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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 691 388

  2. finufft finufft Public

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

    C++ 378 93

  3. DeepFRI DeepFRI Public

    Deep functional residue identification

    Python 333 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 128 23

Repositories

Showing 10 of 213 repositories
  • nemos Public

    NEural MOdelS, a statistical modeling framework for neuroscience.

    flatironinstitute/nemos’s past year of commit activity
    Python 106 MIT 11 126 (2 issues need help) 3 Updated Oct 10, 2025
  • stan-playground Public

    Run Stan models in the browser

    flatironinstitute/stan-playground’s past year of commit activity
    TypeScript 49 Apache-2.0 1 11 1 Updated Oct 9, 2025
  • Cryo-EM-Heterogeneity-Challenge-1 Public

    The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge

    flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1’s past year of commit activity
    Jupyter Notebook 10 MIT 1 31 5 Updated Oct 9, 2025
  • figpack Public

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

    flatironinstitute/figpack’s past year of commit activity
    TypeScript 8 Apache-2.0 0 3 0 Updated Oct 9, 2025
  • CaImAn Public

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

    flatironinstitute/CaImAn’s past year of commit activity
    Python 691 GPL-2.0 388 72 (1 issue needs help) 12 Updated Oct 8, 2025
  • cryojax-ensemble-optimization Public
    flatironinstitute/cryojax-ensemble-optimization’s past year of commit activity
    Python 0 MIT 0 7 0 Updated Oct 8, 2025
  • dmk Public

    A Dual-space Multilevel Kernel-splitting (DMK) Framework for Discrete and Continuous Convolution

    flatironinstitute/dmk’s past year of commit activity
    C++ 10 2 12 (1 issue needs help) 1 Updated Oct 7, 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 Oct 6, 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 102 Apache-2.0 7 9 4 Updated Oct 6, 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 Oct 6, 2025
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