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Brain connectomic software tools

The structure of the nervous system is extraordinarily complicated because individual neurons are interconnected to hundreds or even thousands of other cells in networks that can extend over large volumes. Mapping such networks at the level of…
BrainSpan
Dataset

BrainSpan

Provides several data which are freely-accessible for understanding human brain…

Provides several data which are freely-accessible for understanding human brain development. BrainSpan contains de novo references atlases and a high resolution magnetic resonance imaging (MRI). This…

PrAGMATiC
Web

PrAGMATiC Probabilistic And Generative Model of Areas Tiling the Cortex

Provides a detailed semantic atlas. PrAGMATiC determines where functional areas…

Provides a detailed semantic atlas. PrAGMATiC determines where functional areas appear on the cortical sheet and determines how the cortical map is produced from an arrangement of areas. It can be…

AAL
Desktop

AAL Automated Anatomical Labeling

Offers a reference frame for activation labeling. AAL is based on an anatomical…

Offers a reference frame for activation labeling. AAL is based on an anatomical parcellation of the Montreal Neurological Institute (MNI) single-subject brain. It makes the correspondence between the…

FSL
Desktop

FSL FMRIB Software Library

Allows users to work about magnetic resonance imaging (MRI) brain imaging data.…

Allows users to work about magnetic resonance imaging (MRI) brain imaging data. FSL can realize functional magnetic resonance imaging (FMRI) analysis (brain extraction, smoothing, statistics,…

webKnossos
Web
Desktop

webKnossos

Allows 3D image data annotation in various 3D image analysis settings in…

Allows 3D image data annotation in various 3D image analysis settings in connectomics and other fields. webKnossos is an in-browser annotation tool. The software accelerates human 3D data interaction…

BrainPrint
Desktop

BrainPrint

Allows construction of a similarity measure between brain scans. BrainPrint…

Allows construction of a similarity measure between brain scans. BrainPrint facilitates the statistical analysis by computing distances between shape descriptors without the need for establishing…

The Virtual…
Desktop

The Virtual Brain

Simulates the dynamics of large-scale brain networks with biologically…

Simulates the dynamics of large-scale brain networks with biologically realistic connectivity. The Virtual Brain uses tractographic data (DTI/DSI) to generate connectivity matrices and build cortical…

BrainSuite
Desktop

BrainSuite

Enables largely automated processing of magnetic resonance images (MRI) of the…

Enables largely automated processing of magnetic resonance images (MRI) of the human brain. BrainSuite provides a sequence of low-level operations that can produce accurate brain segmentations in…

HummosEtAl2014
Dataset

HummosEtAl2014

Provides an integrative model of the intrinsic hippocampal theta rhythm. This…

Provides an integrative model of the intrinsic hippocampal theta rhythm. This model can be used to quantify the relative contributions of each of generators to theta power, across different…

Hammersmith…
Dataset

Hammersmith atlas

Provides a maximum probability map in stereotaxic space, which retains…

Provides a maximum probability map in stereotaxic space, which retains quantitative information regarding inter-subject variability. Hammersmith atlas is based on 83 entirely manually delineated…

ANIMAL
Desktop

ANIMAL Automatic Nonlinear Image Matching and Anatomical Labeling

Provides method to evaluate design choices and to choose parameter values.…

Provides method to evaluate design choices and to choose parameter values. ANIMAL method assists users to realize comparison between competing spatial normalization algorithms. This method is based…

Dipy
Desktop

Dipy Diffusion Imaging in Python

Allows to study diffusion Magnetic Resonance Imaging (MRI) data. Dipy is a…

Allows to study diffusion Magnetic Resonance Imaging (MRI) data. Dipy is a program allowing users to share their code and experiments. One of its objectives is to provide transparent implementations…

Neurosynth
Web

Neurosynth

Generates a large database of mappings between neural and cognitive states.…

Generates a large database of mappings between neural and cognitive states. Neurosynth uses text mining, meta-analysis and machine learning techniques. It can automatically conduct large-scale,…

CBS Tools
Desktop

CBS Tools

Allows ultra-high-resolution brain segmentation at 7 Tesla (T). CBS Tools is an…

Allows ultra-high-resolution brain segmentation at 7 Tesla (T). CBS Tools is an automated computational framework for brain segmentation and cortical reconstruction at the ultra-high resolution of…

BrainMaps
Dataset

BrainMaps

Stores megapixels of scanned images of serial sections of both primate and…

Stores megapixels of scanned images of serial sections of both primate and non-primate brains. BrainMaps is a brain atlas which gives access to complete brain datasets for various species. The…

NEURON
Desktop

NEURON

Provides a simulation environment for modeling individual neurons and networks…

Provides a simulation environment for modeling individual neurons and networks of neurons. NEURON provides tools for conveniently building, managing, and using models in a way that is numerically…

Topographica
Desktop

Topographica

Helps researchers understand brain function at the level of the topographic…

Helps researchers understand brain function at the level of the topographic maps that make up sensory and motor systems. Topographica is a software package for computational modeling of neural maps.…

neuroConstruct
Desktop

neuroConstruct

Facilitates the creation, visualization, and analysis of networks of…

Facilitates the creation, visualization, and analysis of networks of multicompartmental neurons in 3D space. neuroConstruct provides a graphical user interface (GUI) which allows model generation and…

JRD-fluid
Algorithm

JRD-fluid Jensen-Rényi Divergence fluid

Allows users to study and visualize clinical/anatomical correlations and brain…

Allows users to study and visualize clinical/anatomical correlations and brain deficits in Human Immunodeficiency virus/Acquired Immune Deficiency Syndrome (HIV/AIDS). JRD-fluid is an analysis method…

Nipype
Desktop

Nipype Neuroimaging in Python: Pipelines and Interfaces

Interfaces with existing software for analysis of neuroimaging data and…

Interfaces with existing software for analysis of neuroimaging data and comparative development of algorithms. Nipype is an open-source, community-developed, Python-based software package that…

Neurokernel
Desktop

Neurokernel

Aims to the collaborative development of comprehensive models of the brain of…

Aims to the collaborative development of comprehensive models of the brain of the fruit fly Drosophila melanogaster and their execution and testing on multiple Graphics Processing Units (GPUs).…

PyTorch
Desktop

PyTorch

Offers a computational model of the brain’s visual system. PyTorch is based…

Offers a computational model of the brain’s visual system. PyTorch is based on an unsupervised inference model that can learn representations from complex data. It can be employed to determine and…

SliceMap
Desktop

SliceMap

Enables mapping of anatomically defined regions onto microtome-cut brain…

Enables mapping of anatomically defined regions onto microtome-cut brain slices. SliceMap employs a combination of coarse pre-registration steps and fine elastic registration based on a library of…

BRAPH
Desktop

BRAPH BRain Analysis using graPH theory

Allows connectivity analysis of brain networks derived from structural magnetic…

Allows connectivity analysis of brain networks derived from structural magnetic resonance imaging (MRI), functional MRI (fMRI), positron emission tomography (PET) and electroencephalogram (EEG) data.…

NeuralAct
Desktop

NeuralAct

Visualizes cortical activations on a three-dimensional (3D) model of a brain…

Visualizes cortical activations on a three-dimensional (3D) model of a brain surface. NeuralAct provides researchers working with Electrocorticography (ECoG) the means to observe the activity on…

MCPA
Desktop

MCPA Multi-Connection Pattern Analysis

Evaluates information detected in patterns of interactions between two neural…

Evaluates information detected in patterns of interactions between two neural populations. MCPA is a standalone software which merge functional connectivity and pattern recognition analyses. It…

LONI-IDA
Dataset

LONI-IDA Laboratory of Neuro Imaging Image and Data Archive

An integrated environment for safely archiving, querying and visualizing…

An integrated environment for safely archiving, querying and visualizing imaging data. LONI IDA provides a large-scale archive for neuroimaging, genetics, and phenomic datasets which serves the major…

GC-LDA
Desktop

GC-LDA Generalized Correspondence Latent Dirichlet Allocation

Generates topics that are simultaneously constrained by both anatomical and…

Generates topics that are simultaneously constrained by both anatomical and functional considerations. GC-LDA learns latent topics from the meta-analytic Neurosynth database of over 11,000 published…

TwoRegionsConst…
Desktop

TwoRegionsConstrained

Predicts hard-to-measure interactions across multiple brain regions…

Predicts hard-to-measure interactions across multiple brain regions incorporating relatively easy-to-measure quantities. TwoRegionsConstrained is a theoretical framework to infer hard-to-measure…

PRO
Desktop

PRO Point-process Response Model for Optogenetics

A probabilistic model for optogenetics data analysis. The PRO approach draws on…

A probabilistic model for optogenetics data analysis. The PRO approach draws on successes of existing generalized linear models (GLM) framework for modeling spike train data. The innovation in the…

ALBERT
Dataset

ALBERT A Label-Based Encephalic ROI Template

Offers a set of manually segmented magnetic resonance (MR) images from 5…

Offers a set of manually segmented magnetic resonance (MR) images from 5 term-born and 15 preterm infants imaged at term corrected age. ALBERT offers volume measurements, based on ultimately…

iCafe
Desktop

iCafe intraCranial artery feature extraction

Allows users to quantify morphometric and intensity features of intracranial…

Allows users to quantify morphometric and intensity features of intracranial arteries on MR angiography (MRA) images. iCafe provides a graphic interface for measuring information on large or/and…

SINEAD
Desktop

SINEAD Software Integrating NEuroimaging And other Data

Represents a multimodal machine-learning that uses multi-kernel learning (MKL)…

Represents a multimodal machine-learning that uses multi-kernel learning (MKL) and Dartel techniques. SINEAD assists users to enhance multimodal classification accuracy of imaging scans from AIBL…

GRETNA
Desktop

GRETNA GRaph thEoreTical Network Analysis

Performs comprehensive graph-based topological analyses of brain networks.…

Performs comprehensive graph-based topological analyses of brain networks. GRETNA incorporates network construction, analysis and comparison modules to provide a complete and automatic pipeline for…

FiberWeb
Web

FiberWeb

Provides a platform for diffusion-weighted magnetic resonance imaging (dMRI)…

Provides a platform for diffusion-weighted magnetic resonance imaging (dMRI) and tractography data visualization. FiberWeb allows users to display virtual dissection, streamlines and volumes in real…

LESYMAP
Desktop

LESYMAP

Allows user to study cognitive performance scores and lesion maps from patients…

Allows user to study cognitive performance scores and lesion maps from patients with stroke. LESYMAP permits visualization of the brain areas responsible for the cognitive deficit.

FFBO
Web
Desktop

FFBO Fruit Fly Brain Observatory

Aims to study fruit fly brain function and investigate fruit fly brain disease…

Aims to study fruit fly brain function and investigate fruit fly brain disease models that are highly relevant to the mechanisms of human neurological and psychiatric disorders. FFBO stores and…

GeNN
Desktop

GeNN GPU enhanced Neuronal Network

A framework, which aims to facilitate the use of graphics accelerators for…

A framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that…

ART
Desktop

ART Automatic Registration Toolbox

Allows users an estimation of displacement fields for inter-subject…

Allows users an estimation of displacement fields for inter-subject registration of high-resolution volumetric magnetic resonance imaging (MRI) images. ART contains an inter-subject registration…

dive
Desktop

dive

A deep neural network model architecture that is highly optimized for…

A deep neural network model architecture that is highly optimized for serial-section transmitted electron microscopy image segmentation. We trained a pixel classifier that operates on raw pixel…

Neurodevelopmen…
Dataset

Neurodevelopmental MRI Database

Consists of average magnetic resonance imaging (MRI) templates, segmented…

Consists of average magnetic resonance imaging (MRI) templates, segmented partial volume estimate volumes for GM, WM, T2W-derived CSF. Neurodevelopmental MRI Database is a database of average MRIs…

ECoG…
Desktop

ECoG ClusterFlow

Allows neuroscientists to investigate the major cluster evolution patterns over…

Allows neuroscientists to investigate the major cluster evolution patterns over space and time. ECoG ClusterFlow is a hierarchical multi-scale approach that supports the exploration, comparison and…

ENIGMA-Viewer
Desktop

ENIGMA-Viewer Enhancing Neuro Imaging Genetics through Meta-Analysis Viewer

Allows users to explore multimodality brain data to compare effect sizes and…

Allows users to explore multimodality brain data to compare effect sizes and associated brain anatomical structures and genomics factors. ENIGMA-Viewer is an interactive visualization tool that…

Flybrain
Dataset

Flybrain

Provides access to a range of anatomical data relevant to the structure and…

Provides access to a range of anatomical data relevant to the structure and function of the Drosophila nervous system. Flybrain is an online atlas and database which provides a guide to some of the…

Diffeomorphic…
Desktop

Diffeomorphic Demons

Consists of a non-parametric diffeomorphic registration algorithm.…

Consists of a non-parametric diffeomorphic registration algorithm. Diffeomorphic Demons is an optimization procedure on the entire space of displacement fields. This method can provide non-parametric…

Brian
Desktop

Brian

Provides a simulator for spiking neural networks. Brian can be used to create a…

Provides a simulator for spiking neural networks. Brian can be used to create a network of neurons and synapses connected with a network of astrocytes. This method permits user to focus mainly on the…

CARLsim
Desktop

CARLsim

Provides a Graphic Processing Unit (GPU)-accelerated library for simulating…

Provides a Graphic Processing Unit (GPU)-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of…

Atlaskit
Dataset

Atlaskit

Gathers a probabilistic in-vivo reference atlas about subcortical nuclei…

Gathers a probabilistic in-vivo reference atlas about subcortical nuclei involved in reward learning and decision making. Atlaskit is composed of anatomical images, T1w and T2w templates, as well as…

Day2day
Dataset

Day2day

Provides a large number of scans for multiple individuals. Day2day contains…

Provides a large number of scans for multiple individuals. Day2day contains additional sequences and further behavioural covariates. It was created thanks to 8 volunteers that were scanned 40-50…

MS-HBM
Desktop

MS-HBM Multi-Session Hierarchical Bayesian Mode

Derives functional parcellations of the cerebral cortex within individual…

Derives functional parcellations of the cerebral cortex within individual subjects. MS-HBM takes into account inter-subject and intra-subject functional connectivity variability. It was applied to…

dfcbenchmarker
Desktop

dfcbenchmarker

Allows researchers to measure the quality of their dynamic functional…

Allows researchers to measure the quality of their dynamic functional connectivity (DFC) methods. dfcbenchmarker is based on four simulation methods: (1) the sliding window (SW) method that uses a…

FiberNET
Desktop

FiberNET

Provides a workflow to classify white matter (WM) fibers. FiberNET provides an…

Provides a workflow to classify white matter (WM) fibers. FiberNET provides an automated method with the aim of eliminating false positive fibers from a fiber bundle. It was tested by using a public…

A unified…
Desktop

A unified thalamic model of multiple distinct oscillations

Generates multiple distinct oscillations corresponding to different…

Generates multiple distinct oscillations corresponding to different physiological conditions. This method is a unified model of the thalamus that offers a mechanistic understanding of thalamic…

A A A
CSR model
Desktop

CSR model Chronic Sleep Restriction model

Checks hypothesis that dynamic changes in the concentrations of both adenosine…

Checks hypothesis that dynamic changes in the concentrations of both adenosine molecules and receptors can account for changes in cognitive performance. CSR model can link the sleep homeostatic…

iPlan CMF
Desktop

iPlan CMF

Allows virtual planning of reconstructions. iPlan CMF is a program permitting…

Allows virtual planning of reconstructions. iPlan CMF is a program permitting users to work on complex planning of mid-facial reconstructions and tumor removal, and especially to reproduce…

m2g
Dataset

m2g

Allows users to study human connectomes. m2g is an online resource that offers…

Allows users to study human connectomes. m2g is an online resource that offers possibility to download data about diffusion magnetic resonance imaging (MRI). Users can find on this platform a list of…

SPANOL
Algorithm

SPANOL SPectral ANalysis Of Lobes

Segments a cortical surface in a few parcels that have strong similarities with…

Segments a cortical surface in a few parcels that have strong similarities with brain lobes. Spanol provides a segmentation of cortical surface by using a K-means clustering of Laplace-Beltrami…

GenerateNull
Desktop

GenerateNull

Allows user to generate noise studies. GenerateNull works with a list of foci…

Allows user to generate noise studies. GenerateNull works with a list of foci used usually in the meta-analysis.

Porcupine
Desktop

Porcupine PORcupine Creates Ur PipelINE

Allows creation of neuroimaging pipelines by means of a graphical user…

Allows creation of neuroimaging pipelines by means of a graphical user interface (GUI). Porcupine is a graphical workflow editor that automatically produces analysis code from a graphically composed…

AFQ-Browser
Desktop

AFQ-Browser

Allows researchers to visualize and explore data. AFQ-Browser is a…

Allows researchers to visualize and explore data. AFQ-Browser is a visualization tool for the quantitative analysis of diffusion magnetic resonance imaging (MRI) data in the web browser. It assists…

SdS model
Desktop

SdS model Sync/deSync model

Exhibits theta phase-dependent long-term potentiation and long-term depression.…

Exhibits theta phase-dependent long-term potentiation and long-term depression. SdS model is a spiking neural network of the neo-cortical and hippocampal system that takes inspiration from the…

HagaEtAl2017
Desktop

HagaEtAl2017

Incorporates the effects of dendritic spikes into Hebbian learning.…

Incorporates the effects of dendritic spikes into Hebbian learning. HagaEtAl2017 provides a framework of hippocampal memory processing based on a two-compartment neuron model. It gives a plasticity…

CerebroMatic
Desktop

CerebroMatic

Allows the generation of tissue class priors from infancy to old age.…

Allows the generation of tissue class priors from infancy to old age. CerebroMatic is a toolbox that uses a more flexible statistical approach, namely multivariate adaptive regression splines. It was…

BNRR
Desktop

BNRR Bayesian Nnetwork–Response Regression

Infers flexibly changes in a network-valued random variable with a continuous…

Infers flexibly changes in a network-valued random variable with a continuous trait. BNRR is a network–response regression model, which considers the brain network as an object-type response…

VALiDATe29
Dataset

VALiDATe29 VAnderbiLt Digital ATlas of the squirrel monkey brain

Provides a squirrel monkey brain atlas. VALiDATe29 is based on multiple…

Provides a squirrel monkey brain atlas. VALiDATe29 is based on multiple magnetic resonance imaging (MRI) contrasts acquired on 29 specimens. It was constructed on a basis of 29 young adult to…

Toolbox-Romano-…
Desktop

Toolbox-Romano-et-al

Detects neuronal assemblies into a complete data processing pipeline designed…

Detects neuronal assemblies into a complete data processing pipeline designed for the comprehensive analysis of fluorescence imaging data. The Toolbox-Romano-et-al is a computational package that…

MEG_Alignment
Desktop

MEG_Alignment

Allows to pre-process data and apply multi-set canonical correlation analysis…

Allows to pre-process data and apply multi-set canonical correlation analysis (M-CCA) to combine data from different magnetoencephalography (MEG) subjects. MEG_Alignment’s method was evaluated with…

Magnetoencephal…
Desktop

Magnetoencephalography laminar simulations

Allows to determinate the laminar origin of Magnetoencephalography (MEG) sensor…

Allows to determinate the laminar origin of Magnetoencephalography (MEG) sensor activity. MEG laminar simulations permits to test theories of human cognition that involve laminar- and frequency-…

EyeBallGUI
Desktop

EyeBallGUI

Allows users to inspect and mark multi-channel digitized contents with no…

Allows users to inspect and mark multi-channel digitized contents with no constraint concerning marking periods of data in subsets of channels. The EyeBallGUI interface simplifies users the…

Structural…
Dataset

Structural Connectome Atlas

Delineates fiber pathways within the cerebrum, cerebellum, brainstem, and a…

Delineates fiber pathways within the cerebrum, cerebellum, brainstem, and a subset of cranial nerves. Structural Connectome Atlas is an accurate, high-resolution and normative map of both the…

M-CRIB
Dataset

M-CRIB Melbourne Children's Regional Infant Brain

Provides a high quality parcellated neonatal atlas with detailed delineation in…

Provides a high quality parcellated neonatal atlas with detailed delineation in cortical and subcortical regions. M-CRIB aims to extend brain coverage by complementing cortical neonate schemes with…

ANNarchy
Desktop

ANNarchy Artificial Neural Networks architect

Provides a high-level interface in Python similar to PyNN to facilitate the…

Provides a high-level interface in Python similar to PyNN to facilitate the creation of rate-coded, spike-coded or hybrid neural networks. ANNarchy is a neural simulator designed for distributed…

ARACHNE
Desktop

ARACHNE

Enables the design and exploration of realistic brain networks of arbitrary…

Enables the design and exploration of realistic brain networks of arbitrary complexity incorporating neurons and astroglia. Arachne enable experimental neuroscientists to build, run and explore…

NEST
Desktop

NEST NEural Simulation Tool

Simulates large heterogeneous networks of point neurons or neurons with a small…

Simulates large heterogeneous networks of point neurons or neurons with a small number of compartments. NEST is best suited for models that focus on the dynamics, size, and structure of neural…

LFP analysis
Desktop

LFP analysis

Implements an algorithm to automatically detect the main LFPs features. LFP…

Implements an algorithm to automatically detect the main LFPs features. LFP analysis is a MATLAB software, exploiting Phillips-Tikhonov regularization to automatically detect the first maximum, the…

GridCAT
Desktop

GridCAT Grid Code Analysis Toolbox

Allows researchers to carry out automated analysis of human grid cell codes in…

Allows researchers to carry out automated analysis of human grid cell codes in functional magnetic resonance imaging (fMRI) data. The GridCAT performs all analyses, from estimation and fitting of the…

NMT
Desktop

NMT National Institute of Mental Health Macaque Template

Provides a high-resolution in vivo magnetic resonance imaging template of the…

Provides a high-resolution in vivo magnetic resonance imaging template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and…

MRIQC
Desktop

MRIQC

Provides a series of image processing workflows to extract and compute a series…

Provides a series of image processing workflows to extract and compute a series of no-reference, image quality metrics (IQMs) to be used in quality assessment protocols for magnetic resonance imaging…

CVU
Desktop

CVU Connectome Visualization Utility

Allows users to visualize multi-modal human brain networks. CVU generates…

Allows users to visualize multi-modal human brain networks. CVU generates powerful, interactive visualizations of human brain networks from common matrix and imaging file formats. It is decoupled…

MIBCA
Desktop

MIBCA Multimodal Imaging Brain Connectivity Analysis

A fully automated all-in-one connectivity toolbox that offers pre-processing,…

A fully automated all-in-one connectivity toolbox that offers pre-processing, connectivity and graph theoretical analyses of multimodal image data such as diffusion-weighted imaging, functional…

pyClusterROI
Desktop

pyClusterROI

Provides a set of python scripts for deriving a whole brain parcellation of…

Provides a set of python scripts for deriving a whole brain parcellation of functional magnetic resonance imaging (fMRI) data. The resulting regions are suitable for use as regions of interest (ROIs)…

NeuroML
Dataset

NeuroML

Focuses on the development of an XML (eXtensible Markup Language) based…

Focuses on the development of an XML (eXtensible Markup Language) based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network…

BrainBrowser
Web
Desktop

BrainBrowser

Exposes a set of web-based 3D visualization tools primarily targeting…

Exposes a set of web-based 3D visualization tools primarily targeting neuroimaging. Using open web technologies, such as WebGL and HTML5, BrainBrowser allows for real-time manipulation and analysis…

PyNN
Desktop

PyNN

Proposes a simulator-independent language for building neuronal network models.…

Proposes a simulator-independent language for building neuronal network models. PyNN makes it possible to write a simulation script once, using the Python programming language, and run it without…

Brainlab
Desktop

Brainlab

Leverages Python's strengths for the task of managing the general…

Leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was designed to overcome the major difficulties of working with the…

Cognitive Atlas
Dataset

Cognitive Atlas

Provides a knowledge base for cognitive neuroscience. Cognitive Atlas aims to…

Provides a knowledge base for cognitive neuroscience. Cognitive Atlas aims to provide such a resource that reflects the views of the entire community. It can become the standard ontology for mental…

NeuroVault
Web
Desktop

NeuroVault

Allows researchers to store, share, visualize, and decode statistical maps of…

Allows researchers to store, share, visualize, and decode statistical maps of the human brain. NeuroVault provides informative visualization of data without the need to install additional software.…

EEGNET
Desktop

EEGNET

A software package running under MATLAB and allowing for analysis and…

A software package running under MATLAB and allowing for analysis and visualization of functional brain networks from M/EEG recordings. The main objective of this tool is to cover the complete…

Brain Modulyzer
Desktop

Brain Modulyzer

Allows users to explore and analyze modular functional brain connectivity data.…

Allows users to explore and analyze modular functional brain connectivity data. Brain Modulyzer makes possible to apply visualization techniques to all relevant data representations. It uses…

CMC
Dataset

CMC CommonMind Consortium

Generates functional genomic data in brain samples. The CMC data brain was…

Generates functional genomic data in brain samples. The CMC data brain was obtained from autopsies of cases with and without severe psychiatric disorders. This database includes over 1,150 samples…

BOLD_LFP
Desktop

BOLD_LFP

Accounts for the relationship between BOLD and ECoG data from human visual…

Accounts for the relationship between BOLD and ECoG data from human visual cortex in V1-V3. BOLD_LFP uses the model predictions and data matching in three ways: (i) across stimuli, the BOLD amplitude…

AICHA
Desktop

AICHA Atlas of Intrinsic Connectivity of Homotopic Areas

Covers the whole cerebrum, each having homogeneity of its constituting voxels…

Covers the whole cerebrum, each having homogeneity of its constituting voxels intrinsic activity, and a unique homotopic contralateral counterpart with which it has maximal intrinsic connectivity.…

Brainnetome…
Dataset

Brainnetome Atlas

Contains 210 cortical, 36 subcortical subregions and information on both…

Contains 210 cortical, 36 subcortical subregions and information on both anatomical and functional connections. Brainnetome Atlas provides not only fine-grained subregions based on structural…

NeuroManager
Desktop

NeuroManager

Automates the workflow of simulation job submissions when using heterogeneous…

Automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. NeuroManager is an object-oriented simulation management…

Nengo
Desktop

Nengo

It can create sophisticated neural simulations with sensible defaults in few…

It can create sophisticated neural simulations with sensible defaults in few lines of code. Nengo is a neural simulator based on a theoretical framework called the Neural Engineering Framework (NEF).…

Open…
Web

Open Neuroimaging Laboratory

Enables distributed collaboration around annotation, discovery and analysis of…

Enables distributed collaboration around annotation, discovery and analysis of publicly available brain imaging data. The Open Neuroimaging Laboratory is a collaborative platform that facilitates…

NeuroGFX
Web

NeuroGFX

Aims to elucidate neural circuit function from connectome data in the fruit fly…

Aims to elucidate neural circuit function from connectome data in the fruit fly brain. NeuroGFX proposes a scalable computational modeling methodology that includes i) a brain emulation engine, with…

Brainstorm
Desktop

Brainstorm

Allows to visualize, process, and integrate with anatomical magnetic resonance…

Allows to visualize, process, and integrate with anatomical magnetic resonance imaging (MRI) data, magnetoencephalography (MEG) and electroencephalography (EEG) data. Brainstorm aims to provide a set…

ABIDE
Dataset

ABIDE Autism Brain Imaging Data Exchange

A functional and structural brain imaging data collected from laboratories to…

A functional and structural brain imaging data collected from laboratories to accelerate the understanding of the neural bases of autism. ABIDE is a grassroots consortium aggregating and openly…

iqr
Desktop

iqr

Provides an efficient graphical environment to design large-scale multi-level…

Provides an efficient graphical environment to design large-scale multi-level neuronal systems that can control real-world devices in real-time. iqr provides a means to design complex neuronal models…

Budapest…
Web

Budapest Reference Connectome

Generates the common edges of the connectomes of 96 distinct cortexes, each…

Generates the common edges of the connectomes of 96 distinct cortexes, each with 1015 vertices, computed from 96 MRI data sets of the Human Connectome Project. The user may set numerous parameters…

OpenMEEG
Desktop

OpenMEEG

Solves forward problems related to Magneto- and Electro-encephalography (MEG…

Solves forward problems related to Magneto- and Electro-encephalography (MEG and EEG). OpenMEEG, using symmetric Boundary Element Methods (BEM), is being used for many problems in the field of…

BrainMap
Web
Desktop

BrainMap

Offers databases, software applications, and other associated tools for…

Offers databases, software applications, and other associated tools for supporting and promoting quantitative coordinate-based meta-analysis of the structural and functional neuroimaging literature.…

ConnectomeExplo…
Desktop

ConnectomeExplorer

Allows users to analyze and explore large volumetric neuroscience data sets.…

Allows users to analyze and explore large volumetric neuroscience data sets. ConnectomeExplorer is based on a powerful query algebra, that can be useful for users in connectomics research to answer…

Scikit-Learn
Desktop

Scikit-Learn

Provides implementations of algorithms for non-machine learning experts and…

Provides implementations of algorithms for non-machine learning experts and reusable across scientific disciplines and application fields. Scikit-Learn is a general-purpose machine learning library…

Multimodal…
Dataset

Multimodal brain MR image database

Provides a database of brain images. Multimodal brain MR image database is a…

Provides a database of brain images. Multimodal brain MR image database is a resource that consists of 100 sets of simulated multimodal Magnetic Resonance (MR) images of brains with tumors of varying…

Anatomist
Desktop

Anatomist

Enables objects visualization and handling for medical imaging. Anatomist is…

Enables objects visualization and handling for medical imaging. Anatomist is one of the BrainVisa suite’s softwares. Features are based on management of several types of objects, management of…

NetworkX
Desktop

NetworkX

Allows to create, manipulate, and study the structure, dynamics, and function…

Allows to create, manipulate, and study the structure, dynamics, and function of complex networks. NetworkX provides data structures for graphs or networks, with graph algorithms, generators, and…

JuBrain…
Web

JuBrain Cytoarchitectonic Atlas Viewer

Allows to view cytoarchitectonic probabilistic maps. JuBrain is based on the…

Allows to view cytoarchitectonic probabilistic maps. JuBrain is based on the analysis of cytoarchitectonic areas in histological sections of ten human postmortem brains. The tool offers a very easy…

NeMo
Desktop

NeMo

Uses the Izhikevich neuron model which provides a range of realistic spiking…

Uses the Izhikevich neuron model which provides a range of realistic spiking dynamics while being computationally efficient. NeMo is a platform that allows modelers to simulate large-scale networks…

bgsmtr
Desktop

bgsmtr

Runs the Gibbs sampling algorithm to fit a Bayesian group sparse multi-task…

Runs the Gibbs sampling algorithm to fit a Bayesian group sparse multi-task regression model. bgsmtr is a package which provides approaches for choosing the tuning parameters with computations using…

Preprocessed…
Desktop

Preprocessed Connectomes Project

Aims to systematically preprocess the data from the 1000 Functional Connectomes…

Aims to systematically preprocess the data from the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI) and openly share the results. The…

EEGLAB
Desktop

EEGLAB

Processes continuous and event-related EEG (electro-encephalography) and MEG…

Processes continuous and event-related EEG (electro-encephalography) and MEG (magneto-encephalography). EEGLAB also processes other electrophysiological data incorporating independent component…

Brainwaiver
Desktop

Brainwaiver

Basic wavelet analysis of multivariate time series with a visualisation and…

Basic wavelet analysis of multivariate time series with a visualisation and parametrization using graph theory. Brainwaiver computes the correlation matrix for each scale of a wavelet decomposition,…

eConnectome
Desktop

eConnectome Electrophysiological Connectome

A MATLAB-based toolbox, eConnectome (electrophysiological connectome), for…

A MATLAB-based toolbox, eConnectome (electrophysiological connectome), for mapping and imaging functional connectivity at both the scalp and cortical levels from the electroencephalogram (EEG), as…

GraphVar
Desktop

GraphVar

A user-friendly GUI-based toolbox for comprehensive graph-theoretical analyses…

A user-friendly GUI-based toolbox for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological…

AxonTracker-3D
Desktop

AxonTracker-3D

An interactive 3D axon tracking and labeling tool to obtain quantitative…

An interactive 3D axon tracking and labeling tool to obtain quantitative information by reconstruction of the axonal structures in the entire innervation field. AxonTracker-3D has been developed to…

The MRI…
Dataset

The MRI Standard Brain of Japanese Macaque Monkey

Is used for spatially normalising Japanese macaque brains into a standard…

Is used for spatially normalising Japanese macaque brains into a standard space. The MRI Standard Brain of Japanese Macaque Monkey template is based on T1/T2 weighted, high-resolution 4 T Magnetic…

BBR
Algorithm

BBR Boundary-Based Registration

An alignment procedure by maximizing image contrast across tissue boundaries…

An alignment procedure by maximizing image contrast across tissue boundaries rather than matching intensities between two images or by matching surface shapes. . BBR is more accurate than correlation…

BCT
Desktop

BCT Brain Connectivity Toolbox

A Matlab toolbox for analysis of complex brain networks. The toolbox contains…

A Matlab toolbox for analysis of complex brain networks. The toolbox contains network analysis functions and complex brain network datasets. These measures are increasingly used to characterize…

PANDA
Desktop

PANDA Pipeline for Analyzing braiN Diffusion imAges

A MATLAB toolbox for a comprehensive pipeline processing of dMRI dataset,…

A MATLAB toolbox for a comprehensive pipeline processing of dMRI dataset, aiming to facilitate image processing for the across-subject analysis of diffusion metrics and brain network constructions.…

Mango
Desktop

Mango Multi-image Analysis GUI

Automates regional behavioral analysis of human brain images. Mango provides…

Automates regional behavioral analysis of human brain images. Mango provides analysis tools and a user interface to navigate image volumes. The tool is ease to use, multi-platform Java application…

GAT
Desktop

GAT Graph-Analysis Toolbox

Facilitates analysis and comparison of structural and functional network brain…

Facilitates analysis and comparison of structural and functional network brain networks. GAT provides a graphical user interface (GUI) that facilitates construction and analysis of brain networks,…

BrainNet Viewer
Desktop

BrainNet Viewer

A graph-theoretical network visualization toolbox to illustrate human…

A graph-theoretical network visualization toolbox to illustrate human connectomes as ball-and-stick models. Within this toolbox, several combinations of defined files with connectome information can…

Connectome…
Desktop

Connectome Mapping Toolkit

A set of free and extensible open source neuroimaging tools written in Python.…

A set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to…

MSM
Algorithm

MSM Multimodal Surface Matching

Conducts surface registration from multiple sources of information. MSM…

Conducts surface registration from multiple sources of information. MSM represents displacement of each surface vertex in form of a discrete set of possible rotations. It offers a regularization term…

BrainWeb
Web

BrainWeb

Hosts a Simulated Brain Database (SBD) and allows users to run custom MRI…

Hosts a Simulated Brain Database (SBD) and allows users to run custom MRI simulations with any of several pulse sequences and source digital phantoms, and arbitrary values of the acquisition…