jafyvilla / brayns

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

Brayns

One of the keys towards understanding how the brain works as a whole is visualisation of how the individual cells function. In particular, the more morphologically accurate the visualisation can be, the easier it is for experts in the biological field to validate cell structures; photo-realistic rendering is therefore important.

The Blue Brain Project has made major efforts to create morphologically accurate neurons to simulate sub-cellular and electrical activities, e.g. molecular simulations of neuron biochemistry or multi-scale simulations of neuronal function. Ray-tracing can help to highlight areas of the circuits where cells touch each other and where synapses are being created. In combination with ‘global illumination’, which uses light, shadow, and depth of field effects to simulate photo-realistic images, this technique makes it easier to visualise how the neurons function.

Brayns is a minimalistic visualiser that can perform ray-traced rendering of neurons. It provides an abstraction of the underlying rendering engines, so that the best possible acceleration libraries can be used for the relevant hardware. (https://github.com/BlueBrain/Brayns.git).

To keep track of the changes between releases check the changelog.

Contact: [email protected]

Architecture

About

The following platforms and build environments are tested:

• Linux: Ubuntu 14.04, RHEL 6.5 (Makefile, x64)

The API documentation can be found on bluebrain.github.io.

Building from Source

Prerequisites

In order to ease the application compilation process, we recommend using the following tree structure:

- src
  +- ispc-v1.9.0-linux
  +- OSPRay
  +- BRayns

Intel ISPC compiler

Download and extract ISPC compiler 1.9.0 archive.

OSPRay

Clone OSPRay in the same folder level as ISPC compiler

  git clone https://github.com/BlueBrain/OSPRay.git
  mkdir OSPRay/Build
  cd OSPRay/Build
  cmake .. -DCMAKE_INSTALL_PREFIX=<Brayns_installation_folder>
  make install

Brayns

  git clone https://github.com/BlueBrain/Brayns.git
  mkdir Brayns/Build
  cd Brayns/Build
  cmake .. -DOSPRAY_ROOT=<Brayns_installation_folder> -DCMAKE_INSTALL_PREFIX=<Brayns_installation_folder>
  make install

A number of dependencies are optional, and are related to some specific Brayns features:

Enable/Disable assimp supported mesh file loader (.obj, .ply, etc.)

cmake .. -DBRAYNS_ASSIMP_ENABLED=ON:OFF

Enable/Disable Brion supported

morphology file loader (.h5, .swc, BlueConfig, CircuitConfig)

cmake .. -DBRAYNS_BRION_ENABLED=ON:OFF

Enable/Disable Deflect for

streaming to Tide, the Tiled Interactive DisplayWall environment.

cmake .. -DBRAYNS_DEFLECT_ENABLED=ON:OFF

Enable/Disable ImageMagick image loading

cmake .. -DBRAYNS_IMAGEMAGICK_ENABLED=ON:OFF

Enable/Disable HTTP/REST interface.

Servus, ZeroBuf, Lexis, LibJpegTurbo and ZeroEQ. See documentation for REST API details.

cmake .. -DBRAYNS_REST_ENABLED=ON:OFF

Running Brayns viewer

export PATH=<Brayns_installation_folder>/bin:$PATH
export LD_LIBRARY_PATH=<Brayns_installation_folder>/lib:$LD_LIBRARY_PATH
braynsViewer

Running Brayns off-screen service

export PATH=<Brayns_installation_folder>/bin:$PATH
export LD_LIBRARY_PATH=<Brayns_installation_folder>/lib:$LD_LIBRARY_PATH
braynsService

Known Bugs

Please file a Bug Report if you find new issues which have not already been reported in Bug Report page. If you find an already reported problem, please update the corresponding issue with your inputs and outputs.