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How to Get Reeled into NeuroDuino – a Mathematician’s Guide (Part II)

Neuroduino
A NeuroDuino, Backyard Brains’ latest prototype

Hi there, it’s Natalia Díaz again with an update to my neuromathematical (yes, such a thing exists!) project. If you don’t remember me, I’m a student of Mathematical Engineering at the University of Santiago de Chile and I’m doing my internship here in BackyardBrains.

Since the last time we met (you and I, that is), BYB co-founder Tim Marzullo sent me some cool stuff. Not that it’s an exclusive privilege of interns, mind you! Anyone can find them in the “Muscle SpikerShield Bundle” kit.

With this bundle, you can do several very entertaining experiments such as seeing on your smartphone the action potentials that are produced when you move your muscles. You can also use the Muscle SpikerShield to control video games, robotics, and musical instruments.

It took a while for my board to pass customs, but it managed to arrive and we got to work right away. What I was most excited about was the arrival of new prototype from Backyard Brains – their very own customized Arduino board – codenamed NeuroDuino. (See above how handsome it is!)

Ben Antonellis, a guy who works for Backyard Brains, had created certain functions for a new interface called “NeuroBoard” that will make it easier for users to write working code for the Muscle SpikerShield / NeuroDuino. But the functions needed to be tested and verified by someone other than the principal developer. So, Tim asked me to do the testing and document the process.

Then came testing, testing, testing…

Testing Neuroduino
Natalia, Tim, Python and masks

So what we did at the beginning was try to understand the code that Ben created, where he explained to us a bit what each function should do. For this, we use the Arduino and C ++ programs. For example, we have commands to:

  • Start measurements
  • Find the greatest value of the channel measurements
  • Define the channel that we are going to use (if we select a different one from the one used, there will be no measurements)
  • Function to determine which button is pressed
  • Etc. (Still letting our imagination run wild!)

At first, we had a little trouble at understanding the commands and nomenclature, but we managed to test several of the pre-made functions. However, some did not work for us, so we asked Ben to help us figure out what we were doing wrong.

Ben helped us right away, tweaked the code a bit, and finally the three of us were able to test all the functions. Most of them worked well and some have yet to be modified. But we made a breakthrough, and now most of the code is tested and verified save for a relay function that’s still patiently waiting for its 15 minutes (or hours) of fame.

We are almost done with this phase of my internship, and for the rest of February, my final month, I will be looking into some custom Python analysis scripts.

Tim and I have been working remotely for the past two months, but we finally had a chance to work face-to-face this week (with social distancing and masks of course). The picture above shows how it went.

Stay tuned for my final blog post update at the end of February!


How to Get Reeled in By Neuroscience – a Mathematician’s Guide (Part I)

how to get reeled in by neuroscience

What lies at the intersection of math and medicine? Why many things, of course. Certainly more than could possibly fit into a blog post! But today, I am going to talk about the connection between brain function and numbers.

My name is Natalia Díaz and I am a student of Mathematical Engineering at the University of Santiago de Chile. Ever since I can remember, I have been tantalized by mathematics and medicine (especially brain function). The opportunity to mix both subjects finally arose when I entered college. That is how Neuroscience popped into my life!

To get my degree, I must complete my internship and my thesis. That’s how I started working with my mentors Dr. Patricio Rojas (University of Santiago) and Dr. Patricio Orio (University of Valparaíso). We are investigating, through numerical simulations, the effect of the electrical synapse topology between inhibitory neurons.

For this, we use a neural mathematical model of a mixed network of inhibitory and excitatory neurons of the cerebral cortex, and we study different types of topology (“all with all” or lattice style) of connection between inhibitory neurons characterizing the patterns obtained.

For example, the figure below shows a significant difference in network synchronization using different topologies. In the first yellowy-whitish graph, there is no gap junction (electrical synapse). The second shows a gap junction with a lattice topology, and in the last one we apply a gap junction with an all-to-all topology. To plot this, we use different values for the mean synaptic strength between excitatory neurons (mGsynE) and for the mean synaptic strength between inhibitory neurons (mGsynI). Lots of abbreviations, I know. But I promise they are fun!

neuroscience math medicine
The network synchronization using different topologies of connection between inhibitory neurons.

As I was researching internship opportunities, Dr. P. Rojas told me about Backyard Brains, a go-to company for those who want to tackle neuroscience through mathematics. As for my project, I will be working on our next generation interface products. Coding Neural Interfaces for beginners can be difficult to understand, so I’ll help make the interface by testing an Arduino library Backyard Brains has developed, seeing how easy it is to use, trying to “break” it, and improving the documentation on the library.

This way, someone using our Arduino -based products won’t have to start from scratch as they learn to control devices like robotics, computers, musical instruments, and video games with the signals of their bodies (EOG, EMG, EKG, and EEG). My project will last until the end of January, and depending on my time, I may roll up my sleeves and get into some Python data analysis programming, a long-standing data analysis dream for the Backyard Brains team.

In my spare time (before COVID), I used to travel to my mother’s house in Pichidegua (VI Region), where we’ve always got together as a family and had a good time, as you can see in the above photo. Yes, there are many of us – try to find me! But now due to the quarantine, I have only been in Santiago, which I also love because I can spend time with my boyfriend, Luis. He is very funny, and he’s also a mathematician.