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CaImAn
Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.DeepFRI
Deep functional residue identificationfinufft
Non-uniform fast Fourier transform library of types 1,2,3 in dimensions 1,2,3CaImAn-MATLAB
Complete Matlab pipeline for large scale calcium imaging data analysisNoRMCorre
Matlab routines for online non-rigid motion correction of calcium imaging datadeepblast
Neural Networks for Protein Sequence AlignmentFMM3D
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.cufinufft
Nonuniform fast Fourier transforms of types 1 and 2, in 1D, 2D, and 3D, on the GPUnemos
NEural MOdelS, a statistical modeling framework for neuroscience.jax-finufft
JAX bindings to the Flatiron Institute Non-uniform Fast Fourier Transform (FINUFFT) librarysparse_dot
Python wrapper for Intel Math Kernel Library (MKL) matrix multiplicationsciware
Learning materials for scientific software developmentmountainsort
Spike sorting softwareinferelator
Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.mountainlab-js
MountainLab is data processing, sharing and visualization software for scientists. It is built around MountainSort, spike sorting software, but is designed to be more generally applicable.bayes-kit
Bayesian inference and posterior analysis for Pythonneurosift
Browser-based NWB visualization and DANDI explorationonline_psp
A collection of computationally efficient algorithms for online subspace learning and principal component analysisspikeforest2
SpikeForest -- spike sorting analysis for website -- version 2mcmc-monitor
Monitor MCMC runs in the browsernixpack
nix+spack = nixpack (spanix?)nifty-ls
A fast Lomb-Scargle periodogram. It's nifty, and uses a NUFFT!figurl
Shareable, interactive scientific figures in the clouddisBatch
Tool to distribute a list of computational tasks over a pool of compute resources. The pool can grow or shrink.mountainsort5
MountainSort spike sorting algorithm, version 5st_gridnet
A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.mountainsort_examples
Examples of using MountainSort spike sorting software.SkellySim
Hydrodynamic Cytoskeleton Simulatorfmm2d
This codebase is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in two dimensions, on a multi-core shared-memory machine.catvae
Categorical Variational Autoencodersonline_psp_matlab
Benchmark of online PCA algorithmsspikeforest
Spike sorting benchmarking systemslurm-prometheus-exporter
Prometheus exporter for slurm job/node datakachery-cloud
dendro
Analyze neuroscience data in the cloudcomptools24
Computational Tools for PDEs with Complicated Geometries and Interfaces workshop materials, June 10-14, 2024.aLENS
a Living ENsemble Simulator -- a lens to help you watch biophysicsspikeforest_old
SpikeForest -- spike sorting analysis for websitebaobzi
An adaptive fast function approximator based on tree searchisosplit5
ISO-SPLIT clustering (stand-alone version)bio-sfa
Code for reproducing the experiment from the paper "A biologically plausible neural network for Slow Feature Analysis"pytorch-finufft
Pytorch wrappers for the FINUFFT librarysf_benchmarks
Special function benchmarksmantis
Manifold-tiling Localized Receptive Fields are Optimal in Similarity-preserving Neural Networksflathub
A simple elasticsearch frontend for serving astrophysical simulation catalog dataccq-software-build
CCQ software build scriptsEnsemble-reweighting-using-Cryo-EM-particles
PointCloud_Regression
Point Cloud regression with new algebraic representation on ModelNet dataset (ICCV 2023)public_www
Basic templates for individual user pages in the public/_www directoryinferelator-prior
Gene regulatory network inference using DNA-binding motifs and chromatin accessibility data.boxcodes3d
This repository contains box codes for evaluating volume potentials for Laplace, Helmholtz, Maxwell, and Stokesbio-nica
Code for reproducing the experiments in the paper "Bio-NICA: A biologically inspired single-layer network for Nonnegative Independent Component Analysis"cppdlr
Discrete Lehmann representation of imaginary time Green's functionsnix-modules
nixpkgs-based module builds of cluster packagesbio-cca
Code accompanying the paper "A biologically plausible neural network for multi-channel Canonical Correlation Analysis"reactopya
React components paired with Python classes for backend computationclair
Clair (Clang Introspection and Reflection) tools. A set of clang tools developed for Flatiron/CCQadapol
Adaptive Pole Fitting for Quantum Many-Body PhysicsDLR_DMFT_scripts
kbucket
System for sharing data for scientific researchccn-template
Template repository for CCN software projectsneutorch
neuron segmentation and synapse detection using PyTorchSlurmUtil
slurm monitoring tools and interfaceq2-matchmaker
A qiime2 plugin for case-control differential abundance analysismountainlab
Scientific data analysis, sharing, and visualizationleast_absolute_regression
Least absolute error regression implemented using Linear Programming, primarily to illustrate repository structure conventions.neuropixels-data-sep-2020
Example neuropixels datasets for purposes of developing spike sorting algorithmsephys-viz
Neurophysiology visualization components deployable to the notebook, web, or desktopinverse-obstacle-scattering2d
This repository contains codes for solving inverse obstacle scattering problems to recover the shape of the obstacle for sound soft, sound hard, and penetrable objectscryoSBI
kachery-p2p
Peer-to-peer content-addressable file sharing using kacherygp-shootout
Benchmark and compare large-scale Gaussian process regression methods in 1D, 2D, and 3D, from MATLABccn-software-fens-2024
Materials for CCN software workshop at FENS 2024looking_glass_3d_test
Test of displaying 3d genomic data using webgl in a "Looking glass" holographic displaycaiman_central
Central hub for resources related to Caiman calcium imaging analysis package.labbox-ephys
FREYA
Canine breast cancer analysis pipelinespikesortercomparison
Notes on metrics and datasets for community spike sorting comparison and validationhither
Run batches of Python functions in containers and on remote serversILCnetworks
Gene regulatory networks for intestinal innate lymphoid cellsFermi_surface_visualization
Interactive visualization of Fermi surfaces representing electron energies and velocities in crystal structures.flatiron-coffee
Meet your colleagues across the Institutespike-front
Front end tool for benchmarking spike sorting algorithms.ccm_widgets
Reactopya widgets of relevance to the Center for Computational Mathematics, Flatiron InstituteCryo-EM-Heterogeneity-Challenge-1
The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challengekvsstcp
Key value storage server. Light weight (single python module with no non-standard module dependencies). Simple protocol minimizes effort needed to write a client (example for C and FORTRAN provided).bio-lda
Code accompanying the paper "A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment"Baobzi.jl
Wrapper library for Baobzi interpolator libraryftk
Factorization of the translation kernel for fast rigid image alignmentsciware-testing-cpp
binary_classification_metrics
Visualizations and other code for exploring binary classification metrics.inverse-volume-scattering2d
This repository contains beta MATLAB codes for data generation of forward medium problems using a hybrid HPS-HBS solver, and an inverse medium solverstan-playground
Run Stan models in the browserqt-mountainview
Visualization of spike sorting experiments to be used as a plugin package to mountainlab-jsfgt2d
This repository contains codes for evaluating sums and integrals of gaussians in two dimensionsspikeforest_recordings
Ephys recordings for the SpikeForest projectquantum_rosetta_private
Playing with quantum computing algorithms for protein and peptide design and structure prediction, with interfaces for the Rosetta software suite. (Repository created by Vikram K. Mulligan, [email protected]).mcmc-monitor-old
Monitor MCMC runsh5_to_json
Represent hdf5 files via json, separating out large binary content into individual filesmountainsort_examples-old
Examples for getting started with MountainSort spike sorting softwareLove Open Source and this site? Check out how you can help us