• dipy: DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.
• nrn: NEURON Simulator. (iv required for the GUI)
• CyKit: Python 3x server to deliver neural EEG data to browser and generic clients via TCP stream.
• incdb-poc: INcDb Proof of Conept
• LiviaNET: This repository contains the code of LiviaNET, a 3D fully convolutional neural network that was employed in our work: "3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study"
• 3D-F-CNN-BrainStruct: This repository contains materials employed in our work to segment subcortical brain structures by employing a 3D fully Convolutional Neural Network.
• brainiak: Brain Imaging Analysis Kit
• ibllib: IBL core shared libraries
• eeg-database: EEG/ERP portal enables community researchers to store, update, download and search data and metadata from EEG/ERP experiments. The system is developed as a standalone product; the database access is available through a web interface.
• life: Please use the new version of LiFE: www.github.com/brain-life/encode
• C-PAC: Configurable Pipeline for the Analysis of Connectomes
• neuroquery: None
• SnPM-devel: Statistical NonParametric Mapping, development version
• hcp2nipype-hack2015: The outcomes of the HCP to Nipype project at the OHBM Hackathon 2015.
• CoSMoMVPA: A lightweight multivariate pattern analysis (MVPA) toolbox in Matlab / Octave
• BrainImagingPipelines: BIPs
• datalad: Keep code, data, containers under control with git and git-annex
• PythonDataCourse: [WIP] Course on Python data pipelines
• neuropower-core: This repository contains the core functions from neuropower in a python package.
• nilearn_tutorials: Nilearn tutorials for OHBM 2016 educational course
• FSL-scripts: Script-framework using FSL, Freesurfer and AFNI functionality for automatization and high-throughput processing of MRI data in clustered environments.
• klustakwik: UNMAINTAINED - use klusta instead
• quickNAT_pytorch: PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
• nsviewer: Neurosynth viewer
• DeepPoseKit: a toolkit for pose estimation using deep learning
• cbrain: CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.
• Psychtoolbox-3: Psychophysics Toolbox Version 3 (PTB-3) is a free set of Matlab and GNU Octave functions for vision and neuroscience research.
• tvb-library: DEPRECATED: Use tvb-root. The science behind The Virtual Brain
• microdraw: Collaborative vectorial annotation tool for ultra high resolution data
• automaticanalysis: Automatic analysis
• mindboggle: Automated anatomical brain label/shape analysis software (+ website)
• python-mrcz: Python module for compressed MRCZ-file format
• NeuroVault: Easy to use web database for statistical maps.
• qa-athena: Quality assessment of Athena pipeline images
• dcmstack: DICOM to Nifti conversion with meta data preservation
• neuropower-web: sample size calculations for fMRI
• sortingQuality: Functions to assess quality of spike sorting results
• quality-assessment-protocol: Scripts and documentation for the PCP's protocol for assessing data quality.
• neupy: NeuPy is a Tensorflow based python library for prototyping and building neural networks
• BROCCOLI: BROCCOLI: Software for Fast fMRI Analysis on Many-Core CPUs and GPUs
• poldracklab-base: Repo for general-purpose code in the poldrack lab
• CaImAn: Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
• affinewarp: An implementation of piecewise linear time warping for multi-dimensional time series alignment
• nibabel: Python package to access a cacophony of neuro-imaging file formats
• spikeforest2: SpikeForest -- spike sorting analysis for website -- version 2
• django-dicom-review: None
• brainbrowser: Web-based visualization tools for neurological data.
• ipfx: computes intrinsic cell features from intracellular electrophysiology data
• fmri: :exclamation: This is a read-only mirror of the CRAN R package repository. fmri — Analysis of fMRI Experiments. Homepage: http://www.wias-berlin.de/software/imaging/
• phy: Interactive electrophysiological data analysis package
• HCPpipelines: Processing pipelines for the HCP
• nwb-jupyter-widgets: Explore the hierarchical structure of NWB 2.0 files and visualize data with Jupyter widgets.
• cmp: Connectome Mapper
• spikeinterface: A Python-based module for creating flexible and robust spike sorting pipelines.
• pycortex: Pycortex is a python-based toolkit for surface visualization of fMRI data
• spiketoolkit: Python-based tools for pre-, post-processing, validating, and curating spike sorting datasets.
• MobilECG-II: Open source ECG holter
• datman: scripts for managing xnat, QC, and data analysis
• SimpleITK: SimpleITK: a simplified layer build on top of the Insight Toolkit (ITK), intended to facilitate its use in rapid prototyping, education and interpreted languages.
• deepflow: This code contains the neural network implementation from the nature communication manuscript NCOMMS-16-25447A.
• pynetdicom: A pure Python DICOM network implementation
• ANTs: Advanced Normalization Tools (ANTs)
• bisweb: This is the repository for the BioImage Suite Web Project
• neurokernel: Neurokernel Project
• jupyter-omeroanalysis-desktop: Run OMERO clients in a Linux desktop using Jupyter
• openNeuroData: A proposal for data standardization in neurophysiology
• birthdaycard: Program to generate birthday cards from structural brain scans.
• font-brain: font symbols for brain imaging analyses
• pyconto: Python Connectome Toolbox
• OctaveMVPA: An All-in-One Princeton MVPA, AFNI-for-MATLAB, and SPM Distro: All Converted for Use in Octave
• Suite2P: Tools for processing 2P recordings
• Compress_SSL: Repository for rotation projects with Liam Paninski/John Cunningham
• SPM_connectome: Analysis of the data from the human connectome with SPM
• freshMRI: a collection of resources to set up a neuroimaging data analysis environment
• simba: SimBA (Simple Behavioral Analysis), a plug-and-play pipeline and GUI for developing supervised behavioral classifiers
• DeepLabCut: Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals
• TME: This code package is for the Tensor-Maximum-Entropy (TME) method. This method generates random surrogate data that preserves a specified set of first and second order marginal moments of a data tensor, which makes it well equipped to test for the null hypothesis that a structure in data is an epiphenomenon of these specified set of primary features of the data tensor. The random surrogate data are sampled from a maximum entropy distribution. This distribution unlike traditional maximum entropy method have constraints on the marginal first and second moments of the tensor mode.
• neuroglancer: WebGL-based viewer for volumetric data
• csg_mri_pipelines: MRI preprocessing and analysis pipelines and tools for the study of disorders of consciousness
• nidb: NeuroInformatics Database
• nwb-schema: Data format specification schema for the NWB neurophysiology data format
• Scalable-Brain-Atlas: Source code of the Scalable Brain Atlas website (scalablebrainatlas.incf.org)
• fslr: FSL-R Interface package
• psacnn: None
• neurospinqc: None
• nipype: Workflows and interfaces for neuroimaging packages
• bctpy: brain connectivity toolbox for python
• BEaST: C implementation of Brain Extraction based on nonlocal Segmentation Technique
• visbrain: A multi-purpose GPU-accelerated open-source suite for brain data visualization
• brainx: Tools for analysis of brain imaging-derived networks, based on NetworkX
• brain-age-prediction: Notes on developmental trajectories, predicting brain maturation, effects of head motion on sMRI, and qMRI and brain development
• heudiconv: A flexible DICOM converter for organizing brain imaging data into structured directory layouts
• myconnectome: Code for the myconnectome project
• ICA-AROMA: ICA-AROMA Software Package: a data-driven method to identify and remove head motion-related artefacts from functional MRI data.
• PowerGrid: GPU accelerated non-Cartesian magnetic resonance imaging reconstruction toolkit
• leap: LEAP is now deprecated -- check out its successor SLEAP!
• real-life: None
• WhitakerLabProjectManagement: This repository contains issues related to the management of all Whitaker Lab projects
• CNMF_E: Constrained Nonnegative Matrix Factorization for microEndoscopic data
• fmriprep: fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
• neurosynth-data: None
• projectMatlab: Interface R, Matlab, SPM
• neurocaas: IaC codebase for the NeuroCAAS Platform
• owmeta: Unified, simple data access python library for data & facts about C. elegans anatomy
• afni: Official AFNI source and documentation
• workbench: Connectome Workbench
• dcm2niix: dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC
• Z-Brain: Z-Brain Viewer and Analysis Scripts for MAP-Mapping
• fieldtrip: The MATLAB toolbox for MEG, EEG and iEEG analysis
• nSTAT: Neural Spike Train Analysis Toolbox for Matlab
• niak: GNU Octave library for connectivity analysis in large fMRI datasets
• fmri-analysis-vm: A VM setup for use in fMRI analysis and education
• fs-cwl: Common workflow language wrappers and workflow for FreeSurfer
• CiftiLib: C++ Library for reading and writing CIFTI-2 and CIFTI-1 files
• Papaya: A pure JavaScript medical research image viewer.
• Dartmouth-OpenBCI-Hackathon: Open BCI demo
• _neurolib_deprecated: A library for neuroscientists by neuroscientists
• spm12w: Spm12w is a set of tools and scripts to automate various aspects of fMRI preprocessing and GLM analysis in SPM12.
• biananes: Scalable fMRI Data Analysis
• epitome: scriptit modules for fmri analysis
• phy: phy: interactive visualization and manual spike sorting of large-scale ephys data
• course-website: Spring 2020 | Python for Neuroscience Data
• yass: YASS: Yet Another Spike Sorter
• sima: Python package for analysis of dynamic fluorescence microscopy data
• najafi-2018-nwb: Conversion of Churchland's dataset to NWB 2.0 format
• GUI: Software for electrophysiology data acquisition (deprecated)
• spyking-circus: Fast and scalable spike sorting in python
• ismrmrd: ISMRM Raw Data Format
• ACE: Tools for automatic extraction of activation coordinates from published neuroimaging articles.
• nipy: Neuroimaging in Python FMRI analysis package
• Naplib: None
• studycentric: StudyCentric - research DICOM viewer
• spykes: Tools for spike data analysis and visualization
• ffn: Flood-Filling Networks for instance segmentation in 3d volumes.