NeuroScheme

Introduction

NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations.

Dependencies

• Required dependencies:

  • ShiFT (requires FiReS and Boost) (1)
  • scoop (1)
  • Qt5
  • Eigen3

• Optional dependencies:

  • nsol: needed to load data via nsol. In order to load BlueConfig files nsol has to be built with Brion support. (2)
  • ZeroEQ & Lexis: enables syncing selections, syncing camera position and sending binary cell set operations (2)
  • (TODO) gmrvlex: enables sending focus messages
  • (TODO) Deflect: enables streaming the main window of the app

• (1) Automatically downloaded and build

• (2) Automatically downloaded and build uncommenting .gitsubprojects entry

In order to check which optional dependencies have been used the following command can be used:

./NeuroScheme --version

Download binary packages

There are binaries for x64 architecture for GNU/Linux, MS Windows and MacOSX available for download in http://vg-lab.es/apps/NeuroScheme/

Building from source

NeuroScheme has been successfully built and used on Ubuntu 16.04/18.04, Mac OSX Yosemite/Sierra and Windows 7/8/10 Visual Studio 2015 Win64. The following steps should be enough to build it just with the required dependencies.

git clone --recursive https://github.com/vg-lab/NeuroScheme
mkdir NeuroScheme/build && cd NeuroScheme/build
cmake .. -DCLONE_SUBPROJECTS=ON -DCMAKE_BUILD_TYPE=Release
make

Updating

If you have already built NeuroScheme and want to update to the latest available version, after pulling the repository and before building, you will have to update the automatically downloaded dependencies. This can be done just running make rebase

cd neuroscheme_source_dir
git pull
cd build
make rebase
make

Running

At the moment NeuroScheme running options have to be defined via command line interface. To take a look to the arguments NeuroScheme accepts you can run the following:

./bin/NeuroScheme --help

NeuroScheme accepts different domains (for example, cortex and congen domains) which can be selected when GUI is started or via the "-d" parameter. Each domain can have its own specific parameters, which can be displayed with --help argument.

Loading and exporting data

All domains

All domains can import from and export to a custom JSON format, accessible via a menu or using CLI arguments (only for importing).

./bin/NeuroScheme -d domain --json /path/to/file.json

Cortex domain

Loading data in cortex domain can be done from both nsol's XML scene and BlueBrain's BlueConfig files. If you have built NeuroScheme with nsol support (explained in the Dependencies section) you can try to visualize a very simple scene by running:

./bin/NeuroScheme -d cortex -xml nsol/testData/scene.xml

Congen domain

For congen domain you can try to visualize a very simple example scene by running.

./bin/NeuroScheme -d cortex -xml ../doc/examples/congen-example.json

Congen domain also allows importing and exporting data to NeuroML. Please note that exporting to NeuroML removes the hierarchy. In case you want to keep the created hierarchy please export it to JSON as explained previously.

Importing and exporting to NeuroML operations are available through the GUI menu and also importing is available through CLI arguments.

./bin/NeuroScheme -d congen -x /path/to/neuroML.xml

Interacting with data

Once a dataset has been loaded you can navigate through the hierarchy or visualize the grouped items right-clicking in the representation and selecting the proper option (if available in the specific dataset). The new visualization can be shown in the same panel or in a new one (horizontal or vertical pane splitting can be selected under "Panes" menu).

When clicking in the toolbar "gear" icon a side panel is shown containing the options regarding layouts, filtering and sorting capabilities.

Clicking in the toolbar "drawer" icon a side panel is shown containing the options regarding stored selections.

Note: The "free movement layout" and the "multi-panel" are still in early development and may cause some bugs.

Key modifiers

• Moving items. By holding shift key while clicking over an item and moving the mouse, NeuroScheme automatically changes the layout to "free movement layout".

• Inspecting items. By holding ctrl key while passing the mouse over an item, the inspector is opened (or updated in case it was already opened) showing the attributes of the item and also allowing to edit and save them.

Creating data

The creating feature is still in a development stage. If you want to try it out you can start with a clear canvas or load a dataset as specified before. To create entities you can click on the background of the canvas, select the type of entity and define its properties in the side panel. To edit or duplicate an entity right click on its representation and select the apropriated option. You can also define connection relationships between entities using drag and drop. To visualize connections you have to enable the option in the toolbar or under the menu "Scene".