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.

The Arduino Sleeps with the Fishes

[Eric Dirgahayu] wanted to explore underwater with some sensors and cameras. First, he needed a platform to carry them. That led to his Arduino-controlled swimming fish. The fish is made from PVC and some waterproof servos. From the video (see below) it isn’t clear how much control the fish has, but it does swim with an undulating motion like a real fish.

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Tissue-Engineered Soft Robot Swims Like a Stingray

We’re about to enter a new age in robotics. Forget the servos, the microcontrollers, the H-bridges and the steppers. Start thinking in terms of optogenetically engineered myocytes, microfabricated gold endoskeletons, and hydrodynamically optimized elastomeric skins, because all of these have now come together in a tissue-engineered swimming robotic stingray that pushes the boundary between machine and life.

In a paper in Science, [Kevin Kit Parker] and his team at the fantastically named Wyss Institute for Biologically Inspired Engineering describe the achievement. It turns out that the batoid fishes like skates and rays have a pretty good handle on how to propel themselves in water with minimal musculoskeletal and neurological requirements, and so they’re great model organisms for a tissue engineered robot.

The body is a laminate of silicone rubber and a collection of 200,000 rat heart muscle cells. The cardiomyocytes provide the contractile force, and the pattern in which they are applied to the 1/2″ (1.25cm) body allows for the familiar undulating motion of a stingray’s wings. A gold endoskeleton with enough stiffness to act as a spring is used to counter the contraction of the muscle fibers and reset the system for another wave. Very clever stuff, but perhaps the coolest bit is that the muscle cells are genetically engineered to be photosensitive, making the robofish controllable with pulses of light. Check out the video below to see the robot swimming through an obstacle course.

This is obviously far from a finished product, but the possibilities are limitless with this level of engineering, especially with a system that draws energy from its environment like this one does. Just think about what could be accomplished if a microcontroller could be included in that gold skeleton.

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Hackaday Prize Semifinalist: Better DIY Aquaculture

The theme of this year’s Hackaday Prize is ‘build something that matters’. For a lot of the teams entering a project, that means solving world hunger, specifically though agriculture. Grains are great, but proteins generally taste better and [Michael Ratcliffe] is focusing his project on aquaculture, or farming fish and other aquatic life.

The problem [Michael] decided to tackle is feeding fish at regular intervals according to water temperature, the age of the fish, and how much food is already floating in the tank. This is actually a difficult problem to solve; fish grow better when they’re fed more than once a day. Currently, most aquaculture setups feed fish once a day simply because it’s so time-consuming.

[Michael] is using Pis, Arduinos, USB cameras, and a lot of experience in automation and control systems to feed fish in the most efficient way. The possibilities of the project are interesting; the best research says a more efficient feeding schedule can translate into a 20% increase in production, which is a lot of extra food for the world.

You can check out [Michael]’s introductory video below.

The 2015 Hackaday Prize is sponsored by:

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Hacklet 50 – Hydroponic Projects

Growing plants without soil has been has been amazing people for centuries. First written about in the 1600’s, hydroponics has become an industry with numerous techniques for germinating and sustaining both plant and animal life. It comes as no surprise then that hackers, makers, engineers, and scientists have been working with and improving hydroponic systems for centuries. Hydroponic plant growth is a project you can really sink your teeth into, as there’s nothing sweeter than eating the fruits and vegetables of your labor. This week’s Hacklet is all about the best hydroponic projects on Hackaday.io!

hydropwnWe start with HydroPWNics, [Adam Vadala-Roth’s] entry in The 2015 Hackaday Prize. [Adam] is creating a universal system with will work with both hydroponic and soil based grow systems. The hydroponic setup will consist of plants in a PVC gutter system. Water will be pumped to the top gutter, and flow down via gravity through the plant roots and back to the reservoir. The system will be monitored and controlled by a DyIO controller. Props to [mad.hephaestus] for creating DyIO, a project seeing reuse in the Hackaday.io community!

 

hydro2Next up is [Justin] with AAGriculture, an Automated Aquaponic Garden. AAGriculture is aquaponic system, which means it uses a symbiotic relationship between plants and fish to make more food for humans to eat. The fish in this case are bluegill and bullhead. A Raspberry Pi controls the system, while A Teensy-LC is used to help out with some of the real-time duties, like monitoring a PH probe. [Justin] is even using CO2 tanks to keep dissolved gasses in check. He must be doing something right, as his tomatoes are now over 23″ tall!

 

homer[Em] brings us 5g Aquaponics. 5g aquaponics isn’t a next generation cellular system, nor a 5.8 GHz WiFi setup, it’s an aquaponic system in a 5 Gallon bucket. Anyone from the US  will recognize the orange “Homer Bucket” from Home Depot. 5g Aquaponics includes a window, allowing the underwater workings to be monitored. Speaking of monitoring, 5g aquaponics is a manual affair – [Em] hasn’t used any electronics here. The idea is to create a system that is easy to get up and running for those who are new to Hydro/Aquaponic setups. [Em] is using a dual zone root system. The plant grows in dirt within a burlap fabric. The fabric then sits in a water bath which also houses the fish. Air pumped through an airstone keeps everything circulating. [Em’s] initial version of the project worked a bit too well. The tomato plant grew so large that the roots strangled the fish! Hopefully both flora and fauna are happy with this new rev 2.0!

 

smartAquaFinally we have [Kijani grows] with Smart Aquaponics, which was [Kijani’s] entry in The 2014 Hackaday Prize. One wouldn’t expect fish, plants and Linux to mix, but that is exactly what is going on here. Linux runs on the popular Wr703n router, while a custom ATmega328 Arduino compatible board keeps track of the sensors.  The second version of the system will run on an ATmega2560 and an AR9331 module, all housed on one board. The system does work, and it’s been expanded from a single fish tank to a large flood/drain table complete with grow lights, all kept at [Kijani’s] office. The biggest problems [Kijani] has run into are little things like misplaced resistors masquerading as kernel bugs.

Still haven’t eaten your veggies? Want to see more hydroponic projects? Check out our new hydroponic projects list! That’s it for this week’s Hacklet, As always, see you next week. Same hack time, same hack channel, bringing you the best of Hackaday.io!

Training Fish to feed Themselves

We’ve featured quite a few aquarium and fish feeder hacks on our blog. [RoboPandaPDX] thought of taking it up a notch and make an interactive fish feeder. He built a Fish feeder that train’s them to feed themselves.

A copper bar hangs from the middle of a metal cylinder – much like a bell. The end of the bar has a fish lure. When a fish pushes the lure, the copper bar touches the metal cylinder and  closes the circuit. This signal goes to an Arduino. To catch the attention of the fishes and to “teach” them, an RGB LED is used. The fish need to figure out that the feeder will dispense food only when the LED is ON and the Lure is pushed. If the fish figure that out, and push the lure when the LED is on, a servo is activated which pushes the feeder to deliver 1 unit of fish food. While at it, he added a couple of bells and whistles. A buzzer to indicate when the Lure switch is closed and a 2 line LCD shows how many times the switch has been activated and how long the program has been running.

A Sparkfun  open logger stores the hit count and the minutes and seconds of the hit for data analysis later on. The good news is that it seems to be working. The current code activates the feeder for 30 to 60 minutes every day, which is indicated by the LED. At the end of 9 days,  [RoboPandaPDX] found that the goldfish would hit the Lure when the LED turned on, and then turn around to face where the feeder would dispense food in to the tank. His next plan is to put up some obstacles along the path to see if the fish learn some new tricks. His schematic looks a little iffy (the Lure switch is connected to the RST pin of the Arduino), and it seems he cannot remember why he ever did that. He’s happy that it works though, but we’re sure that’s not the right way to wire it up.

[RoboPandaPDX] is looking for suggestions on improving his interactive feeder, so if you have any, do add them in the comments below.

If you need some more fish feeder ideas, check out this and this that we blogged about earlier.

3D Printed Fish Feeder

[Helios Labs] recently published version two of their 3D printed fish feeder. The system is designed to feed their fish twice a day. The design consists of nine separate STL files and can be mounted to a planter hanging above a fish tank in an aquaponics system. It probably wouldn’t take much to modify the design to work with a regular fish tank, though.

The system is very simple. The unit is primarily a box, or hopper, that holds the fish food. Towards the bottom is a 3D printed auger. The auger is super glued to the gear of a servo. The 9g servo is small and comes with internal limiters that only allow it to rotate about 180 degrees. The servo must be opened up and the limiters must be removed in order to enable a full 360 degree rotation. The servo is controlled by an Arduino, which can be mounted directly to the 3D printed case. The auger is designed in such a way as to prevent the fish food from accidentally entering the electronics compartment.

You might think that this project would use a real-time clock chip, or possibly interface with a computer to keep the time. Instead, the code simply feeds the fish one time as soon as it’s plugged in. Then it uses the “delay” function in order to wait a set period of time before feeding the fish a second time. In the example code this is set to 28,800,000 milliseconds, or eight hours. After feeding the fish a second time, the delay function is called again in order to wait until the original starting time.