Discover BlueBrain/MorphIO Open Source project

Visualizer for large-scale and interactive ray-tracing of neurons

675

Brayns

Blue Brain Nexus - A knowledge graph for data-driven science

284

nexus

Blue Brain Python Optimisation Library

269

BluePyOpt

Simulator optimized for large scale neural network simulations.

196

CoreNeuron

A lightweight, interactive, extensible and cross-platform framework for building, visualizing and analyzing digital reconstructions of neuronal morphology skeletons extracted from microscopy stacks.

135

NeuroMorphoVis

Neuronal Morphology Analysis Tool

126

NeuroM

Electrophys Feature Extraction Library

102

eFEL

The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration

BioExplorer

Code Generation Framework For NEURON MODeling Language

nmodl

Tiled Interactive Display Environment

Tide

Reference data for the "Simulation Neuroscience:Neurons and Synapses" Massive Online Open Course

MOOC-neurons-and-synapses-2017

Blue Brain text mining toolbox for semantic search and structured information extraction

REST and websockets C++ library

Rockets

Building and Using Knowledge Graphs made easy

nexus-forge

Topological Neuron Synthesis

NeuroTS

A lightweight, interactive, extensible and cross-platform framework for building, visualizing and analyzing vasculature (or blood vessels) morphologies.

VessMorphoVis

Python framework for graph analytics and co-occurrence analysis

BlueGraph

Large-scale Interactive Volume Rendering Engine

Livre

Interactive visualization framework for geometrically detailed neuron simulations

RTNeuron

A python package for the topological analysis of neurons.

TMD

Public tutorials around electrophysiological simulations

SimulationTutorials

Reconstruction of watertight meshes, annotated volumes and center line skeletons of neuroscience spatial structures from non-watertight inputs, segmented masks, skeletons of NGV morphologies and volumes.

Ultraliser

Natural Language Processing Toolkit for Neuroscience

bluima

Java

Brion

Blue Brain C++ File IO Library

C++ library for building applications to stream pixels to Tide

Deflect

Blue Brain Project nixpkgs configuration - Build a brain with Nix

bbp-nixpkgs

Nix

snap

The Blue Brain Pythonic Simulation and Network Analysis Productivity layer

Search, download, and prepare brain atlas data.

Atlas-Download-Tools

Nexus Web is the interface of Blue Brain Nexus

nexus-web

TypeScript

nexus-kg

Nexus KnowledgeGraph Service

Desktop application (GUI) to perform systematic and collaborative curation of neuroscientific literature.

neurocurator

OSG render bins for transparent geometry

osgTransparency

BluePyEfe

BluePyEfe: Blue Brain Python E-feature extraction

Runs cells from stand-alone packages.

EModelRunner

Biologically detailed neural network simulations and analysis API

BlueCelluLab

Blue Brain Python Cell Model Management

BluePyMM

Framework to facilitate SIMD programming, without any tedious SIMD intrinsics.

cyme

A python and C++ interface to the SONATA format

libsonata

Blue Brain multi-modal registration and alignment toolbox

atlas-alignment

dash

Data Access and Sharing

BlueBrain's recipe writer to parameterize structure and logic of a mouse whole-neocortex connectome

Long-range-micro-connectome

A set of JavaScript libraries built on top of Nexus

nexus-js

TypeScript

bluebrain.github.com

API documentation for BlueBrain projects:

HTML

nexus-bbp-domains

BBP domains specification (schemas, vocabularies)

A collection of tools to repair morphologies

NeuroR

A BBP Simulation Control application for NEURON

neurodamus

Extra tools to work with the Luigi library

singlecell-emodel-suite

luigi-tools

This repository contains the source code of the paper titled "Optimum trajectory learning in musculoskeletal systems with model predictive control and deep reinforcement learning".

learning_musculoskeletal_arm_control

Vasculature blood flow computation and impact of astrocytic endfeet on vessels

AstroVascPy

MOOC-hippocampus-network-simulation-2019

Neuronal morphology preparation and classification using Machine Learning.

morphoclass

Python module to use the annotations created with NeuroCurator, for example in a Jupyter notebook.

nat

morph-tool

Repository of spack external packages

spack-packages

hpc-coding-conventions

Python docstring generation for C++ projects using boost::python

Pydoxine

Simple framework to create data validation workflows.

data-validation-framework

SSCxEModelExamples

SHACL shapes for W3C PROV-O

nexus-prov

Currentscape is a Python tool enabling scientists to easily plot the currents in electrical neuron models. The code is based on the paper Alonso and Marder, 2019.

Currentscape

The Searchable Knowledge-Graph Application

nexus-search-webapp

JavaScript

nexus-python-sdk

A Python API to interface with Nexus REST API

Tools to work with voxel based brain atlases.

voxcell

Manage entities within the knowledge graph

bluepyentity

Multiple simulations analysis tool

blueetl

nexus-iam

Deep-Atlas

dir-content-diff

Simple tool to compare directory contents and get differences using smart comparators.

ConnectomeUtilities

Connectome Utilities

me-features-to-mo-ID-mapping

Interactive Supercomputing Tools and Library

Monsteer

Blue Brain Python Electrical Modeling Pipeline

BluePyEModel

hippocampus-workshop

A web environment for the simulation of brain molecular networks.

morphology-suite

BlueNaaS-Subcellular

Vue

atlas-annotation

Align and improve brain annotation atlases

Workflows used for morphology processing.

morphology-workflows

C++11 Graph Storage library

basalt

The Blue Brain Project's documentation theme.

sphinx-bluebrain-theme

HTML

codash

Collage-based distribution of DASH entities

The neuromapp library reproduces the algorithms of the main software of the BBP as a collection of mini-apps

neuromapp

EMSim is a library that compute different electro-magnetic effects like LPF and VSD.

EMSim

Tools to compute direction vectors in the context of brain atlases.

atlas-direction-vectors

Building blocks commonly used in Nexus services

nexus-service

Generalisation of electrical models of neurons with MCMC

emodel-generalisation

Morphology Specifications used at BBP

morphology-documentation

Makefile

RenderingResourceManager

A Python based service managing rendering resources for visualization web services

A Command Line Interface (CLI) for Nexus

nexus-cli

An SBT Plugin for building Nexus Scala based projects

sbt-nexus

DMT

Tools to compute densities in the context of brain atlases.

atlas-densities

Synthesize diameters of neuronal morphologies

git-cmake-format

CMake

diameter-synthesis

Converter for mod files to C code

mod2c

neurox

A parallel & distributed asynchronous simulator of extended Hodgkin-Huxley neuron models

LLM agent made to communicate with different neuroscience related tools

neuroagent

me-types-mapper