Brayns plugins

Introduction

Brayns architecture allows it to be used for almost any kind of visualization purpose. For this reason, the core of Brayns knows nowthing about any science-specific modeling.

To load specific functionality, the Brayns backend service must be launched by specifiying plugins, which will add extra functionality.

Circuit Explorer plugin

The Circuit Explorer plugin is the main Brayns plugin for neuroscientific visualization. It provides Brayns with extra features, such as, but not limited to:

  • Loading neuronal circuits based on CircuitConfig / BlueConfig

  • Load morphology files (Ascii, SWC or H5)

  • Loading simulations in the form of compartment or spike reports

  • Load circuit-specific features, such as synapses

  • Provides multiple renderers for different kind of visualizations that highlight circuit specific features

The Circuit Explorer plugin also provides a python class within the Brayns python client that encapsulates its functionality and eases the usage of the API exposed by this plugin. For further information on the Circuit Explorer’s python API, refer to Circuit Explorer API

To load the Circuit Explorer plugin when launching the Brayns backend service, use the following argument in the command line:

--plugin braynsCircuitExplorer

Circuit Info plugin

The Circuit Info plugin provides circuit-specific information. It is used by the brayns web interface WebBrayns. Nonetheless, it can be used within the python API as well, if desired, to query some circuit information, such as:

  • List of GIDs (all, or from a list of target)

  • List of targets

  • List of compartment reports, and report-specific information

  • Spike report information

  • List of projections

  • Efferent and afferent synapses for a set of GIDs

  • Projected efferent synapses for a set of GIDs and a projection

For information on the Circuit Info python API, refer to Circuit Info API

To load the Circuit Info plugin when launching the Brayns backend service, use the following argument in the command line:

--plugin braynsCircuitInfo

Diffusion Tensor Imaging plugin

The DTI plugin adds functionality to load streamlines into Brayns, as well as to attach a spike report simulation to them to be visualized.

This plugin accept a file with extension .dti, with the following format:

streamlines=<path to streamlines file .row>
gids_to_streamline_row=<path to GID to streamlines file row mapping .mapping>

The streamlines property points to a file with all the streamlines to load. Each row corresponds to a streamline defined by a set of points, with the following format:

<number of points> <point 1 x> <point 1 y> <point 1 z> <point 2 x> <point 2 y> ...

The gids_to_streamline_row property points to a file that maps cell GIDs to rows to in the streamlines file, with the following format:

<GID> <row_index>

For information on the DTI python API, refer to DTI API

To load the DTI plugin when launching the Brayns backend service, use the following argument in the command line:

--plugin braynsDTI

Fluorescence plugin

The Fluorescence plugin allows for fluorescent staining visualization. It works by sending the Brayns backend service a specific generated volume that will use to render fluorescent scattering and decaying.

Attention

This plugin requires a specific rendering engine to allow for its usage, the pbrt-v2 engine.

For information on the Fluorescence python API, refer to Fluorescence API

To load the Fluorescence plugin when launching the Brayns backend service, use the following arguments in the command line, which will load the appropiate render engine along the plugin:

--engine pbrtv2 --plugin braynsFluorescence

Physically based volumes plugin

The PBR Volumes plugin allows to load volumes into Brayns with physically based properties.

Attention

This plugin requires a specific rendering engine to allow for its usage, the pbrt-v3 engine.

For information on the PBR Volumes python API, refer to PBR Volumes API

To load the PBR Volumes plugin when launching the Brayns backend service, use the following arguments in the command line, which will load the appropiate render engine along the plugin:

--engine pbrt --plugin braynsPBRVolumes