GSoC Project Idea 4.2: Reusable visualization tools for Jupyter

jupyter
webgl
ipywidgets
python
#1

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.

Skills: Python, WebGL, IPyWidgets, Jupyter

Mentors: Lia Domide & Paula Popa, The Virtual Brain project.

2 Likes
#2

Check these preview:
https://github.com/the-virtual-brain/tvb-documentation/blob/master/manuals/UserGuide/screenshots/visualizer_dual_seeg_and_regions.jpg
https://github.com/the-virtual-brain/tvb-documentation/blob/master/manuals/UserGuide/screenshots/simulator_phase_plane_interactive.jpg

#3

Hello there.

My name is umar harun abdullahi.
I am the one selected to participate on this project.

WEEKLY REPORT.

  1. What did you get done this week?
    Write TVB visualization list/inventory recommended by mentor.
  2. What do you plan on doing next week?
    Finished the visualization and start the actual project.
  3. Are you blocked on anything?
    No.

#GSoC_2019 #gsoc

#4

Hi Umar, thanks for posting. Could you please put the ‘GSoC_2019’ category on this, so it pops up in the students-mentors group for 2019?

Thanks
Malin

#6

Hi, I’ve added you to the GSoC_Students group. This group has access to the private mentor+students 2019 group in the category GSoC_2019. Please put that tag on your future posts!

Best
Malin

#7

WEEKLY REPORT.

1. What did you get done this week?
Start writing the skeleton of anatomical visualization to become reusable to
jupyter notebook with the support of webgl(XTK).

2. What do you plan on doing next week?
Continue with the anatomical visualization.

3. Are you blocked on anything?
No.

#GSoC_2019 #gsoc

#9

WEEKLY REPORT.

1. What did you get done this week?
Working on XTK https://xtk.github.io to run Jupiter notebook latest version.

2. What do you plan on doing next week?
Finalize the running on xtk on Jupiter

3. Are you blocked on anything?
No

@GSoC_2019 #gsoc

#10

WEEK (4) WEEKLY REPORT.

1. What did you get done this week?
Finalize the running on xtk on Jupiter and continue working on tvb notebooks visualization method inventory

2. What do you plan on doing next week?
Finalize the TVB notebooks visualization method inventory and start another branch of the project

3. Are you blocked on anything?
No

#GSOC_2019 #gsoc