napari-flowreg 0.1.0a2

napari plugin for Flow-Registration motion correction

🚧 Under Development

This project is still in an alpha stage. Expect rapid changes, incomplete features, and possible breaking updates between releases.

• The API may evolve as we stabilize core functionality.
• Documentation and examples are incomplete.
• Feedback and bug reports are especially valuable at this stage.

napari-FlowReg

This repository contains the napari wrapper for the Flow-Registration toolbox, which is a toolbox for the compensation and stabilization of multichannel microscopy videos. The publication for this toolbox can be found here and the project website with video results here.

Related projects

• PyFlowReg: https://github.com/FlowRegSuite/pyflowreg
• Original Flow-Registration repo: https://github.com/FlowRegSuite/flow_registration
• ImageJ/Fiji plugin: https://github.com/FlowRegSuite/flow_registration_IJ

Installation via pip and conda

To install the plugin via conda, you can create a new environment and install napari along with the plugin:

conda create -n flowreg -c conda-forge python=3.12.0 napari

You can then install napari-flowreg via [pip]:

pip install napari[all] napari-flowreg

or from the directly from the GitHub repository:

pip install git+https://github.com/flowregsuite/napari-flowreg.git

Dataset

The dataset which we used for our evaluations is available as 2-Photon Movies with Motion Artifacts.

Citation

Details on the original method and video results can be found here.

If you use parts of this code or the plugin for your work, please cite

“Pyflowreg,” (in preparation), 2025.

and

P. Flotho, S. Nomura, B. Kuhn and D. J. Strauss, “Software for Non-Parametric Image Registration of 2-Photon Imaging Data,” J Biophotonics, 2022. doi:https://doi.org/10.1002/jbio.202100330

BibTeX entry

@article{flotea2022a,
    author = {Flotho, P. and Nomura, S. and Kuhn, B. and Strauss, D. J.},
    title = {Software for Non-Parametric Image Registration of 2-Photon Imaging Data},
    year = {2022},
  journal = {J Biophotonics},
  doi = {https://doi.org/10.1002/jbio.202100330}
}