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
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
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
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
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!
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.
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
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
studycentric: StudyCentric - research DICOM viewer
spykes: Tools for spike data analysis and visualization
ffn: Flood-Filling Networks for instance segmentation in 3d volumes.
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