Hackaday Links: December 18, 2022

December 18, 2022 by Dan Maloney 27 Comments

By now everyone has probably seen the devastation wrought by the structural failure of what was once the world’s largest free-standing cylindrical aquarium. The scale of the tank, which until about 5:50 AM Berlin time on Friday graced the lobby of the Raddison Blu hotel, was amazing — 16 meters tall, 12 meters in diameter, holding a million liters of saltwater and some 1,500 tropical fish. The tank sat atop a bar in the hotel lobby and was so big that it even had an elevator passing up through the middle of it.

But for some reason, the tank failed catastrophically, emptying its contents into the hotel lobby and spilling the hapless fish out into the freezing streets of Berlin. No humans were killed by the flood, which is miraculous when you consider the forces that were unleashed here. Given the level of destruction, the displaced hotel guests, and the fact that a €13 million structure just up and failed, we’re pretty sure there will be a thorough analysis of the incident. We’re pretty interested in why structures fail, so we’ll be looking forward to finding out the story here.

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Fourteen-Legged Cell Carries Nature’s Tiny Computer

October 16, 2022 by Al Williams 12 Comments

Computers are, after all, frighteningly complex state machines. Quite of bit of the software we write can be modeled as a state machine, too. A great technological achievement by humans? Turns out, state machines exist in some of nature’s tiniest natural computers, according to biologists studying Euplotes eurystomus, a kind of water-dwelling eukaryote. This single-cell organism uses fourteen protolegs known as cirri that move in a particular gait, in response to certain stimuli.

As you might expect, a single-celled organism doesn’t have the infrastructure to support a brain, so scientists wondered what could control the way the beast walks using the cirri. The answer was fibers made of bundles of microtubles that acted as a mechanical state machine.

While we are used to state machines using bi-stable electronic elements, older machines often used cams and microswitches along with a timing motor. For example, a phone answering machine might have a three-minute motor. One cam would depress a micro switch to run the outgoing message for 15 seconds. Then another cam would depress a microswitch to start recording, and a final switch and cam would keep the motor running until the very end. To start the process, a ringing phone would goose the motor so that that last cam engaged. Simple and no computer needed. The “brain fibers” of the Euplotes seem to work in a similar way. They enforce which states can be reached from what other states and react to outside stimuli, as well.

Is any of this practical? Maybe not, although we often see technology mimic biological systems. But we can’t help but wonder if future microscopic-scale machines might not need this same sort of mechanical state machine for many purposes, including locomotion.

You can apparently make single-cell organisms your servants, more or less. We’ve covered state machines many times if you need a refresher.

Tube Tumbler Provides The Perfect Culture

March 27, 2022 by Brian McEvoy 2 Comments

We’ve all had to shake jars of nail polish, model paint, or cell cultures. Mixing paint is easy – but bacteria and cells need to be agitated for hours. Happily, laboratory tube tumblers automate this for us. The swishing action is handled with rotation. The vials are mounted at angles around a wheel. The angular offset means the tubes are inclined as they rise, and declined as they fall. This causes the liquid in the tube to slosh from one side to the other as the wheel rotates. [Sebastian S. Cocioba] aka [ATinyGreenCell] released his plans through Tinkercad and GitHub, and with a name like Sir Tumbalot, we know he must be cultured indeed.

Grab your monocles. Version 2 features a driven wheel lined with magnets to attach tube adapters, and he’s modeled 50mL and twin 15mL tube holders. The attachment points look like a simple beveled rectangle with a magnet pocket, so if you’re feeling vigorous for vials, you can whip up custom sockets and tumble any darn thing. A Trinamic StealthChop chip on a custom PCB controls the pancake stepper, and the whole shebang should cost less than $50USD. We’re wondering what other purposes this modular design could have, like the smallest rock tumbler or resin print rinser.

Making lab equipment is phenomenal for saving money for things that just spin up to a biotech lab.

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PiSpy, The Camera Setup Designed To Make Biological Observations Better

March 24, 2022 by Dan Maloney 3 Comments

Back in grad school, we biology students were talking shop at lunch one day. We “lab rats” were talking about the tools of the trade, which for most of us included things like gel electrophoresis, restriction endonucleases, and polymerase chain reaction. Not to be left out, a fellow who studied fire ants chimed in that his main tool was a lawn chair, which he set up by a Dumpster in a convenience store parking lot to watch a fire ant colony. Such is the glamor of field biology.

Ants on the march. Tough luck for the crickets, though.

What our colleague [Mike] wouldn’t have given for something like PiSpy, the automated observation tool for organismal biology by [Greg Pask] of Middlebury College, et al. As discussed in the preprint abstract, an automated imaging platform can be key to accurate observations of some organisms, whose behavior might be influenced by the presence of a human observer, or even a grad student in a lawn chair. Plus, PiSpy offers all the usual benefits of automation — it doesn’t get tired, it doesn’t need to take bathroom breaks, and it can even work around the clock. PiSpy is based on commonly available components, like laser-cut plywood and a Raspberry Pi and camera, so it has the added advantage of being cheap and easy to produce — or at least it will be when the Pi supply picks back up again. PiSpy takes advantage of the Pi’s GPIO pins to enable triggering based on external events, or controlling peripherals like lights or servos.

While built for biological research, there are probably dozens of uses for something like PiSpy. It could be handy for monitoring mechanical testing setups, or perhaps for capturing UI changes during embedded device development. Or you could just use it to watch birds at a feeder. The source is all open-sourced, so whatever you make of PiSpy is up to you — even if it’s not for watching fire ants.

When Hacking And Biosensing Collide

December 24, 2021 by Elliot Williams 2 Comments

[Prof. Edwin Hwu] of the Technical University of Denmark wrote in with a call for contributions to special edition of the open-access scientific journal Biosensors. Along the way, he linked in videos from three talks that he’s given on hacking consumer electronics gear for biosensing and nano-scale printing. Many of them focus on clever uses of the read-write head from a Blu-ray disc unit (but that’s not all!) and there are many good hacks here.

For instance, this video on using the optical pickup for the optics in an atomic force microscope (AFM) is bonkers. An AFM resolves features on the sub-micrometer level by putting a very sharp, very tiny probe on the end of a vibrating arm and scanning it over the surface in question. Deflections in the arm are measured by reflecting light off of it and measuring their variation, and that’s exactly what these optical pickups are designed to do. In addition to phenomenal resolution, [Dr. Hwu’s] AFM can be made on a shoestring budget!

Speaking of AFMs, check out his version that’s based on simple piezo discs in this video, but don’t neglect the rest of the hacks either. This one is a talk aimed at introducing scientists to consumer electronics hacking, so you’ll absolutely find yourself nodding your heads during the first few minutes. But then he documents turning a DVD player into a micro-strobe for high speed microfluidics microscopy using a wireless “spy camera” pen. And finally, [Dr. Hwu’s] lab has also done some really interesting work into nano-scale 3D printing, documented in this video, again using the humble Blu-ray drive, both for exposing the photopolymer and for spin-coating the disc with medium. Very clever!

If you’re doing any biosensing science hacking, be sure to let [Dr. Hwu] know. Or just tear into that Blu-ray drive that’s collecting dust in your closet.

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Microfluidics For Biohacking Hack Chat

July 5, 2021 by Dan Maloney 2 Comments

Join us on Wednesday, July 7 at noon Pacific for the Microfluidics for Biohacking Hack Chat with Krishna Sanka!

“Microfluidics” sounds like a weird and wonderful field, but one that doesn’t touch regular life too much. But consider that each time you fire up an ink-jet printer, you’re putting microfluidics to work, as nanoliter-sized droplets of ink are spewed across space to impact your paper at exactly the right spot.

Ink-jets may be mundane, but the principles behind them are anything but. Microfluidic mechanisms have found their way into all sorts of products and processes, with perhaps the most interesting uses being leveraged to explore and exploit the microscopic realms of life. Microfluidics can be used to recreate some of the nanoscale biochemical reactions that go on in cells, and offer not only new ways to observe the biological world, but often to manipulate it. Microfluidics devices range from “DNA chips” that can rapidly screen drug candidates against thousands of targets, to devices that can rapidly screen clinical samples for exposure to toxins or pathogens.

There are a host of applications of microfluidics in biohacking, and Krishna Sanka is actively working to integrate the two fields. As an engineering graduate student, his focus is open-source, DIY microfluidics that can help biohackers up their game, and he’ll stop by the Hack Chat to run us through the basics. Come with your questions about how — and why — to build your own microfluidics devices, and find out how modern biohackers are learning to “go with the flow.”

Our Hack Chats are live community events in the Hackaday.io Hack Chat group messaging. This week we’ll be sitting down on Wednesday, July 7 at 12:00 PM Pacific time. If time zones have you tied up, we have a handy time zone converter.

[Featured image: Cooksey/NIST]

Webcam Heart Rate Monitor Brings Photoplethysmography To Your PC

December 25, 2020 by Adam Zeloof 31 Comments

It seems like within the last ten years, every other gadget to be released has some sort of heart rate monitoring capability. Most modern smartwatches can report your BPMs, and we’ve even seen some headphones with the same ability hitting the market. Most of these devices use an optical measurement method in which skin is illuminated (usually by an LED) and a sensor records changes in skin color and light absorption. This method is called Photoplethysmography (PPG), and has even been implemented (in a simple form) in smartphone apps in which the data is generated by video of your finger covering the phone camera.

The basic theory of operation here has its roots in an experiment you probably undertook as a child. Did you ever hold a flashlight up to your hand to see the light, filtered red by your blood, shine through? That’s exactly what’s happening here. One key detail that is hard to perceive when a flashlight is illuminating your entire hand, however, is that deoxygenated blood is darker in color than oxygenated blood. By observing the frequency of the light-dark color change, we can back out the heart rate.

This is exactly how [Andy Kong] approached two methods of measuring heart rate from a webcam.

Method 1: The Cover-Up

The first detection scheme [Andy] tried is what he refers to as the “phone flashlight trick”. Essentially, you cover the webcam lens entirely with your finger. Ambient light shines through your skin and produces a video stream that looks like a dark red rectangle. Though it may be imperceptible to us, the color changes ever-so-slightly as your heart beats. An FFT of the raw data gives us a heart rate that’s surprisingly accurate. [Andy] even has a live demo up that you can try for yourself (just remember to clean the smudges off your webcam afterwards).

Method 2: Remote Sensing

Now things are getting a bit more advanced. What if you don’t want to clean your webcam after each time you measure your heart rate? Well thankfully there’s a remote sensing option as well.

For this method, [Andy] is actually using OpenCV to measure the cyclical swelling and shrinking of blood vessels in your skin by measuring the color change in your face. It’s absolutely mind-blowing that this works, considering the resolution of a standard webcam. He found the most success by focusing on fleshy patches of skin right below the eyes, though he says others recommend taking a look at the forehead.

Every now and then we see something that works even though it really seems like it shouldn’t. How is a webcam sensitive enough to measure these minute changes in facial color? Why isn’t the signal uselessly noisy? This project is in good company with other neat heart rate measurement tricks we’ve seen. It’s amazing that this works at all, and even more incredible that it works so well.