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  1. CaImAn CaImAn Public

    Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

    Python 698 390

  2. finufft finufft Public

    Non-uniform fast Fourier transform library of types 1,2,3 in dimensions 1,2,3

    C++ 380 94

  3. DeepFRI DeepFRI Public

    Deep functional residue identification

    Python 334 85

  4. CaImAn-MATLAB CaImAn-MATLAB Public

    Complete Matlab pipeline for large scale calcium imaging data analysis

    MATLAB 258 149

  5. NoRMCorre NoRMCorre Public

    Matlab routines for online non-rigid motion correction of calcium imaging data

    MATLAB 152 97

  6. deepblast deepblast Public

    Neural Networks for Protein Sequence Alignment

    Python 131 23

Repositories

Showing 10 of 216 repositories
  • figpack Public

    A Python package for creating shareable, interactive, browser-based visualizations

    flatironinstitute/figpack’s past year of commit activity
    TypeScript 11 Apache-2.0 0 3 0 Updated Nov 3, 2025
  • neurosift Public

    Browser-based NWB visualization and DANDI exploration

    flatironinstitute/neurosift’s past year of commit activity
    TypeScript 60 Apache-2.0 13 46 1 Updated Nov 3, 2025
  • disBatch Public

    Dynamic dispatch of a list of command-line tasks, locally or on a cluster. Supports retrying failed tasks, and adding/removing compute resources on-the-fly.

    flatironinstitute/disBatch’s past year of commit activity
    Python 46 Apache-2.0 9 7 0 Updated Nov 2, 2025
  • nemos Public

    NEural MOdelS, a statistical modeling framework for neuroscience.

    flatironinstitute/nemos’s past year of commit activity
    Python 108 MIT 12 127 (2 issues need help) 2 Updated Nov 1, 2025
  • jax-finufft Public

    JAX bindings to the Flatiron Institute Non-uniform Fast Fourier Transform (FINUFFT) library

    flatironinstitute/jax-finufft’s past year of commit activity
    Python 104 Apache-2.0 7 8 2 Updated Nov 1, 2025
  • nifty-ls Public

    A fast Lomb-Scargle periodogram. It's nifty, and uses a NUFFT!

    flatironinstitute/nifty-ls’s past year of commit activity
    Python 44 Apache-2.0 5 4 0 Updated Nov 1, 2025
  • neurorse-workshops Public

    Built workshop materials for the NeuroRSE packages

    flatironinstitute/neurorse-workshops’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Oct 31, 2025
  • ccn-software-sfn-2025 Public

    Materials for CCN software workshop at SfN, Nov 2025

    flatironinstitute/ccn-software-sfn-2025’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 31, 2025
  • finufft Public

    Non-uniform fast Fourier transform library of types 1,2,3 in dimensions 1,2,3

    flatironinstitute/finufft’s past year of commit activity
    C++ 380 94 45 (3 issues need help) 6 Updated Oct 31, 2025
  • ManifoldEM Public

    Python package for determination of conformational continua of macromolecules from single-particle cryo-EM data

    flatironinstitute/ManifoldEM’s past year of commit activity
    Python 13 GPL-3.0 2 5 0 Updated Oct 30, 2025
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