PyCorre

Fast, GPU-accelerated rigid and piecewise-rigid motion correction for calcium-imaging recordings. PyCorre implements the NoRMCorre algorithm, which is the same phase-correlation + upsampled-DFT method used by CaImAn, but rewritten in PyTorch. The whole stack is corrected in batched operations that run on CPU or GPU from a single, dependency-light codebase.

Installation

pip install pycorre

The only runtime dependencies are torch, numpy, and tqdm. GPU support is whatever your PyTorch build provides (install the appropriate CUDA wheel of torch for your machine).

Quickstart

import numpy as np
from pycorre import RigidMotionCorrection, PWRigidMotionCorrection

# A recording of shape (n_frames, height, width); numpy array or torch tensor.
frames = ...

# Rigid correction on the GPU.
model = RigidMotionCorrection(device="cuda")  # or "cpu" / "auto"
corrected = model.fit_transform(frames)

# Piecewise-rigid (non-rigid) correction.
model = PWRigidMotionCorrection(device="cuda", strides=(96, 96), overlaps=(32, 32))
corrected = model.fit_transform(frames)

The API follows scikit-learn's fit / transform / fit_transform pattern. fit estimates the template (unless you pass one) and finds the per-frame shifts; transform applies them. Inputs may be numpy arrays or torch tensors; numpy in and numpy out.

Performance

The table below shows the rigid correction throughput on a real recording with resolution 360x640 for 1800 frames.

On this sample, PyCorre is ~22x faster than CaImAn and ~3x faster than jnormcorre. On CPU alone, with no GPU at all, PyCorre still leads, running ~4.5x faster than the CaImAn reference and ~2.9x faster than jnormcorre.

The scaling curve can be seen here:

Author

PyCorre is written and maintained by Ryan 'RyanIRL' Peters (@ryanirl).

Citation

If you use PyCorre in your research, please cite it:

@software{peters_pycorre,
  author = {Peters, Ryan},
  title  = {{PyCorre}: GPU-accelerated rigid and piecewise-rigid motion correction for calcium imaging},
  url    = {https://github.com/ryanirl/pycorre},
  year   = {2026}
}

PyCorre implements the NoRMCorre algorithm; if you use it, please also cite the original method:

Pnevmatikakis, E. A., & Giovannucci, A. (2017). NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data. Journal of Neuroscience Methods, 291, 83-94. https://doi.org/10.1016/j.jneumeth.2017.07.031

License

pycorre is released under the MIT License (see LICENSE).