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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 711 393
finufft finufft Public

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

C++ 398 97
DeepFRI DeepFRI Public

Deep functional residue identification

Python 347 87
CaImAn-MATLAB CaImAn-MATLAB Public

Complete Matlab pipeline for large scale calcium imaging data analysis

MATLAB 258 152
NoRMCorre NoRMCorre Public

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

MATLAB 153 97
deepblast deepblast Public

Neural Networks for Protein Sequence Alignment

Python 135 23

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Showing 10 of 222 repositories

cryojax-ensemble-optimization Public

flatironinstitute/cryojax-ensemble-optimization’s past year of commit activity

Jupyter Notebook 4 MIT 1 7 1 Updated Feb 5, 2026
neurorse-workshops Public
Built workshop materials for the NeuroRSE packages

flatironinstitute/neurorse-workshops’s past year of commit activity

Jupyter Notebook 0 MIT 0 0 0 Updated Feb 5, 2026
ccn-software-feb-2026 Public
Materials for CCN software workshop at Flatiron, Feb 2026

flatironinstitute/ccn-software-feb-2026’s past year of commit activity

Python 0 MIT 0 0 0 Updated Feb 5, 2026
nemos Public
NEural MOdelS, a statistical modeling framework for neuroscience.

flatironinstitute/nemos’s past year of commit activity

Python 119 MIT 15 126 (1 issue needs help) 10 Updated Feb 5, 2026
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++ 398 97 43 (3 issues need help) 6 Updated Feb 5, 2026
FMM3D Public
Flatiron Institute Fast Multipole Libraries --- This codebase is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.

flatironinstitute/FMM3D’s past year of commit activity

Fortran 133 52 23 1 Updated Feb 5, 2026
dmk Public
A Dual-space Multilevel Kernel-splitting (DMK) Framework for Discrete and Continuous Convolution

flatironinstitute/dmk’s past year of commit activity

C++ 18 4 12 (1 issue needs help) 1 Updated Feb 4, 2026
scc-viswall-prom Public
Generates plots of cluster usage data for the Flatiron viswall by scraping Prometheus

flatironinstitute/scc-viswall-prom’s past year of commit activity

Python 0 Apache-2.0 0 0 0 Updated Feb 4, 2026
neuroRSE Public
Website for CCN's neuroRSE group

flatironinstitute/neuroRSE’s past year of commit activity

CSS 1 MIT 0 0 0 Updated Feb 4, 2026
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

C++ 114 Apache-2.0 11 14 2 Updated Feb 3, 2026

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