Repositories list

• nemos

  Public
  NEural MOdelS, a statistical modeling framework for neuroscience.

  Python

  •

  MIT License

  •11•102•122•3•Updated Aug 21, 2025Aug 21, 2025

• walnuts

  Public
  Within-orbit Adaptive Leapfrog No-U-Turn Sampler

  samplingstanmcmc+ 1hmc

  C++

  •

  MIT License

  •0•10•7•3•Updated Aug 21, 2025Aug 21, 2025

• neurosift

  Public
  Browser-based NWB visualization and DANDI exploration

  TypeScript

  •

  Apache License 2.0

  •13•59•42•3•Updated Aug 19, 2025Aug 19, 2025

• finufft

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

  C++

  •

  Other

  •92•370•43•7•Updated Aug 18, 2025Aug 18, 2025

• flathub

  Public
  A simple elasticsearch frontend for serving astrophysical simulation catalog data

  Haskell

  •

  Apache License 2.0

  •8•10•14•0•Updated Aug 18, 2025Aug 18, 2025

• cryoSBI

  Public
  Python

  •1•12•15•2•Updated Aug 13, 2025Aug 13, 2025

• pytorch-finufft

  Public
  Pytorch wrappers for the FINUFFT library

  Python

  •

  MIT License

  •0•14•6•2•Updated Aug 12, 2025Aug 12, 2025

• CaImAn

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

  2-photoncalcium-imagingmotion-correction+ 3source-extractiondeconvolutioncnmf

  Python

  •

  GNU General Public License v2.0

  •386•680•71•12•Updated Aug 11, 2025Aug 11, 2025

• jax-finufft

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

  Python

  •

  Apache License 2.0

  •6•100•10•3•Updated Aug 11, 2025Aug 11, 2025

• septin_AH_analysis

  Public
  Analysis script for septin AH paper.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Aug 11, 2025Aug 11, 2025

• nifty-ls

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

  time-serieslomb-scargle-periodogramspectral-analysis

  Python

  •

  Apache License 2.0

  •5•43•4•0•Updated Aug 10, 2025Aug 10, 2025

• vintch-v1-model

  Public
  Implementation of V1 model from Vintch et al., 2015

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

• stan-playground

  Public
  Run Stan models in the browser

  TypeScript

  •

  Apache License 2.0

  •1•47•11•1•Updated Aug 8, 2025Aug 8, 2025

• CryoLike

  Public
  Python

  •

  MIT License

  •6•9•8•11•Updated Aug 7, 2025Aug 7, 2025

• RocketSHP

  Public
  Fast structural heterogeneity estimation

  Jupyter Notebook

  •

  MIT License

  •1•8•0•0•Updated Aug 6, 2025Aug 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.

  distributed-computingbatch-processing

  Python

  •

  Apache License 2.0

  •9•46•7•0•Updated Aug 4, 2025Aug 4, 2025

• lineage_viewer

  Public
  Graphical interface for editing a lineage and viewing related microscopy images

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•7•0•Updated Aug 4, 2025Aug 4, 2025

• neuroRSE

  Public
  Website for CCN's neuroRSE group

  CSS

  •

  MIT License

  •0•1•0•0•Updated Aug 4, 2025Aug 4, 2025

• clair

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

  C++

  •

  Apache License 2.0

  •2•16•2•0•Updated Aug 3, 2025Aug 3, 2025

• c2py

  Public
  Clair/c2py low level library

  C++

  •

  Apache License 2.0

  •1•1•0•0•Updated Aug 3, 2025Aug 3, 2025

• Cryo-EM-Heterogeneity-Challenge-1

  Public
  The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge

  Jupyter Notebook

  •

  MIT License

  •1•8•31•5•Updated Jul 31, 2025Jul 31, 2025

• sparse_dot

  Public
  Python wrapper for Intel Math Kernel Library (MKL) matrix multiplication

  pythonsparsesparse-matrix+ 4numpymatrix-multiplicationscipymkl

  Python

  •

  MIT License

  •11•88•3•0•Updated Jul 28, 2025Jul 28, 2025

• PyBenchFramework

  Public
  BenchmarkToolkit is a Python library designed to simplify and streamline benchmarking tasks. This library provides a high-level abstraction over various benchmarking functions, allowing developers to easily perform performance testing and analysis with minimal setup.

  Python

  •1•0•0•1•Updated Jul 28, 2025Jul 28, 2025

• adapol

  Public
  Adaptive Pole Fitting for Quantum Many-Body Physics

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•11•0•0•Updated Jul 27, 2025Jul 27, 2025

• nixpack

  Public
  nix+spack = nixpack (spanix?)

  Nix

  •

  MIT License

  •4•47•1•4•Updated Jul 25, 2025Jul 25, 2025

• spack

  Public
  A flexible package manager that supports multiple versions, configurations, platforms, and compilers.

  Python

  •

  Other

  •2.4k•2•0•12•Updated Jul 25, 2025Jul 25, 2025

• capture_lock

  Public
  Modular Visual-Odometry research platform built on COLMAP for testing our algebraic solvers (e.g., DRaM-LHM, ICCV 2025) in multiview geometry.

  slampnppose-estimation

  C++

  •0•3•0•0•Updated Jul 24, 2025Jul 24, 2025

• simple_ans

  Public
  Simple ANS (Asymmetric Numeral Systems) implementation in Python/C++

  C++

  •

  Apache License 2.0

  •4•3•0•1•Updated Jul 24, 2025Jul 24, 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.

  C++

  •

  GNU Affero General Public License v3.0

  •0•1•0•0•Updated Jul 10, 2025Jul 10, 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.

  C++

  •

  GNU Affero General Public License v3.0

  •1•4•0•0•Updated Jul 10, 2025Jul 10, 2025