Brain Voyager 🚀🧠

transparent img

Overview

What ?

We created Brain Voyager, a way to view data visualizations in a 3D space.

We have made 3 data visualizations:

  • Loose Representation of the Brain (Allen Dataset)
  • Live Updating Bar Graphs (SynapTech Data)
  • Brain Representation

Why ?

To encourage data literacy by providing an engaging medium to view and understand important data.

Context on the allen dataset

The Allen Mouse Brain Connectivity Atlas provides comprehensive information about the connectivity patterns of neural circuits in the mouse brain. This dataset includes anatomical tracing data, synaptic connectivity maps, and connectivity matrices for different brain regions. Visualizing brain connectivity patterns in VR can help users explore the structural and functional organization of neural circuits and understand how information flows through the brain.

Check out the Allen Mouse Brain Dataset Below

mouse friend

Our Process

Selecting a dataset

We chose the Allen Mouse Brain Connectivity because we were the most interested in looking at how brain connectivity works!

Preprocessing Data

We followed sample code from Allen SDK to get all the relevant data.

Model Creation

From the data we extracted in our processing, we used the x, y, and z coordinates to create a 3D model of corresponding squares, which is a loose representation of the brain. We generated obj files based on regions of brain as well as Shader files for colors of each region.

For our second visualizations, live brain data updating, we created around 40 bargraphs at different instants of time to string together in an animation.

Creating the Visualization

To create the actual visualization, we imported our models into Unity.

rocket

Future Goals

Being able to browse through different datasets

We hope also hope to add the ability to view other datasets! Here are some examples that are also from the Allen Institute

  • Allen Human Brain Atlas
  • Allen Cell Database
  • Allen Brain Observatory

Making a More Robust Model

Due to time constraints, we weren't able to make our mouse brain 3D model as robust as we would`ve hoped!

Specifically we hope to:

  • Get nrrd files of the mouse brain from Allen SDK
  • Use package “pynrrd” to transfer nrrd to numpy arrays
  • Generate obj files that can be used in Unity with the numpy arrays
  • Have a human brain model thats color coded by region

Recording Live Brain Data

Finding a way to record live brain data, with something like Open BCI, to be able to contiunuously update the brain data that is viewed.

Skills Learned / Used / Practiced

Languages

  • C#
  • Bash
  • Python

Modeling

  • SolidWorks
  • F3D
  • Blender
  • Unity
  • GPU Programming

Processing_Data

  • Allen SDK
  • Excel

Website

  • JS (React, Next.js, Node.js)
  • CSS (TailwindCSS)
  • HTML

Photo Gallley

  • graphic

    Loose Representation of the Brain

  • graphic

    In the future we hope to maken a 3D model of a color-coded (by section) human brain!

  • graphic

    Process Photo - trying to get one consistent face.

  • graphic

    Process Photo - trying to get one consistent face part 2!

1 of 5