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Incorporate new features into an advanced, cross-platform 3D viewer for NeuroML cells and networks

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Status:
Active, Closed for joining
Contributor/Mentors

Contributor: Giannis D

Mentors: Ankur Sinha (he/him/his), Padraig Gleeson

About

The project is about incorporating new features into an existing 3D viewer which allows for visualisation of cells and networks using the NeuroML standard. Right now the viewer is limited to only viewing the model, whether it is a single cell or a complete network, but at the end of the project it should be a fully equipped 3D viewer with GUI to interface with the user. The user should be able to get as many information as he can about the model using an intuitive GUI with a short learning curve, using “on click” or “on selection” methods to provide according information and providing easy access to views of cells showing ion channel distributions, segment groups, etc. A critical aspect of the project is to ensure high performance with the Vispy viewer to allow visualization of large scale networks. Being able to interact with a model, significantly boosts the understanding of its structure and dynamics. Furthermore, the additional information that will be added can make this viewer an invaluable tool both for an experienced scientist and a beginner in the field, as long as they have some knowledge of python, by providing the capability of exploring new models in a fast, efficient and intuitive manner. Additionally, the Vispy viewer should be embedded into NeuroMLLite-GUI. Options for using the Vispy viewer inside Jupyter notebooks/JupyterLab should also be investigated, as Jupyter notebooks are gaining popularity rapidly.

Deliverables
2024
  • Incorporating new features into an existing 3D viewer which allows for visualisation of cells and networks using the NeuroML standard
2024