Hi! I’m Shreya and I just graduated from the Dwarkadas J. Sanghvi College of Engineering affiliated to the University of Mumbai in Electronics Engineering. During the last two years of my undergraduate study, I spent most of my vacations, free time and some weekends working as a research intern at the Indian Institute of Technology (IIT) Bombay where I completed several computer programming and embedded electronics projects. My undergraduate capstone project had me working with Artificial Neural Networks for ECG beat classification. This project was also completed at and funded by IIT Bombay.
Me on a train in India (during our final year class trip to Rishikesh)
Recently I have been really interested in neuroscience and EEGs, which is how I discovered Backyard Brains. I had been following their blog and Facebook posts for a few months, and that’s how I found out about this internship! I joined Backyard Brains on 12th June (got delayed because of final exams!) and I will be working on the Electric Fish project here for six months. This is my first time in the USA and so far, it’s been great! I’ve been enjoying the climate here – it’s a good change from the intense summer heat in Mumbai. I also love how Ann Arbor has so many different flower species!
Me and some beautiful flowers in Ann Arbor
Electric fish are a really interesting type of animal that can generate and detect electric fields around them to either stun prey or to communicate with other electric fish, detect objects and navigate. However, finding them and tracking them can be difficult, and many species have yet to be discovered! This project is aimed at building a device which can be deployed into the freshwater rivers of South America to detect and record the Electric Organ Discharges (EOD) of weakly electric fish as they swim past it. Each species has a unique EOD, which can be either wave-type or pulse-type. So, based on the nature of the recorded EOD, the species of the fish can be estimated and it can also be used to study the behaviour of the fish. This project is based on the research that Dr. Eric Fortune of the New Jersey Institute of Technology conducted in Ecuador. I will be using the Elephant Nose fish to test the device while prototyping.
Elephant Nose fish (source: Wikimedia Commons)
The Elephant Nose fish produces EODs which look like spikes when recorded using electrodes. So far, I have been able to amplify and see these spikes on an oscilloscope. I will be improving the filter and amplifier, using an Arduino to detect spikes in the recorded data, and saving this information along with time stamps on an SD card. Some of the challenges I will be facing while designing this are that the device needs to be waterproof and it should have power saving capabilities since it might have to run on batteries or solar energy for months at a time to be able to detect any electric fish.
Below are some of the spikes I recorded from the Elephant Nose fish as seen on an oscilloscope (along with 60 Hz noise).
I’m really enjoying working on this project here, at Backyard Brains, and I look forward to finishing this project!
Over the course of the next 10 weeks, I will be designing and running a neuroethological study on the electrical behavior of the South American weakly electric fish. My goal is to develop a Backyard Brains-esque tool to listen to, record, and manipulate the electrical discharge of the electric fish. I will be posting routine updates on my progress, documenting the successes and failures that I run into along the way.
For some basic background, weakly electric fish are capable of generating electric fields which allow them to navigate the environment and communicate with other electric fish.
Eigenmmania Virescens – Glass Knifefish (Photo by. Nadia Milan)
Weakly electric fish have an electric organ, typically located in their tail. This is what allows them to generate electric signals, also known as Electric Organ Discharge (EOD). These electric signals are in the range of millivolts and are used to communicate with other fish and in electrolocation, a process of navigating the environment by means of detecting objects and sources of external electric fields. What separates weakly electric fish from strongly electric fish is the strength of the EOD – strongly electric fish such as electric eels and rays can use their EODs to stun prey or defend themselves.
Electric Organ Discharge?
When in close contact with another fish emitting a similar frequency, weakly electric fish are effectively “blinded” (Watanabe & Takeda, 1963). In order to cope, the weakly electric fish has developed a jamming avoidance response (JAR) in which the fish will adjust their emitted frequencies to diminish electric field disturbances. For example, if two fish emit signal frequencies of 300 Hz and 304 Hz, the beat frequency will be too low (4 Hz) and cause too much interference between the fish. In this case, the fish with the lower frequency might push its frequency down to 292 Hz while the other pushes its frequency up to 312 Hz, resulting in a more ideal beat frequency of 20 Hz.
I plan to experiment with the JAR to further understand the neural mechanisms of these fish – I plan to stimulate the water to mimic the presence of other fish in the tank as a means to investigate. I would like test out the absolute range for these fish and figure out how to reliably set a fish at a certain frequency. There are many more interesting aspects of the weakly electric fish that I have yet to talk about, so stay tuned for more!
By. Davis Catolico
Hello my name is Bailey! I am a junior majoring in electrical engineering at Michigan State University and am doing an internship at Backyard Brains this summer. Sorry I missed the first blog post, I was travelling in Japan with my sister!
Left-my sister, Right-me
I know it doesn’t look like it from the picture, but I was doing some important background research for my project.
I mean…circuits were involved
Ok, so it was just for fun.
After getting over my jetlag it was time to get back to work. My project this summer involved mormyrid fishes. What’s so special about these fish? Mormyrid fish are awesome because they both emit and detect electric signals. Unlike an electric eel, however, their electrical discharges are too weak to harm other fish. Instead, they use electric signals to navigate their environment, which is naturally very cloudy, and communicate with each other. A lot can be learned about these fishes’ behavior and even evolutionary history just by studying their electric organ discharges (EODs). Unfortunately the equipment used to record their EODs is quite costly, often prohibitively so-especially for those who live in the same area as the fish. This is where we come in. My goal this summer was to build an inexpensive, easy to use, and open source device that can record EODs from weakly electric fish.
Since the EODs occur at very high frequencies, a simpler microcontroller like an Arduino is not sufficiently powerful to record their EODs in real time. Enter the BeagleBone Black.
The BeagleBone Black has a 1GHz processor and 4GB of storage (that can be supplemented with a micro SD card) as well as running a full Linux OS, making it perfect for collecting the EOD data.
Now I need something to convert the analog EOD signals to digital so that the BeagleBone can process them. For this project I am using the MCP3008 analog to digital converter. Initially, I started by using a cape that had the chip on it.
Analogs, prepare to be converted!
The cape worked well for testing the setup with low frequency sine waves, however, the inputs it normally connected to on the BeagleBone were not able to handle the high speed data collection I needed and the data was not being recorded in real time. To work around this issue, I had to individually connect each pin to the appropriate input on the BeagleBone. This lead to the setup appropriately nicknamed “The Shiva”.
Not pictured: the additional arms I grew to operate this setup
This setup allowed me to access the programmable real time units (PRUs) on the BeagleBone. PRUs are essentially microprocessors within a microprocessor that sit around eagerly awaiting a program to execute. Unlike the main CPU, the PRUs do not run Linux, allowing them to collect the data in real time. Now that I had my setup I was only missing one thing-the fish! A quick trip to the Electric Fish Lab at MSU and the newest additions to the Backyard Brains Petting Zoo, Tina and Taco, were ready for some data collection.
The one on the right with the goatee is Taco. Tina is on the left
I started recording by using the example code from chapter 13 on the Exploring BeagleBone website. The code filled up the PRU memory with data from the recording, and then used another program to read the data from the memory. Although this worked well, it was not what I wanted in terms of a final product. Using the example code as a basis, Stanislav Mircic, Backyard Brains’ ultra-programmer, and I modified it to continuously write the data to a circular buffer as well as simultaneously read the buffer and check if an EOD has occurred.
Now the program will record only the EODs, which is what we are ultimately interested in, instead of all of the raw data. Here’s an example of the output:
Now that I’ve verified what the circuit needs to be, I have to draw out the schematic so that a board can be printed in a form that can snap onto the BeagleBone.
My drawing of the circuit
And finally the actual board.
Goodbye Shiva! Only two arms needed for this one.
For the rest of the summer I will be modifying the circuit design to better suit the goal, such as altering the gain to match the type of recordings we’ll be getting, and preparing the device for field work by building a portable power source and a case that it can float in. Soon we hope for the device to be picking up lots of fish conversations from around the world! Stay tuned!