GSoC 2020 project idea 3: TVB: Reusable visualization tools for Jupyter

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 relevant 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:

  1. anatomical visualization (surface, connectivity)
  2. time series viewer
  3. 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. Documentation and usage examples for all created classes.

Skills: Python, WebGL, IPyWidgets, Jupyter

Mentors: Gabriel Florea, Bogdan Valean

2 Likes

Hello. Interested to work on this project. Could you please let me know how to start with it?

Hello Shubhank, I’m tagging @liadomide who will ping her mentors and/or get back to you. In the meantime, TVB has lots of demos here to hep you get more familiar with the platform: http://docs.thevirtualbrain.org/demos/Demos.html# /Malin, org admin

Thank you, Malin, you gave the very good first step.
I would add to that a further step, particular for this project, by pointing to our existing, but very slim module for ploting in the notebooks: https://github.com/the-virtual-brain/tvb-root/tree/master/scientific_library/tvb/simulator/plot
This module is something we want redone, but it can be regarded as a starting point, to learn from it.

Hi, are there any Pre-GSoC issues to begin with?

Thanks for sharing the module, it helps to better understand the project.

We have no other issue for the student then to study the package and write a good proposal for GSOC submit.
We appreciate to have the proposal draft shared in advance, for being able to comment, ask early questions or be able to guide the student.

This is Sanjiban Sengupta, sophomore in Computer Engineering from IIIT Bhubaneswar, India, would like to contribute to INCF for GSoC’20, I have practical and working knowledge of C, C++, Python and Java, for web, I am familiar with HTML, CSS, JS, Bootstrap and frameworks such as ReactJS and NodeJS, also i am acquainted with concepts of ML and AI, Linux Kernel and know the technicalities to apply these to solve modern real life problems.

On going through the project proposals, I found the project TVB: Reusable visualization tools for Jupyter interesting to work upon and contribute and thus will be thankful for your kind guidance.

Thus I request the mentors to kindly guide me for the beginning processes.

Hi There.
Sadly I am not able to completed the project last year, I wish to completed it this year.

1 Like

hello to everyone.
i’m very interested in this project.
actually my graduation project is reconstructing images from human brain activity.
so i know how important is the visualization in projects like this . this is why i’m very interested about the project.
but i’m too late is there any chance that i will be able to write a good proposal and get accepted???
thank you in advance.

yah you can give it a try.

thanks for your reply.
but i will definitely need your help to write the proposal
thanks in advance.

Ok No problem, I will, count me in.

is there’s an easier way to communicate with you???

Sorry for the late Reply, and its almost 5 minutes remains.

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