ebrains-collaboratory

The EBRAINS Collaboratory (initially known as Collaboratory 2.0) offers researchers and developers an environment to work in teams and share their work with users, teams or all of the Internet. Workspaces in the Collaboratory are known as collabs. The Collaboratory is composed of a collection of software for web services.

The IAM service of the Collaboratory manages user identification and team management for EBRAINS services. Users can be grouped into units, groups and collab teams for simpler management.

The Wiki service of the Collaboratory hosts the main interface to access all other Collaboratory services. It also offers a handy way of documenting your work with a simple wiki user interface.

The Drive service offers each collab its own storage space for files. The drive provides easy access to files from Jupyter Notebooks. All files are under version control. The Drive is intended for smaller files that change more often.

The Lab service provides a JupyterLab environment for your notebooks with official releases of EBRAINS tools pre-installed. It’s a great way of programming interactively and of sharing your notebooks with other users.

The Office service handles Office documents (Word, PowerPoint or Excel) which can be edited collaboratively online. Whether it is for taking live minutes in a meeting or to finalize/review a report, the collaborative mode is very handy.

The Bucket service offers each collab its own storage space for large files. The bucket provides programmatic access to files from Jupyter Notebooks via the bucket API. Datasets, videos and other files too large for the Drive should be stored here.

The Chat service offers instant messaging with all users that have an EBRAINS account and that have entered the chat at least once. The chat offers channels, discussions and direct messaging. Client apps are available for desktop and mobile devices. Users that are not active in the Chat also receive notifications by email.

Other software

All software

3D Slicer

3D Slicer is: A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy. A free, open source software available on multiple operating systems: Linux, MacOSX and Windows Extensible, with powerful plug-in capabilities for adding algorithms and applications. Features include: Multi organ: from head to toe. Support for multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy. Bidirectional interface for devices. There is no restriction on use, but Slicer is not approved for clinical use and intended for research. Permissions and compliance with applicable rules are the responsibility of the user.

Data analysis and visualisation

3DSpineMFE

A MATLAB® toolbox that given a three-dimensional spine reconstruction computes a set of characteristic morphological measures that unequivocally determine the spine shape.

Modelling and simulation

3DSpineS

Dendritic spines of pyramidal neurons are the targets of most excitatory synapses in the cerebral cortex and their morphology appears to be critical from the functional point of view. Thus, characterizing this morphology is necessary to link structural and functional spine data and thus interpret and make them more meaningful. We have used a large database of more than 7,000 individually 3D reconstructed dendritic spines from human cortical pyramidal neurons that is first transformed into a set of 54 quantitative features characterizing spine geometry mathematically. The resulting data set is grouped into spine clusters based on a probabilistic model with Gaussian finite mixtures. We uncover six groups of spines whose discriminative characteristics are identified with machine learning methods as a set of rules. The clustering model allows us to simulate accurate spines from human pyramidal neurons to suggest new hypotheses of the functional organization of these cells.

Data analysis and visualisationData

Other software

3D Slicer

3DSpineMFE

3DSpineS

Make the most out of EBRAINS