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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 688 388

  2. finufft finufft Public

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

    C++ 371 93

  3. DeepFRI DeepFRI Public

    Deep functional residue identification

    Python 332 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 127 22

Repositories

Showing 10 of 212 repositories
  • stan-playground Public

    Run Stan models in the browser

    flatironinstitute/stan-playground’s past year of commit activity
    TypeScript 48 Apache-2.0 1 11 4 Updated Sep 23, 2025
  • clair Public

    Clair (Clang Introspection and Reflection) tools. A set of clang tools developed for Flatiron/CCQ

    flatironinstitute/clair’s past year of commit activity
    C++ 16 Apache-2.0 3 3 1 Updated Sep 23, 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 9 MIT 1 31 6 Updated Sep 23, 2025
  • masala_public Public

    The public repository for the Core library of the Masala software suite. Masala is a set of free and open-source tools for biomolecular modelling, with a plugin-based infrastructure that makes it easy to extend other software.

    flatironinstitute/masala_public’s past year of commit activity
    C++ 5 AGPL-3.0 1 0 0 Updated Sep 23, 2025
  • masala_public_standard_plugins Public

    Public fork of the Standard Masala Plugins library. The Masala macromolecular modelling suite has a modular, plugin-based architecture; common modelling tasks are handled by the "standard" plugins that most users will want. But they're in a separate repo to ensure that plugin devs don't have to touch the core code.

    flatironinstitute/masala_public_standard_plugins’s past year of commit activity
    C++ 1 AGPL-3.0 0 0 0 Updated Sep 23, 2025
  • neuroRSE Public

    Website for CCN's neuroRSE group

    flatironinstitute/neuroRSE’s past year of commit activity
    CSS 1 MIT 0 0 0 Updated Sep 23, 2025
  • cppdlr Public

    Discrete Lehmann representation of imaginary time Green's functions

    flatironinstitute/cppdlr’s past year of commit activity
    C++ 11 Apache-2.0 6 2 1 Updated Sep 22, 2025
  • baobzi Public

    An adaptive fast function approximator based on tree search

    flatironinstitute/baobzi’s past year of commit activity
    C++ 16 Apache-2.0 4 13 1 Updated Sep 22, 2025
  • nemos Public

    NEural MOdelS, a statistical modeling framework for neuroscience.

    flatironinstitute/nemos’s past year of commit activity
    Python 105 MIT 11 123 (2 issues need help) 2 Updated Sep 22, 2025
  • aLENS_analysis Public

    Postprocessing & analysis scripts for aLENS data

    flatironinstitute/aLENS_analysis’s past year of commit activity
    Jupyter Notebook 0 2 0 0 Updated Sep 22, 2025
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