GSoC 2019
There are several modeling studies using brain network models which incorporate biologically realistic macroscopic connectivity (the so-called connectome) to understand the global dynamics observed in the healthy and diseased brain measured by different neuroimaging modalities such as fMRI, EEG and MEG.
For this particular modelling approach in Computational Neuroscience, open source frameworks enabling the collaboration between researchers with different backgrounds are not widely available. The Virtual Brain is, so far, the only neuroinformatics project filling that place.
Several open issues addressed by the following proposals involve
- UI (web, concept, modernize)
- Notebook (integration)
Description: Data visualization plays a crucial role in TVB's neuroinformatics platform, and a Structural Connectivity (connectome) is a core datatype, modelling full brain regions and their connections. An interaction paradigm needs to be proposed, as well as the implementation to be done for such a connectivity visualizer in the browser client of TVB. We need to easily display and interact with up to 1000 regions in a connectivity (1000^2 adjacency matrix) in 2D and 3D. Rendering performance as well as per-element interaction is important. Interaction from the user: rotate, zoom, move, edit edges, etc. are all necessary.
The current implementation is documented here: http://docs.thevirtualbrain.org/manuals/UserGuide/UserGuide-UI_Connectivity.html#long-range-connectivity
Expected Results: Completely redo and improve a section of TVB front-end (Connectivity Cockpit) from UX design, down to implementation, web technologies and optimization for extremely large data structures.
Skills: HTML5, React JS and Python
Mentors: Lia Domide, Paula Popa
Description: TVB's web-based UI provides several very useful visualization tools, which are setup for full screen use. As TVB is used in wider contexts (HBP collaboratory, Jupyter notebooks), it is important to ensure the relevent visualization tools are present everywhere.
This project is to rewrite the widgets in TVB UI to become reusable components which can be employed from a Jupyter notebook for use in the HBP collaboratory, while maintaining compatibility with the existing TVB framework. Tools are to be refactored, choice up to the student, in order of priority
- anatomical visualization (surface, connectivity)
- time series viewer
- the phase plane tool
Use of WebGL (in particular Python/notebook oriented GL tools) are encouraged, where numerous interesting opportunities for optimization are present, e.g. XTK for anatomy, vispy for time series.
Expected results: A set of classes usable within Jupyter notebook, for displaying common data objects via WebGL or WebGL-based libraries.
Skills: Python, WebGL, IPyWidgets, Jupyter
Mentors: Lia Domide, Paula Popa
TVB's main web site is http://www.thevirtualbrain.com/ and more technical documentation can be found at http://docs.thevirtualbrain.com/
We intend to participate in GSOC 2019 under the INCF organization, as we did in the past years. We thank INCF org admins for making this great experience possible for us! https://www.incf.org/collaborate/tool-development/google-summer-of-code