Autoreward2

The motivation to start this project arises when we started to include a new behavioral paradigm in the lab, an alternation T-mace with return arms (like the one in Wood et al. 2000). We wanted a clean performance, as well as a clean video record, so we consider necessary to interfere neither with the animal attention (mice, how they are!) nor the camera’s field of view. I decided then to give a try to the new hobby I was getting into, “Do-It-Yourself” (DIY) stuff.

In my head, it was pictured very simple. At the end of the day, I just needed a) something to detect the animal passing by, b) something to deliver a drop of water and c) something to make it happen in a coordinated way. And that’s what Autoreward2 is, no more, no less.

Well perhaps it is a bit more. So far, the project can:

  • Detect when the animal reaches the end of any of the two arms.
  • Deliver a small drop of fluid through the corresponding licking port (easy to make it happen in the opposite, if wanted).
  • Give visual cues to the experimenter, indicating which arm has been reached.
  • Allow to select different modes of working for different working protocols: ‘Waiting for selection’, ‘Habituation’, ‘Training’, ‘Experimental’ and “Filling and cleaning” modes (and is ready to include more!).

To achieve it, I decided for very simple approach. A couple of cheap infrared emitters are continuously read by an UNO R3 board. Breaking any of the beams triggers the signal to open the corresponding solenoid valve, connected to the fluid tank. That lets the liquid flow by gravity for around 75 milliseconds, resulting in a single drop at the tip of the licking port.

There is a delay after each detection, to avoid repetitive delivery if animals don’t leave the area. A couple LEDs mounted in the bare-board (out of animal sight) light up when the process is triggered, one for each side. They also work as indicators for the ‘Waiting for selection’ mode, when they are continuously on, meanwhile no option is choose or the ‘return to waiting mode action’ is pressed.

The selection is made through a 4×4 membrane keypad. Right now, only options 1 to 4 are programmed, making up to 12 more programs available! When any section is made, the in-built LED blinks the corresponding times and the system is ready to work. At any moment, pressing any key makes the system reset to the waiting mode. As easy as that.

Everything is powered by a regular 9V wall adapter, giving 3.3V to the LEDs and Infrared detectors, and 9V to the solenoids. Of course, it is possible to use a 9V batterie to power it. To avoid damage coming from the solenoid discharges, the circuit is protected by a couple of diodes at this level.

And that’s all, it’s simple. The most important thing: it works. The other most important thing: it costs around 80€. Here is the to-buy list (or equivalent):

  • Elegoo UNO R3 (I found them for 10€, with USB cable)
  • BreadBoard + Acrylic base (7€)
  • 9V 1A Wall power supply (9€)
  • 2x InfraRed beams, 5mm (15€ both, the 3mm ones are even cheaper)
  • 2x Mini-Solenoid valves (10€ both)
  • 2x red LEDs
  • 4x 1 KΩ resistors
  • 2x TIP120 Transistors
  • 2x 1N4001 diodes
  • Wiring (set of jumpers for less than 10€)
  • ‘Velcro’ to attach the acrylic base where the boards are mounted.
  • Plastic tubing and laboratory sample tubes, modified with turning siringe tips to attach/deattach the tubing easily.
  • 2x or 4x weak magnets to fix the tubes to the walls.

Feel free to access the Github page or the Arduino forum post to obtain the code, check for the circuit sketch, and see some pictures.

PD: If someone is scandalized by the code, I am getting better on it, it is not my main strength. Please, improve it! Of course, I have in mind many possible upgrades such as a screen, a SD card port, to change the Keypad for a wireless interface (tactile?) … Did someone say smartphone plus Bluetooth? Going fancy, a barcode reader to easily introduce subjects’ data… And here is where I relay in the open-access idea, I offer it and hopefully someone implement any of the ideas. If so, remember to share!

Jesús J. Ballesteros

New collaboration between PLOS and Open Neuroscience

We are happy to announce that a new Open Source toolkit channel went live today at https://channels.plos.org/open-source-toolkit.
This channel is a joint collaboration from Open Neuroscience, Trend in Africa and PLOS. There you will find several open source projects related to science. They range all disciplines and comprehend both software and hardware. It is open for suggestions and interaction from the community!

Channel’s front page

new pages Jan/2017

The following projects/pages were curated and added to open neuroscience on Dec/16-Jan/17:

Attys: https://wp.me/P82mzJ-lu

Allen Brain Map: https://wp.me/P82mzJ-l8

Vision Egg: https://wp.me/P82mzJ-lc

Frontiers collection on Python for Neurosciences: https://wp.me/P82mzJ-kA

PySpace: https://wp.me/P82mzJ-kW

BackLog: https://wp.me/P82mzJ-5S

Backlog

On an attempt to make things even more open at Openeuroscience.com and take a little bit of the publishing delay away, we’ve decided to create the backlog page.

In this page you’ll find all projects that we are planning to upload to the website but didn’t get a chance yet! This way we are not stopping the information spread, and people get to make comments about the projects before they are curated.

From: https://thegrimbrothers.files.wordpress.com/2011/02/back-log-a.jpg
From: https://thegrimbrothers.files.wordpress.com/2011/02/back-log-a.jpg

Companies selling open source hardware/software

Two companies have incorporated the open source philosophy into their business models and are now providing products for neuroscience released under know open source licenses:

Sanworks: After the success and demand of PulsePal, Josh Sanders founded Sanworks, a company dedicated to providing systems for neuroscience research. A brief description on the company’s website follows:

Sanworks, L.L.C. develops automated systems for Neuroscience research, and streamlines access to them through an online assembly service. Our goal is to make Neuroscience tools open, affordable and accessible. We are especially focused on embedded systems for exploring the links between brain function and behavior.

Spike Gadgets: Also dedicated to providing systems for neuroscience, Spike Gadgets is focusing at electrophysiology systems and providing a complete solution with hardware and software. Although only their software is open source, this already opens doors to a lot of interesting customization/changes. A brief description from the company’s website:

SpikeGadgets is trying something new. Our hybrid approach is to design and sell powerful hardware that interfaces with an open-source software platform supported by a large community of scientists and developers. Our goal is to support the efforts of the open-source community in a commercially-sustainable way.

One of the founders, Mattias Karlsson, was kind enough to provide a brief description of their software, which can be found here.

 

The Hackaday citizen prize winners are out! And FlyPi made the cut!

We live in a time of unparalleled access to technology and this has the power to make life better for everyone. Today we are excited to announce twenty spectacular builds that use access to technology to move scientific exploration within the reach of all. These are the winners of the Citizen Scientist challenge of the…

via Hackaday Prize: 20 Projects that Make Us All Citizen Scientists — Hackaday

Flypi -100$ microscope/behavioural setup!

We’ve been working in collaboration with the folks of TrendinAfrica (trendinafrica.org) to develop a cheap, yet reliable, open source microscopy system to be used by scientists and DIY biologists. It is called Flypi, since its original focus were experiments with Drosophila and it uses the Raspberry pi computer as its “brains”.
The project has been going quite well and we feel it is mature enough to gain some public attention (and hopefully adoption!) and also to enter the hackaday.io competition, which would help us further develop it! So please, visit the project page, share it with your networks and show us some love by giving us “skulls” @ https://hackaday.io/project/5059-flypi-100-microscopeexperimental-setup. Also check out the paper we are writing about it: https://open-labware.net/projects/flypi/

Center for Reproducible Neuroscience

scan
from http://reproducibility.stanford.edu/

The Center for reproducible Neuroscience was founded in 2015 with the aim of helping researchers make their science stand the test of time, by making it more open and reproducible (aka better science). The starting point of the center is neuroimaging, as they provide computational power, databanks for storing and sharing data and data analysis platform (to be launched in 2016), tuned to the field.

Open source projects for neuroscience!