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Flatiron Institute

@simonsfoundation

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New York City
https://flatironinstitute.org/

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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
finufft finufft Public

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

C++ 380 94
DeepFRI DeepFRI Public

Deep functional residue identification

Python 334 85
CaImAn-MATLAB CaImAn-MATLAB Public

Complete Matlab pipeline for large scale calcium imaging data analysis

MATLAB 258 149
NoRMCorre NoRMCorre Public

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

MATLAB 152 97
deepblast deepblast Public

Neural Networks for Protein Sequence Alignment

Python 130 23

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Showing 10 of 216 repositories

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 44 (3 issues need help) 6 Updated Oct 31, 2025
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 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
neuroRSE Public
Website for CCN's neuroRSE group

flatironinstitute/neuroRSE’s past year of commit activity

CSS 1 MIT 0 0 0 Updated Oct 30, 2025

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