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The Top 623 Neuroscience Open Source Projects on Github

CategoriesΒ >Β ScienceΒ >Β Neuroscience
Course Content ⭐ 1,969
NMA Computational Neuroscience course
Mne Python ⭐ 1,673
MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
Psychopy ⭐ 1,119
For running psychology and neuroscience experiments
Awesome Neuroscience ⭐ 774
A curated list of awesome neuroscience libraries, software and any content related to the domain.
Nengo ⭐ 620
A Python library for creating and simulating large-scale brain models
Brian2 ⭐ 589
Brian is a free, open source simulator for spiking neural networks.
Fieldtrip ⭐ 532
The MATLAB toolbox for MEG, EEG and iEEG analysis
Brainflow ⭐ 456
BrainFlow is a library intended to obtain, parse and analyze EEG, EMG, ECG and other kinds of data from biosensors
Dcm2niix ⭐ 412
dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC
Csinva.github.io ⭐ 377
Slides, paper notes, class notes, blog posts, and research on ML πŸ“‰, statistics πŸ“Š, and AI πŸ€–.
Eyeloop ⭐ 343
EyeLoop is a Python 3-based eye-tracker tailored specifically to dynamic, closed-loop experiments on consumer-grade hardware.
Pyriemann ⭐ 325
Python package for covariance matrices manipulation and Biosignal classification with application in Brain Computer interface
Pyphi ⭐ 266
A toolbox for integrated information theory.
Moabb ⭐ 256
Mother of All BCI Benchmarks
Open Computational Neuroscience Resources ⭐ 255
A publicly-editable collection of open computational neuroscience resources
Neurokit.py ⭐ 253
A Python Toolbox for Statistics and Neurophysiological Signal Processing (EEG, EDA, ECG, EMG...).
Brayns ⭐ 248
Visualizer for large-scale and interactive ray-tracing of neurons
Brainiak ⭐ 242
Brain Imaging Analysis Kit
Brainrender ⭐ 238
a python based software for visualization of neuroanatomical and morphological data.
Neurodocker ⭐ 227
Generate custom Docker and Singularity images, and minimize existing containers
Neurotech Course ⭐ 220
CS198-96: Intro to Neurotechnology @ UC Berkeley
Neurolib ⭐ 214
Easy whole-brain modeling for computational neuroscientists πŸ§ πŸ’»πŸ‘©πŸΏβ€πŸ”¬
Bmtk ⭐ 191
Brain Modeling Toolkit
Erplab ⭐ 180
ERPLAB Toolbox is a free, open-source Matlab package for analyzing ERP data. It is tightly integrated with EEGLAB Toolbox, extending EEGLAB’s capabilities to provide robust, industrial-strength tools for ERP processing, visualization, and analysis. A graphical user interface makes it easy for beginners to learn, and Matlab scripting provides enormous power for intermediate and advanced users.
Opensesame ⭐ 180
Graphical experiment builder for the social sciences
Dvid ⭐ 177
Distributed, Versioned, Image-oriented Dataservice
Suite2p ⭐ 177
cell detection in calcium imaging recordings
Nrn ⭐ 175
NEURON Simulator
Kilosort ⭐ 173
Fast spike sorting with drift correction for up to a thousand channels
Fooof ⭐ 169
Parameterizing neural power spectra into periodic & aperiodic components.
Awesome Computational Neuroscience ⭐ 166
A list of schools and researchers in computational neuroscience
Bluepyopt ⭐ 154
Blue Brain Python Optimisation Library
Eegrunt ⭐ 147
A Collection Python EEG (+ ECG) Analysis Utilities for OpenBCI and Muse
Visbrain ⭐ 143
A multi-purpose GPU-accelerated open-source suite for brain data visualization
Entropy ⭐ 142
EntroPy: complexity of time-series in Python (DEPRECATED)
Tapas ⭐ 139
TAPAS - Translational Algorithms for Psychiatry-Advancing Science
Catmaid ⭐ 135
Collaborative Annotation Toolkit for Massive Amounts of Image Data
Uncertainpy ⭐ 131
Uncertainpy: a Python toolbox for uncertainty quantification and sensitivity analysis, tailored towards computational neuroscience.
Brainpy ⭐ 121
A flexible and extensible framework for brain modeling
Analyzing_neural_time_series ⭐ 114
python implementations of Analyzing Neural Time Series Textbook
Mne Cpp ⭐ 114
MNE-CPP: A Framework for Electrophysiology
Spikeextractors ⭐ 112
Python-based module for extracting from, converting between, and interfacing with many common file formats in extracellular recording.
Psycho.r ⭐ 110
An R package for experimental psychologists
Elephant ⭐ 107
Elephant is the Electrophysiology Analysis Toolkit
Pynwb ⭐ 106
A Python API for working with Neurodata stored in the NWB Format
Workbench ⭐ 104
Connectome Workbench
Clinica ⭐ 101
Software platform for clinical neuroimaging studies
Twpca ⭐ 98
πŸ• Time-warped principal components analysis (twPCA)
Cortex V2 Example ⭐ 98
Example with Cortex V2 API
B Soid ⭐ 97
Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is a pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.
Expyriment ⭐ 96
Platform-independent lightweight Python library for designing and conducting timing-critical behavioural and neuroimaging experiments
Braingraph ⭐ 94
Graph theory analysis of brain MRI data
Cellfinder ⭐ 94
Automated 3D cell detection and registration of whole-brain images
Canlabcore ⭐ 93
Core tools required for running Canlab Matlab toolboxes. The heart of this toolbox is object-oriented tools that enable interactive analysis of neuroimaging data and simple scripts using high-level commands tailored to neuroimaging analysis.
Euclidean Distance Transform 3d ⭐ 90
Euclidean distance transform for multi-label 3D anisotropic images using marching parabolas.
Wave_clus ⭐ 89
A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering
Coreneuron ⭐ 89
Simulator optimized for large scale neural network simulations.
Dcm2bids ⭐ 84
Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
Tnn ⭐ 84
Biologically-realistic recurrent convolutional neural networks
Openbci Dashboard ⭐ 80
A fullstack javascript app for capturing and visualizing OpenBCI EEG data
Artificial Intelligence And Machine Learning ⭐ 72
A repository for implementation of artificial intelligence algorithm which includes machine learning and deep learning algorithm as well as classical AI search algorithm
Spikeinterface ⭐ 72
A Python-based module for creating flexible and robust spike sorting pipelines.
Segregated Dendrite Deep Learning ⭐ 71
Deep learning in a spiking neural network using segregated dendrites.
Nengo Gui ⭐ 70
Nengo interactive visualizer
Kfs ⭐ 69
Keras for Science
Cochlea ⭐ 67
Inner ear models for Python
Rastermap ⭐ 67
A multi-dimensional embedding algorithm
Nengo Dl ⭐ 67
Deep learning integration for Nengo
Deepeeg ⭐ 66
Deep Learning with Tensor Flow for EEG MNE Epoch Objects
Pytorch_connectomics ⭐ 65
PyTorch Connectomics: segmentation toolbox for EM connectomics
Open Science Resources ⭐ 64
A publicly-editable collection of open science resources, including tools, datasets, meta-resources, etc.
Epfl ⭐ 63
EPFL summaries & cheatsheets over 5 years (computer science, communication systems, data science and computational neuroscience).
Arbor ⭐ 62
The Arbor multi-compartment neural network simulation library.
Nix ⭐ 62
Neuroscience information exchange format
Python Meegkit ⭐ 61
πŸ”§πŸ§  MEEGkit: M/EEG processing toolkit in Python πŸ§ πŸ”§
Labhacks ⭐ 61
Resources for data driven neuroscientists.
Pyabf ⭐ 60
pyABF is a Python package for reading electrophysiology data from Axon Binary Format (ABF) files
Vame ⭐ 60
Variational Animal Motion Embedding
Psyneulink ⭐ 60
A block modeling system for cognitive neuroscience
Spyking Circus ⭐ 58
Fast and scalable spike sorting in python
Mne Bids ⭐ 57
MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.
Knossos ⭐ 56
KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
Snntorch ⭐ 56
Deep and online learning with spiking neural networks in Python
Facemap ⭐ 56
matlab/python GUI for unsupervised video analysis of rodent behavior (capable of processing multiple camera views)
Autopilot ⭐ 55
Distributed behavioral experiments
Pulse2percept ⭐ 54
A Python-based simulation framework for bionic vision
Miniscope V4 ⭐ 53
All things Miniscope v4
Openneuro ⭐ 52
A free and open platform for analyzing and sharing neuroimaging data
Multipy ⭐ 52
Multiple hypothesis testing in Python
Mne Bids Pipeline ⭐ 52
Automatically process entire electrophysiological datasets using MNE-Python.
Visualqc ⭐ 51
VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.
Nat ⭐ 51
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
Jatos ⭐ 51
Just Another Tool for Online Studies
Awesome Cogsci ⭐ 49
An Awesome List of Cognitive Science Resources
Teneto ⭐ 49
Temporal Network Tools
Spiketoolkit ⭐ 49
Python-based tools for pre-, post-processing, validating, and curating spike sorting datasets.
Oat ⭐ 48
Real-time position tracker for behavioral research
Spectral_connectivity ⭐ 48
Frequency domain functional and directed connectivity analysis tools for electrophysiological data
Quicknatv2 ⭐ 47
Fast Whole Brain Segmentation (Layers, codes and Pre-trained Models)
Pyprep ⭐ 45
A Python implementation of the Preprocessing Pipeline (PREP) for EEG data
1-100 of 623 projects

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Applications πŸ“¦Β 181
Artificial Intelligence πŸ“¦Β 72
Blockchain πŸ“¦Β 70
Build Tools πŸ“¦Β 111
Cloud Computing πŸ“¦Β 79
Code Quality πŸ“¦Β 28
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Command Line Interface πŸ“¦Β 48
Community πŸ“¦Β 81
Companies πŸ“¦Β 60
Compilers πŸ“¦Β 60
Computer Science πŸ“¦Β 74
Configuration Management πŸ“¦Β 39
Content Management πŸ“¦Β 167
Control Flow πŸ“¦Β 197
Data Formats πŸ“¦Β 77
Data Processing πŸ“¦Β 266
Data Storage πŸ“¦Β 132
Economics πŸ“¦Β 60
Frameworks πŸ“¦Β 198
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Messaging πŸ“¦Β 97
Networking πŸ“¦Β 304
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Operations πŸ“¦Β 120
Package Managers πŸ“¦Β 52
Programming Languages πŸ“¦Β 229
Runtime Environments πŸ“¦Β 96
Science πŸ“¦Β 42
Security πŸ“¦Β 375
Social Media πŸ“¦Β 26
Software Architecture πŸ“¦Β 70
Software Development πŸ“¦Β 68
Software Performance πŸ“¦Β 57
Software Quality πŸ“¦Β 127
Text Editors πŸ“¦Β 45
Text Processing πŸ“¦Β 131
User Interface πŸ“¦Β 310
User Interface Components πŸ“¦Β 465
Version Control πŸ“¦Β 29
Virtualization πŸ“¦Β 68
Web Browsers πŸ“¦Β 38
Web Servers πŸ“¦Β 25
Web User Interface πŸ“¦Β 194
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