batch2p

Batch 2-photon preprocessing pipeline. Runs configurable source extraction (suite2p or suite3d) from a single JSON configuration file.

This package streamlines source extraction from tiff files (at the moment ScanImage files are supported). Suite2p and Suite3d are currently supported, with features like:

• file concatenation
• flexible parameters handling (also including parameter "sweeps")
• creation of batch files for SLURM
• if the experiment used totalsync for synchronization, imaging and other experimental data (eg. behavioral) are automatically synchronized.

Installation

From PyPI

pip install batch2p

From source (using pip)

git clone https://github.com/NeuroNetMem/batch2p.git
cd batch2p
pip install . # (or uv pip install ".[all]" )

this will install batch2p without GUI support, (which is suitable for headless servers). To install the GUI, replace the last line with

pip install ".[gui]" # (or uv pip install ".[gui]" )

From source (using uv)

git clone https://github.com/NeuroNetMem/batch2p.git
cd batch2p
uv pip install .

suite3d (optional)

If you need suite3d support, install it manually from source after installing batch2p. See instructions at https://github.com/alihaydaroglu/suite3d.

Briefly,

• Clone the suite3d repository (in a different directory):

git clone https://github.com/alihaydaroglu/suite3d.git

cd suite3d 
pip install ".[all]" # (or uv pip install ".[all]" )

Then, install the suite3d cuda dependencies:

pip install "cupy-cuda13x" # for CUDA 13.X, for other CUDA versions change accordingly

Usage

Detailed usage documentation can be found in the docs directory.

• batch2p — single-session pipeline
• batch2p-multi — multi-session batch runner
• batch2p-gui — graphical interface