Octopus Learning and Behavior

Hi, I’m Ilya Chugunov, a rising sophomore at UC Berkeley, majoring in Electrical Engineering and Computer Science. My hobbies include: hiking, archery, and pondering deeply about why my code doesn’t compile. As a member of the Backyard Brains fellowship this summer I will be studying the fascinating, and possibly unseen, behaviors of the California Two Spot Octopus (Octopus Bimaculoides).

Classifying and understanding animal behavior has been a hot-topic endeavor of biologists since even before the great Charles Darwin, but historically has very often been assays with pen on paper note taking. With recent developments in both the processing power of your average computer and the mathematics behind this processing, machine-learning has sprung up as a powerful tool to help us see beyond what our brains can comprehend. We now have the novel ability to find patterns in everything from the behaviors of lab rats or communication of cuttlefish chromatophores without having to introduce the arduous task of a scientist to list through thousands of frames of video.

With my project I plan to do exactly this, to collect a plethora of video data of Bimac Octopodes and use computer-vision and machine-learning techniques to extract behaviors from this video without biasing it via human intervention.

Below is an example of some of my work so far; using background subtraction, erosion, and Gaussian filtering I am able to transform a recording of a moving animal (in this case a squid) into an easily trackable contour entity, and then create a graph of its movement pattern (on the bottom).

 Additionally, I have a working algorithm to detect and quantify breathing patterns in a resting octopus. It transforms the video stream of the octopus (top) into a graph of detected motion vs frame number (center), which when then smoothed with the Blackman-Harris window function, allows us easily to deduce the time between breaths, in this case, 6.67 seconds (bottom).

I hope to continue to develop tools for octopus video analysis in this coming month and to discover more and more the hidden patterns in this beautiful animal’s behavior. I am especially excited to look into quantifying their problem-solving skills through various intellect challenging exercises (like letting them explore a maze!).

Welcome 2017 Backyard Brains Fellows!

From left to right: Top: Greg Gage (Not a Fellow), Zachary, Jaimie, Spencer, Nathan, Ilya Bottom: Joud, Christy, Haley

It’s early on a warm Ann Arbor morning and the office is buzzing with excitement! Our Summer 2017 research fellows are here! Today, our fellows are getting to know the staff and space at Backyard Brains, but more importantly, they’re planning, because for the next ten weeks they will be working on neuroscience and engineering research projects. The projects include work with Squids, Songbirds, Dragonflies, Mosquitoes, EEG recordings, and Electric Fish. The fellows work to create inexpensive, DIY methodology (the BYB way) to tackle their research problems and then present their findings at a poster presentation and in a journal publication. The fellows also develop experimental-grade versions of their projects so that other students and teachers can perform the experiments themselves!

Meet the Fellows, See the Projects

The fellows are off to a great start! Check out their blog posts introducing their projects:

• Zach – Identifying Bird Songs
• Ilya – Octopus Learning and Behavior
• Spencer –Optogenetics with the FlyPad
• Jaimie – Electrophysiology of Dragonflies
• Nathan – Decoding Images in the Brain
• Christy – Behavioral Study of Baby Squids
• Joud – Improving Memory Formation During Sleep
• Haley – Learning about the Mosquito Love Song

Progress

 The team has been working hard to bring their projects to life. Check out these blog posts on their rig construction and data collection efforts!

• Zach – When Computers Hear the Birds Sing
• Ilya – Studying Aggressive Behavior in Octopodes
• Spencer –The Taste Preferences of Fruit Flies
• Jaimie – Recording from the Visual Neurons in a Dragonfly
• Nathan – Detecting the Detection of Faces
• Christy – Recording the Behavior of Squid Hatchlings
• Joud – Learning and Deep Sleep
• Haley – Harmonics of Mosquito Mating

After a morning of introductions and orientation, we took a quick break for lunch, then hurried back to the office to perform some recordings. For many of our fellows, working with our SpikerBoxes was their first opportunity to perform real neuron recordings! This is just the beginning of a summer of hands on science, rapid prototyping, troubleshooting, and data collection.

Quick Italian Buffet for Lunch

Recording from Earthworm neurons. Spikes!

As part of the fellowship, the students will be keeping you updated with frequent blog posts. These posts are a great window in the world of research! From start to finish, you can follow along with our fellows as they experience the triumphs and pitfalls of scientific inquiry.

You’ll be hearing a lot about our fellows and their projects for the next ten weeks. They’re excited to introduce themselves and their projects to you soon. Keep an eye out here, on our Facebook page, and Twitter for project updates and more!