline Steps:

1. Motion Correction
   • Template creation
   • Rigid registration
   • Piecewise-rigid registration
2. Segmentation
   • Iterative CNMF segmentation
   • Deconvolution
   • Refinement
3. Collation
   • Lateral offset correction (between z-planes)
   • Collate images and metadata into a single volume

Requirements

• caiman
• mesmerize-core
• numpy
• scipy

Optional:

• fastplotlib
• mesmerize-viz