Tag: Microcontroller

Feeding Experimentation Device (FED) part 2: new design and code

fed-front3           fed-gif-3

The Feeding Experimentation Device (FED) is a free, open-source system for measuring food intake in rodents. FED uses an Arduino processor, a stepper motor, an infrared beam detector, and an SD card to record time-stamps of 20mg pellets eaten by singly housed rodents. FED is powered by a battery, which allows it to be placed in colony caging or within other experimental equipment. The battery lasts ~5 days on a charge, providing uninterrupted feeding records over this duration.  The electronics for building each FED cost around $150USD, and the 3d printed parts cost between $20 and $400, depending on access to 3D printers and desired print quality.

The Kravitz lab has published a large update of their Feeding Experimentation Device (FED) to their Github site (https://github.com/KravitzLab/fed), including updated 3D design files that print more easily and updates to the code to dispense pellets more reliably.  Step-by-step build instructions are available here: https://github.com/KravitzLab/fed/wiki

Hao Chen lab, UTHSC – openBehavior repository

The openBehavior github repository from Hao Chen’s lab at UTHSC aims to establish a computing platform for rodent behavior research using the Raspberry Pi computer. They have buillt several devices for conducting operant conditioning and monitoring enviornmental data.

The operant licking device can be placed in a standard rat home cage and can run fixed ratio, various ratio, or progressive ratio schedules. A preprint describing this project, including data on sucrose vs water intake is available. Detailed instructions for making the device is also provided.

The environment sensor can record the temperature, humidity, barometric pressure, and illumination at fixed time intervals and automatically transfer the data to a remote server.

There is also a standard alone RFID reader for the EM4100 implantable glass chips, a motion sensor addon for standard operant chambers, and several other devices.

Automated Home-Cage Functional Imaging

Timothy Murphy and his colleagues at the University of British Columbia have developed an automated system for mesoscopic functional imaging that allows subjects to self-initiate head-fixation and imaging within the home-cage. In their 2016 paper, “High-throughput automated home-cage mesoscopic functional imaging of mouse cortex,” Dr. Murphy and his colleagues present this device and demonstrate its use with a group of calcium indicator transgenic mice. The supplementary material to this paper includes a diagram of the hardware, a graphic representation of the training cage, several videos of subjects interacting with the device and sample imaging data. The Python source code and 3D print files can be found on Dr. Murphey’s UBC webpage.

Murphy, T. H., Boyd, J. D., Bolaños, F., Vanni, M. P., Silasi, G., Haupt, D., & LeDue, J. M. (2016). High-throughput automated home-cage mesoscopic functional imaging of mouse cortex. Nature Communications, 7, 11611.

Nose-Poke System – Kelly Tan Research Group

The Kelly Tan research group at the University of Basel, Switzerland investigates the neural correlates of motor behavior, focusing on the role of the basal ganglia in controlling various aspects of motor actions. To aid in their investigation, the group has developed an open-source nose-poke system utilizing an Arduino microcontroller, several low-cost electronic components, and a PVC behavioral arena. These researchers have shared the following information about the project:

Giorgio Rizzi, Meredith E. Lodge, Kelly R Tan.
MethodsX 3 (2016) 326-332
Operant behavioral tasks for animals have long been used to probe the function of multiple brain regions. The recent development of tools and techniques has opened the door to refine the answer to these same questions with a much higher degree of specificity and accuracy, both in biological and spatial-temporal domains. A variety of systems designed to test operant behavior are now commercially available, but have prohibitive costs. Here, we provide a low-cost alternative to a nose poke system for mice. Adapting a freely available sketch for ARDUINO boards, in combination with an in-house built PVC box and inexpensive electronic material we constructed a four-port nose poke system that detects and counts port entries.
  • We provide a low cost alternative to commercially available nose poke system.
  • Our custom made apparatus is open source and TTL compatible.
  • We validate our system with optogenetic self-stimulation of dopamine neurons in mice.

IMG_20160126_163648 IMG_20160126_163703 IMG_20160126_163714 IMG_20160126_163725 IMG_20160127_124611 IMG_20160127_124624 IMG_20160127_150643 IMG_20160127_150708


The Kelly Tan research group provides further documentation for this device, including SketchUp design files, Arduino source code, and a full bill of materials, as supplementary data in their 2016 paper.

ArduiPod Box

ArduiPod Box is a simple, comprehensive touchscreen-based operant conditioning chamber that utilizes an iPod Touch in conjunction with an Arduino microcontroller to present visual and auditory stimuli, record behavior in the form of nose-pokes or screen touches, and deliver liquid reward. In his 2014 paper, Oskar Pineño introduces ArduinoPod Box and demonstrates the use of the device in a visual discrimination task.

ArduiPod Box relies on an open-source iOS app named Shaping that can be downloaded for free at the iTunes store, as well as, on Dr. Pineno’s website. Detailed instructions for assembly of the ArduiPod Box are also detailed on the website. In addition, video demonstrating of ArduiPod can be found here.

13428_2013_367_Fig2b_HTML

 


Pineño, Oskar (2014). ArduiPod Box: a low-cost and open-source Skinner box using an iPod Touch and an Arduino microcontroller. Behav Res Methods. 46(1): 196–205

Syringe Pump – Pearce Research Group

In their 2014 paper “Open-Source Syringe Pump Library,” Bas Wijnen, Emily Hunt, Gerald Anzalone, and Joshua Pearce detail an open-source syringe pump apparatus developed in their lab, as well as, validate the performance of the device. The authors write, “This syringe pump was designed using freely available open-source computer aided design (CAD) software and manufactured using an open-source RepRap 3-D printer and readily available parts. The design, bill of materials and assembly instructions are globally available to anyone wishing to use them on the Open-source syringe pump Approdepia page… The cost of the entire system, including the controller and web-based control interface, is on the order of 5% or less than one would expect to pay for a commercial syringe pump having similar performance. The design should suit the needs of a given research activity requiring a syringe pump including carefully controlled dosing of reagents, pharmaceuticals, and delivery of viscous 3-D printer media among other applications.”

Pearce Research group also provides an Open Source Lab page dedicated to low-cost, open-source lab hardware.


Wijnen, Bas; Hunt, Emily; Anzalone, Gerald; Pearce, Joshua (2014). Open-Source Syringe Pump Library. PLoS ONE, 9(9), e107216.

Visual Stimuli Presentation Device

This apparatus is designed to present complex visual stimuli in rodent behavioral experiments, such as visual discrimination tasks, or visually guided choice paradigms. This low-cost device utilizes an Arduino Uno microcontroller, and three (green) 8×8 LED matrices to present a montage of visual cues across a behavioral arena. Diffusion filters were used to decrease the luminance of the visual cues in order to render them more suitable for rodent visual discrimination. The present design incorporates three light displays to be mounted above three choice ports (nose pokes, levers, etc.); however as many as 8 light displays can be controlled by a single Arduino. This flexible device can be programmed to display a multitude of distinct static and dynamic visual cues, can easily be integrated into an existing behavioral chamber, and seamlessly interface with commercial systems such as MedPC. The wiring diagram and schematic below detail the configuration of this apparatus in a MedPC-based system; however, this device can be controlled by any comparable system, TTL signal, or other device in a behavioral chamber.

SchematicWiring Diagram

Adafruit provides extensive documentation on assembly and programming of these components on their website.

Please contact openbehavior@gmail.com for Arduino source code and the 3D design files of the mounts used to install this device into a behavioral chamber.

Feeding Experimentation Device (FED)

WP_20160320_003Feeding Experimentation Device (FED) is a home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers a low-cost alternative (~$350) to commercial feeders, with the convenience of use in tradition colony rack caging.

In their 2016 paper, “Feeding Experimentation Device (FED): A flexible open-source device for measuring feeding behavior,” Katrina P. Nguyen, Timothy J. O’Neal, Olurotimi A. Bolonduro, Elecia White, and Alexxai V. Kravitz validate the reliability of food delivery and precise measurement of feeding behavior provided by FED, as well as, demonstrate the application of FED in an experiment examining light and dark-cycle feeding trends, and another measuring optogenetically-evoked feeding.

WP_20160324_10_54_40_Pro

KravitzLab has shared the Arduino scripts for controlling FED, as well as, the python code used to analyze the feeding data collected by FED on the KravitzLab Github. Additionally, build instructions and power considerations are detailed on the FED Wiki page and 3D Design Files provided through TinkerCAD.


Nguyen, Katrina; O’Neal, Timothy; Bolonduro, Olurotimi; White, Elecia; Kravitz, Alexxai (2016). Feeding Experimentation Device (FED): A flexible open-source device for measuring feeding behavior. J Neurosci Methods, 267:108-14.

Rodent Operant Bucket (ROBucket)

Horizontal Figure 1-01The Rodent Operant Bucket (ROBucket), designed by Dr. Alexxai Kravitz and Kavya Devarakonda of the Eating and Addiction Section, Diabetes Endocrinology and Obesity Branch, NIDDK, is an inexpensive and easily assembled open-source operant chamber, based on the Arduino microcontroller platform, that can be used to train mice to respond for a reward.

The apparatus contains two nose pokes, a drinking well, and a solenoid-controlled sucrose delivery system. The chamber can easily run magazine training, fixed ratio and progressive ratio training schedules, and can be programmed to run more complicated behavioral paradigms.

rodent operant bucket

In their 2016 paper, “ROBucket: A low cost operant chamber based on the Arduino microcontroller,” Kavya Devarakonda, Katrina P. Nguyen, and Alexxai V. Kravitz validate ROBucket by demonstrating its application in an operant conditioning paradigm, as well as, detail the hardware comprising ROBucket, and the flexible software controlling it.

Further documentation of this device can be found on the NIDDK website, where Dr. Kravitz and his lab share ROBucket construction instructions, ROBucket design files, ROBucket source code, and 3D printing design files.


 Kavya Devarakonda, Katrina P. Nguyen, Alexxai V. Kravitz (2016). ROBucket: A low cost operant chamber based on the Arduino microcontroller. Behav Res Methods 48(2): 503–509.