NeuroScheme Introduction¶

NeuroScheme is a visual exploratory framework that facilitates the process of knowledge extraction from complex neural scenes. This framework contains a multilevel structure, following the different organizational levels of the brain. Schematic or iconic symbols have been designed to portray the entities at each level, providing graphical representations that emphasize relevant features while hiding less important information. These schematic views, together with a multilevel organization, allow the exploration of the brain at different scales, combining in the same view different levels of abstraction whose entities can be either schematically represented (at different abstraction levels) or geometrically depicted at the finest level of detail.

This documentation is for NeuroScheme version 0.7.6 that can be obtained from the homepage.

External Links¶

The homepage for NeuroScheme is located at NeuroScheme Homepage and the source code for the latest release is available in the Github page. For reporting bugs please use the Github Issues page. If you have any questions or suggestions about ViSimpl refer to dev@vg-lab.es.

NeuroScheme synchronization¶

For NeuroScheme to synchronize with other applications a ZeroEQ discovery provider must be installed in the machine. ZeroEQ applications are linked using automatic discovery based on ZeroConf protocol or through explicit connection addressing using hostname and port because of that a service like Avahi on Linux or dnssd on Mac/Windows (like Bonjour) must be installed. If that service is not present NeuroScheme will still be usable but won’t be able to synchronize events or selection data.

Installation and running¶

NeuroScheme can be downloaded from the NeuroScheme Homepage for Linux and Mac operating systems and executed locally. Additionally it can be executed using a docker image.

Docker containers¶

The docker containers for NeuroScheme can be found on Docker Hub. It’s recommended to use the highest tag number (latest official release) or the git master (represents the latest commit to master branch, and usually are the same as the highest tag number).

Executing locally¶

The application options and parameters are:

OPTION	PARAMETER	DESCRIPTION
`--version`	none	Shows the version of the application.
`--help`	none	Shows the options and arguments used for executing the application.
`-ncl` `--not-colored-log`	none	Do not use colors in the application log.
`-d` `--domain`	cortex\|congen	Specifies the data domain.
`-sc` `--scale`	numerical value	Specifies the scale of the data. Default is 1.0f.
`-l` `--log-file`	path_to_log_file	Specifies the path of the log file.
`--json`	path_to_json_file	Load JSON data file.
`-bc`	path_to_bc_file	Load BlueConfig file. Only valid for cortex domain.
`-xml`	path_to_xml_file	Load XML scene. Only valid for cortex domain.
`-target`	target_label	Specifies target label of the BlueConfig file.
`--no-morphologies` `-nm`	none	No morphologies. Only valid for cortex domain.
`-lc`	none	Load connectivity. Only valid for cortex domain.
`--csv-neuron-stats` `-cns`	path_to_csv_file	Load neuron stats. Only valid for cortex domain.

If the options are incompatible or its parameters invalid the application will abort the execution and will show the help message in the console.

Test dataset¶

A test data for NeuroScheme (for Congen and Cortex domains) can be downloaded from:

Docker example¶

When Using a docker image replace the folder $(pwd)/neuroscheme-example-data by the the local folder with your local data.

 xhost +local:docker
 # Pull the image
 docker pull vglab/neuroscheme:0.7.6-nvidia-ubuntu-16.04
 # Download example data
 mkdir neuroscheme-example-data && cd neuroscheme-example-data
 wget https://vg-lab.es/apps/NeuroScheme/example-data/neuroscheme-congen-example-data.json
 wget https://vg-lab.es/apps/NeuroScheme/example-data/neuroscheme-cortex-example-data.xml
 wget http://neuromorpho.org/dableFiles/allen%20cell%20types/CNG%20version/H16-03-001-01-09-01_559391771_m.CNG.swc
 cd ..
 # Run cortex example
 docker run --gpus 1 -ti --rm -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /etc/machine-id:/etc/machine-id -v $(pwd)/neuroscheme-example-data:/data  --privileged vglab/neuroscheme:0.7.6-nvidia-ubuntu-16.04 /usr/bin/NeuroScheme -d cortex -xml /data/neuroscheme-cortex-example-data.xml
 # Run congen example
 docker run --gpus 1 -ti --rm -e DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /etc/machine-id:/etc/machine-id -v $(pwd)/neuroscheme-example-data:/data  --privileged vglab/neuroscheme:0.7.6-nvidia-ubuntu-16.04 /usr/bin/NeuroScheme -d congen --json /data/neuroscheme-congen-example-data.json