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MATLAB <3 BYB + Arduino

Why buy, when you can build? Madhu Govindarajan of MathWorks recently used one of our old products to make his very own heart rate detector. The Heart & Brain SpikerShield (recently replaced by our Heart and Brain SpikerBox) was designed to help the user view and record the action potentials of their heart easily, and Madhu has harnessed this basic concept to create his own heart rate detector.

In the demo, Madhu explains how to use the MATLAB and Simulink programs to filter the raw ECG, compute the heart rate value, and display it on a thin-film-transistor LCD screen (very high resolution, with a transistor for each pixel), called a TFT screen. The actual TFT screen is available here, and Madhu’s team used the libraries available as well as their own custom modifications to create a recognizable ECG display. Sounds very BYB, if we do say so ourselves.

MATLAB (matrix laboratory) is a programming language developed by MathWorks used by neuroscientists and engineers alike to do a lot of data analysis. It’s a powerful tool that pairs nicely with open source gear like ours, and there are accessible versions available to young coders for learning and development. This example is a higher-level high school or undergrad experiment, and we are excited to see ways in which we can expand use for the high school level! For more information on using MATLAB in schools, check out this Mathworks webpage.

MathWorker Tom Bryan primarily worked on the signal processing code behind the video, and he had this to say about our work: “BYB will be my go-to for neuroscience hardware from now on, because they are the only reliable company making good products.” Thanks for the high praise, Tom!

We love to hear your stories. If you have done something cool with our gear, drop us a note at hello@backyardbrains.com to brag about it a little!


Intracellular recording in Snails Final Update – Juan Ferrada

Hi Everyone. Juan here! My two month tour with Backyard Brains has reached its end, and I’m really grateful to have had the opportunity to work on this project.

I had three activites during the “practica” here at Backyard Brains:

  • Recording from the Ganglia of Snails
  • Helping on the Anemone Project
  • Assisting in Outreach.

The snail recording was my main project at 70% of my time, the anemona project occupied about 10% of my time, and the high school outreach was 20%.

Recording from Snails.

The original aim was to record the intracellular action potential of pacemaker-like cells from the parietal ganglia of Helix aspersa, using Backyard Brains hardware for the optics, acquisition and amplification. From the last blog post you can see that we had no problem with dissecting the ganglia or visualizing the neurons with hand pulled pipettes in the microscope, but we couldn’t get any recordings. Recording electrical activity from the leg of the cockroach is different from the ganglia of the snail. Because of the dry environment of the cockroach leg and the strong signal from the leg nerves, the cockroach leg nerve activity is very easy to record. Buuuuut with the snail, we have a really weak signal in a conductive aqueous salt solution, so we must take a different approach to the experiment, as repeated attempts at the BYB lab did not yield results.

Sooo we went to familiar ground (for me) and replicated the experiment with lab equipment from the Laboratorio de Neurociencias at the University of Santiago (Usach). We had divine intervention from Darwin Contreras, a PhD student who just that day had successfully defended his Ph.D. and happened to only be coming back to the lab to get his motorcycle helmet to go motor on home and relax with his growing family. Using a large Faraday cage, a dissection scope, and a high end manipulator (but yes, a Backyard Brains Neuron SpikerBox Pro), we carefully inserted an insulated  blunt tip silver wire into the ganglia.

 

And we listened to the low background noise coming out from the speaker of the SpikerBox. But….Every now and then there was a rattle, sparse and random enough to not be an artifact, so we recorded it and to the surprise of everyone there it was, spontaneous, asynchronous action potentials. Success!

We witnessed high amplitude spiking (download the raw data if you like!).

And we also witnessed the rhythmic “neuron dying” response.

 

But this was only a partial success, as it was 1) our only successful recording, and 2) made extracellularly instead of intracellularly. We found a shorter electrode, to prevent the antenna effect, and a faraday cage minimized the noise profile, but we are still far away from the original goal, recording intracellularly from the large neurons in the parietal ganglion.

At the moment, we may seek another preparation for intracellular single unit recording, as the snail preparation is a bit tricky. We may go to the intracellular recordings of the muscles of the tail of the crayfish, or perhaps try another mollusk, say a “macha,” a type of clam very common along the Chilean and Peruvian coast, that we looooovvveeee to eat.

Recording from the Nervous System of Anemones

We continue in the long term project to record from sea anemones. We built a harpoon style electrode…

 

but the silver wire wasn’t strong enough to pierce the membrane of the oral disc of the anemone. We had heard that there are more neurons around the oral disc (which, in an anemone, serves as its mouth, anus, and reproductive orifice). We will try tungsten next, which is the classic, strong material for small metal electrodes.

But….we had the idea that maybe we could remove the tentacles, like we remove the leg of the cockroach, and attempt a recording in a more controlled environment under a microscope. To our surprise, the tentacles kept moving for an hour  after we had cut them! We may be on to a new preparation, it is very fascinating to watch. Very primordial success, yet waiting, yet to come. See our video below.

We then inserted an insulated blunt tip silver wire into the open end of the tentacle and tried to see if we could measure spontaneous activity or evoked activity (when we touched the tentacle with a probe).

 

But….we did not get any successful neuron recordings. We are sure there is something here though, there have got to be neurons inside the tentacle. The tentacle is moving, and neurons must be talking to the muscles. The neurons in the anemone tentacle are arranged like sheets between rings of muscle, so it’s a matter of optimizing the preparation. We are always getting closer to the elusive anemone neurophysiology, stay tuned.

Outreach

During the last part of May we taught the students how to build a two stage amplifier circuit from a breadboard, and the students can now recognize the logic of how to manage components like resistors, capacitors, and transistors.

During the last two classes I helped teach about the difference between reactions and reflexes using the knee and elbow.

For the last class, we did experiments measuring the difference between audio and visual reaction times. Data collected in a classroom can be noisy. Supposedly auditory reactions are faster than visual reaction times but we did not observe that difference in the students who had well tabulated data. But I always continue in my experiments. I always continue trying to have compelling data that tells an interesting story.

Bye Guys, Now I have to write my thesis! I’ll miss the late night pizza party experiment sessions with Florencia and Tim and the workshops in the Fablab at the high school Colegio Alberto Blest Gana. I will not miss the cardboard-tasting garlic bread  (pizza delivery company to remain anonymous).

 


Intracellular recording in Snails Midterm Update – Juan Ferrada

Hi! Juan Ferrada here from the University of Santiago again to give you an update on my project with Backyard Brains.

Main Project – Single unit recording from Snail Neurons

First mission – Isolate the Neurons

As we spoke of a month ago, we are trying to record the individual neurons of the giant pacemaker cells of the parietal ganglia of the common garden snail Helix aspersa. Our first step is to isolate this ganglia so we can visualize the famously large F1 neurons, that can reach up to a crazy big 200 um in diameter. After anesthetizing the snail with magnesium chloride, we began the preparation.

Here we can see the exposed cerebral ganglion and parietal ganglion. They are the highly white structures around the yellowish-white esophagus.

We removed the ganglion, and you can see it is surrounded by connective tissue. Using fine #5 forceps, we slowly picked away the tissue…

until, looking at the sample below a RoachScope at high mag, we see what appear to be a cluster of spheres. These, my friends, are the neurons we are looking for.

Second mission – Get an electrode close to the neurons

Now that we have the neurons in our sights, we have to get an electrode near it, not so easy when the sample is under our microscope. Luckily, we used the Backyard Brains Manipulator to move a glass pipette that we made just by holding a hollow borosilicate glass tube (part number 615000 – 1.0 mm x 0.75 mm) over a lighter and pulling it apart in the flame to make a very fine tip. Using the manipulator holding the electrode, we have just enough clearance to move between the sample and the microscope.

We can easily see the pipette tip on our smartphone looking through the RoachScope lens, and we can manipulate the electrode to come close to our neurons, attempting to insert them into the neurons. You can see a brief video of electrode movement below.

Third mission – Get a recording

We have the neurons, we have the electrode, we have the microscope, we have the manipulator. Now it is time to do the recording. This is my trial by fire, the hardest part of the whole experiment. The plan is to stab the cell with a high resistance glass electrode, then listen and record the spontaneous action potentials. Unfortunately, so far we are only getting noise, but we are slowly improving the amplifier setup, experimenting with electrode styles, reducing 50/60 Hz noise, and chasing the dragon of weak signals. We keep trying to catch it. Stay tuned!

Side-Project – Recording from Sea Anemone Tentacles
Since we are dealing with glass microelectrodes and amplifying signal in a noisy watery environment, I have also been working with the Backyard Brains team on a project they have had in mind for a long time – extracellular recordings from the tentacles of sea anemones. The lab has been caring for 9 anemones (taken from the intertidal zone near Algarrobo, Chile, an understudied organism called Anemonia alicemartinae). Over the past four months, the Backyard Brains team has been learning how to maintain a prosperous anemone colony. Since these are Humboldt current creatures, they like their water cold. So we have a trick to keep the aquarium under 20 degrees Celcius by having a fan always blowing air over the water. To further keep the anemones healthy we feed them surf clam meat every day, and clean the tank entirely, replacing and remixing the salt water, every 4-6 weeks.

We were originally using long silver wire (32 gauge) inside our pipette but it turned out to be brittle and the insulation susceptible to breaks and shorts, causing a lot of noise. We switched to flexible 30 gauge copper Minatronics wire that we threaded into a glass pipette, sucked up a tentacle, and recorded….nothing. To try to evoke a response, we touched the anemone trunk with a glass probe, but we did not register any electric activity in the tentacles.

Our next step is to try to insert an electrode near the oral disc, where we have read that more neurons are present.

Outreach

Any Backyard Brains internship has an outreach component, and I have been helping Backyard Brains teach classes in Colegio Alberto Blest Gana in San Ramón, Santiago. In the past few weeks we have been teaching the students, ranging from 11-17, how to read circuit diagrams and use broadboards. We are building electromyogram amplifiers from scratch. I have learned more about electronics in 1 month than all the combined previous months of my life!

Now we are deep in the experiments, and we will update you at the end of May.