Optogenetics for 100 Euros

Larval zebrafish, Drosophila (fruit fly), and Caenorhabditis elegans (roundworm) have become key model organisms in modern neuroscience due to their low maintenance costs and easy sharing of genetic strains across labs. However, the purchase of a commercial solution for experiments using these organisms can be quite costly. Enter FlyPi: a low-cost and modular open-source alternative to commercially available options for optogenetic experimentation.

One of the things that larval zebrafish, fruit flies, and roundworms have in common is that scientists can monitor them individually or in groups in a behavioural arena while controlling the activity of select neurons using optogenetic (light-based) or thermogenetic (heat-based) tools.

FlyPi is based on a 3D-printed mainframe, a Raspberry Pi computer, and a high-definition camera system supplemented by Arduino-based optical and thermal control circuits. FlyPi features optional modules for LED-based fluorescence microscopy and optogenetic stimulation as well as a Peltier-based temperature simulator for thermogenetics. The complete version with all modules costs approximately €200 with a layman’s purchasing habits, but for those of us who live on the dark side of eBay or the depths of Taobao, it shouldn’t cost more than €100.

Once assembled, all of the functions of FlyPi can be controlled through a graphical user interface. As an example for how FlyPi can be used, the authors of the paper document its use in a series of “state-of-the-art neurogenetics experiments”, so go check out the recently published open access paper on PLOS. Everything considered the authors hope that the low cost and modular nature, as well as the fully open design of FlyPi, will make it a widely used tool in a range of applications, from the classroom all the way to research labs. Need more lab equipment hacks? Don’t worry, we’ve got you covered. And while you’re at it, why not take a spin with the RWXBioFuge.

Magnetic Stir Plate is a Hack

If you’ve ever spent any time around a lab, you’ve doubtless seen one of those awesome combination magnetic stirrer and heater plates that scientists use to get liquids mixed and up to temperature. If you’ve ever etched your own PCBs using ammonium persulfate, you’ve experienced the need for both heating and agitation firsthand. Using a stirrer plate for PCB etching is putting two and two together and coming up with four. Which is to say, it’s a good idea that’s not amazingly novel. [acidbourbon] built his own, though, and there’s almost no part of this DIY heater/stirrer that isn’t a hack of some kind or another.

Start off with the temperature controller. Instead of buying a thermocouple or using an LM75 or similar temperature-measurement IC, [acidbourbon] uses a bog-standard 1n4148 diode. The current passed through a diode, at a given voltage, is temperature dependent, which means that adding a resistor and a microcontroller’s ADC yields a quick hacked temperature sensor. [acidbourbon] glued his straight onto the casserole that he uses as an etching tray.

Does the type of person who saves $0.25 by using a diode instead of a temperature sensor go out and buy a stirrer motor? No way. Motor and gears come from a CD-ROM drive. The “fish” — the magnetic bar that spins in the etchant — is made of neodymium magnets lengthened by shrink-wrapping heat-shrinking them together with some capacitors. Who knew that shrinkwrap heat-shrink, fused with pliers, was waterproof? Is that a wall-wart in that box, with the prongs wired to mains electricity?

Anyway, this just goes to show that etching equipment need not be expensive or fancy. And the project also provides a showcase for a bevy of tiny little hacks. And speaking of [acidbourbon]’s projects, this semi-automatic drill press mod has been on our to-do list for two years now. Shame on us! Continue reading “Magnetic Stir Plate is a Hack”

Ask Hackaday: How Do You Make A Hotplate?

Greetings fellow nerds. The Internet’s favorite artificial baritone chemist has a problem. His hotplates burn up too fast. He needs your help to fix this problem.

[NurdRage] is famous around these parts for his very in-depth explorations of chemistry including the best ways to etch a PCB, building a thermometer probe with no instructions, and chemical synthesis that shouldn’t be performed by anyone without years of experience in a lab. Over the past few years, he’s had a problem: hotplates suck. The heating element is usually poorly constructed, and right now he has two broken hotplates on his bench. These things aren’t cheap, either: a bare-bones hotplate with a magnetic stirrer runs about $600.

Now, [NurdRage] is asking for help. He’s contacted a few manufacturers in China to get a hundred or so of these hotplate heating elements made. Right now, the cost for a mica and metal foil hotplate is about $30 / piece, with a minimum order quantity of 100. That’s $3,000 that could be better spent on something a bit more interesting than a heating element, and this is where you come in: how do you build the heating element for a hotplate, and do it cheaply?

If you buy a hotplate from the usual lab equipment supplier, you’ll get a few pieces of mica and a thin trace of metal foil. Eventually, the metal foil will oxidize, and the entire hotplate will stop working. Repairs can be done with copper tape, but by the time that repair is needed, the heating element is already on its way out.

The requirements for this heating element include a maximum temperature of around 350 ºC. That’s a fair bit hotter than any PCB-based heat bed from a 3D printer gets, so consider that line of reasoning a dead end. This temperature is also above what most resins, thermoplastics, and composites can handle, which is why these hotplates use mica as an insulator.

Right now, [NurdRage] will probably end up spending $3,000 for a group buy of these heating elements. That’s really not that bad – for the price of five hotplates, he’ll have enough heating elements to last through the rest of his YouTube career. There must be a better way, though, so if you have an idea of how to make a high-temperature heating element the DIY way, leave a note in the comments.

Lego-Like Chemistry and Biology Erector Set

A team of researchers and students at the University of California, Riverside has created a Lego-like system of blocks that enables users to custom build chemical and biological research instruments. The system of 3D-printed blocks can create a variety of scientific tools.

The blocks, which are called Multifluidic Evolutionary Components (MECs) appeared in the journal PLOS ONE. Each block in the system performs a basic lab instrument task (pumping fluids, making measurements or interfacing with a user, for example). Since the blocks are designed to work together, users can build apparatus — like bioreactors for making alternative fuels or acid-base titration tools for high school chemistry classes — rapidly and efficiently. The blocks are especially well suited for resource-limited settings, where a library of blocks can create a variety of different research and diagnostic tools.

Continue reading “Lego-Like Chemistry and Biology Erector Set”

Take Your Samples for a Spin with the RWXBioFuge

We have a confession to make: we love centrifuges. We’ve used all shapes and sizes, for spinning bags of whole blood into separate components to extracting DNA, and everything in between. Unfortunately, these lab staples are too expensive for many DIY-biologists unless they buy them used or build them themselves. [Pieter van Boheemen] was inspired by other DIY centrifuges and decided to make his own, which he named the RWXBioFuge.

[Pieter] designed the RWXBioFuge using Sketchup, OpenSCAD, and InkScape. It features a Thermaltake SMART M850W ATX power supply, an R/C helicopter Electronic Speed Controller (ESC), and brushless outrunner motor. For user output it utilizes a 16×2 LCD character display with an I2C interface.The frame is laser-cut from 3mm MDF while the 3D-printed PLA rotor was designed with OpenSCAD.

An Arduino handles the processing side of things. [Pieter] used an Arduino Ethernet – allowing a web interface to control the centrifuge’s settings and operation from a distance. We can see this being useful in testing out the centrifuge for any rotor/motor balance issues, especially since [Pieter] states that it can be configured to run >10,000 rpm. We wouldn’t want to be in the room if pieces start flying off any centrifuge at that speed!  However, we feel that when everything’s said and done, you should have a centrifuge you can trust by your side when you’re at your lab bench.

While there are similarities to the Openfuge, the larger RWXBioFuge has rotor capacities of eight to twenty 1.5-2.0ml microcentrifuge tubes. Due to the power supply, it is not portable and a bit more expensive, but not incredibly so. There are some small touches about this centrifuge that we really like. The open lid detector is always a welcome safety feature. The “Short” button is very handy for quick 5-10 second spins.

A current version of the RWXBioFuge is being used at the Waag Society’s Open Wetlab. [Pieter’s] planned upgrades for the next version include a magnetic lid lock, different rotor sizes, an accelerometer to detect an improperly balanced rotor, and optimizing the power supply, ESC, and motor setup. You can never have enough centrifuges in a lab, and we are looking forward to seeing this project’s progress!

Check out a few more pictures of the RWXBioFuge after the break.

Continue reading “Take Your Samples for a Spin with the RWXBioFuge”

DIY Magnetic Stirrer Looks Professional

Stirrers are used in chemistry and biology labs to mix containers full of liquids. Magnetic stirrers are often preferred over the mechanical types because they are more sterile, easier to clean and have no external moving parts. Magnetic stirrers quickly rotate a magnet below the glass beaker containing the liquids that need mixing. The magnetic field travels effortlessly through the glass and reacts against a small magnetic cylinder called the stir bar. The spinning stir bar mixes the contents and is the only part of the mixer that touches the liquids.

[Malcolm] built his own magnetic stirrer. Unlike some DIY stirrers out on the ‘web, this one gets an “A” for aesthetics. It’s clean white lines allow it to look right at home in the professional laboratory. The graduated knob looks good and is functional too as the the potentiometer it is attached to allows multiple mixing speeds. Surprisingly, a D-size battery is all that is needed to power the stirrer. Most of the parts required for this project can be found in your spare parts bin. [Malcolm] has written some excellent instructions on how he made the stirrer including a parts list and schematics.

Want to make a magnetic stirrer but aren’t into chemistry or biology? No worries… I pity the fool who don’t build one of these….

DIY High Stability Timebase Hack for ~$25. Why? Frequency Stability Matters!

DIY High Stability Timebase OCXO

If you have an old “Racal-Dana 199x” frequency counter or similar 10 MHz internally referenced gear with a poor tolerance “standard quartz crystal oscillator” or bit better “temperature compensated crystal oscillator” (TCXO) you could upgrade to a high stability timebase “oven controlled crystal oscillator” (OCXO) for under $25. [Gerry Sweeney] shares his design and fabrication instructions for a DIY OCXO circuit he made for his Racal-Dana frequency counter. We have seen [Gerry] perform a similar upgrade to his HP 53151A, however, this circuit is more generic and can be lashed up on a small section of solderable perf board.

Oven controlled oscillators keep the crystal at a stable temperature which in turn improves frequency stability. Depending on where you’re starting, adding an OCXO could improve your frequency tolerance by 1 to 3 orders of magnitude. Sure, this isn’t as good as a rubidium frequency standard build like we have seen in the past, but as [Gerry] states it is nice to have a transportable standalone frequency counter that doesn’t have to be plugged into his rubidium frequency standard.

[Gerry’s] instructions, schematics and datasheets can be used to upgrade any lab gear which depends on a simple 10 MHz reference (crystal or TXCO). He purchased the OCXO off eBay for about $20 — it might be very old, yet we are assured they get more stable with age. Many OCXO’s require 5 V, 12 V or 24 V so your gear needs to accommodate the correct voltage and current load. To calibrate the OCXO you need a temperature stable variable voltage reference that can be adjusted from 1 to 4 volts. The MAX6198A he had on hand fit the bill at 5 ppm/°C temperature coefficient. Also of importance was to keep the voltage reference and trim pot just above the oven for added temperature stability as well as removing any heat transfer through the mounting screw.

You can watch the video and get more details after the break.

Continue reading “DIY High Stability Timebase Hack for ~$25. Why? Frequency Stability Matters!”