Category: Sensors

MAPLE: a Modular Automated Platform for Large-Scale Experiments

January 8th, 2018 
The de Bivort lab and FlySorter, LLC are happy to share on OpenBehavior their open-source Drosophila handling platform, called MAPLE: Modular Automated Platform for Large-Scale Experiments.

Drosophila Melanogaster has proven a valuable genetic model organism due to the species’ rapid reproduction, low-maintenance, and extensive genetic documentation. However, the tedious chore of handling and manually phenotyping remains a limitation with regards to data collection. MAPLE: a Modular Automated Platform for Large-Scale Experiments provides a solution to this limitation.

MAPLE is a Drosophila-handing robot that boasts a modular design, allowing the platform to both automate diverse phenotyping assays and aid with lab chores (e.g., collecting virgin female flies). MAPLE permits a small-part manipulator, a USB digital camera, and a fly manipulator to work simultaneously over a platform of flies. Failsafe mechanisms allow users to leave MAPLE unattended without risking damage to MAPLE or the modules.

The physical platform integrates phenotyping and animal husbandry to allow end-to-end experimental protocols. MAPLE features a large, physically-open workspace for user convenience. The sides, top, and bottom are made of clear acrylic to allow optical phenotyping at all time points other than when the end-effector carriages are above the modules. Finally, the low cost and scalability allow large-scale experiments ($3500 vs hundreds of thousands for a “fly-flipping” robot).

MAPLE’s utility and versatility were demonstrated through the execution of two tasks: collection of virgin female flies, and a large-scale longitudinal measurement of fly social networks and behavior.

Links to materials:

CAD files

Control Software

Raw data and analysis scripts 

De Bivort Lab Site 


 

ArControl: Arduino Control Platform

January 3rd, 2018

The following behavioral platform was developed and published by Xinfeng Chen and Haohong Li, from Huazhong University of Science and Technology, Wuhan, China


ArControl: Arduino Control Platform is a comprehensive behavioral platform developed to deliver stimuli and monitor responses. This easy-to-use, high-performance system uses an Arduino UNO board and a simple drive circuit along with a stand-along GUI application. Experimental data is automatically recorded with the built-in data acquisition function and the entire behavioral schedule is stored within the Arduino chip. Collectively, this makes ArControl a “genuine, real-time system with high temporal resolution”. Chen and Li have tested ArControl using a Go/No-Go task and a probabilistic switching behavior task. The results of their work show that ArControl is a reliable system for behavioral research.

Source codes and PCB drafts may be found here: ArControl Github

 

 

Pyper

November 28, 2017

Pyper is developed by The Margrie Laboratory.


Pyper provides real-time or pre-recorded motion tracking of a specimen in an open-field. Pyper can send TTL pulses based on detection of the specimen within user-defined regions of interest.  The software can be used through the command line or through a built-in graphical user interface. The live feed can be provided by a USB or Raspberry Pi camera.

Example of Pyper tracking a mouse in an open field


Find more information here.

Manual for Pyper.

3DTracker – 3D video tracking system for animal behavior

November 8th, 2017

Jumpei Matsumoto has submitted the following to OpenBehavior regarding 3D tracker, a 3D video tracking system for animal behavior.


3DTracker-FAB is an open source software for 3D-video based markerless computerized behavioral analysis for laboratory animals (currently mice and rats). The software uses multiple depth cameras to reconstruct full 3D images of animals and fit skeletal models to the 3D image to estimate 3D pose of the animals.


More information on 3D tracker may be found on the system’s website, www.3dtracker.org

Additionally, a dynamic poster on the system was presented on November 12, 2017 at the Society for Neuroscience annual meeting. Click here for more information.

Autonomous Training of a Forelimb Motor Task

November 3, 2017

Greg Silas, from the University of Ottawa, has kindly contributed the following to OpenBehavior.


“Silasi et al developed a low-cost system for fully autonomous training of group housed mice on a forelimb motor task. We demonstrate the feasibility of tracking both end-point as well as kinematic performance of individual mice, each performing thousands of trials over 2.5 months. The task is run and controlled by a Raspberry Pi microcomputer, which allows for cages to be monitored remotely through an active internet connection.”

Click here to submit a piece of open-source software or hardware to OpenBehavior.

Moving Wall Box (MWB)

October 26th, 2017

Andreas Genewsky, from the Max-Planck Institute of Psychiatry, has generously shared the following regarding his Moving Wall Box task and associated apparatus.


“Typicallly, behavioral paradigms which aim to asses active vs. passive fear responses, involve the repeated application of noxius stimuli like electric foot shocks (step-down avoidance, step-through avoidance, shuttle-box). Alternative methods to motivate the animals and ultimately induce a conflict situation which needs to be overcome often involve food and/or water deprivation.

In order to repeatedly assess fear coping strategies in an emotional challenging situation without footshocks, food or water deprivation (comlying to the Reduce & Refine & Replace 3R principles), we devised a novel testing strategy, henceforward called the Moving Wall Box (MWB) task. In short, during the MWB task a mouse is repeatedly forced to jump over a small ice-filled box (10 trials, 1 min inter-trial intervals ITI), by slowly moving walls (2.3 mm/s, over 60 s), whereby the presence of the animal is automatically sensed via balances and analyzed by a microcontroller board which in turn controls the movements of the walls. The behavioral readouts are (1) the latency to reach the other compartment (high levels of behavioral inhibition lead to high latencies) and (2) the number of inter-trial shuttles per trial (low levels of behavioral inhibition lead to high levels of shuttles during the ITI).

The MWB offers the possibility to conduct simultaneous in vivo electrophysiological recordings, which could be later aligned to the behavioral responses (escapes). Therefore the MWB task fosters the study of activity patterns in, e.g., optogenetically identified neurons with respect to escape responses in a highly controlled setting. To our knowledge there is no other available compatible behavioral paradigm.”


OMR Arena

September 7, 2017

Researchers at the National Eye Institute and the University of Oldenberg, Germany, have developed the OMR-arena for measuring visual acuity in mice.


The OMR-arena is an automated measurement and stimulation system that was developed to determine visual thresholds in mice. The system uses an optometer to characterize the visual performance of mice in a free moving environment. This system uses a video-tracking system to monitor the head movement of mice while presenting appropriate 360° stimuli. The head tracker is used to adjust the desired stimulus to the head position, and to automatically calculate visual acuity. This device, in addition to being open-source and affordable, offers an objective way for researchers to measure visual performance of free moving mice.


Kretschmer F, Kretschmer V, Kunze VP, Kretzberg J (2013) OMR-Arena: Automated Measurement and Stimulation System to Determine Mouse Visual Thresholds Based on Optomotor Responses. PLoS ONE 8(11): e78058. 

Autoreward2

May 26th, 2017

Jesús Ballesteros, Ph.D. (Learning and Memory Research Group, Department of Neurophysiology at Ruhr-University Bochum, Germany) has generously his project, called Autoreward2, with OpenBehavior. Autoreward2 is an Elegoo Uno-based system designed to detect and reward rodents in a modified T-maze task.


In designing their modified T-maze, Ballesteros found the need for an automatic reward delivery system. Using open-source resources, he aimed to create a system with the following capabilities:

  • Detect an animal at a certain point in a maze;
  • Deliver a certain amount of fluid through the desired licking port;
  • Provide visual cues that indicate which point in the maze has been reached;
  • Allow different modes to be easily selected using an interface;
  • Allow different working protocols (i.e., habituation, training, experimental, cleaning)

To achieve these aims, he created used an Elegoo UNO

R3 board to read inexpensive infrared emitters. Breaking any infrared beam causes the board to open one or two solenoid valves connected to a fluid tank. The valve remains open for around 75 milliseconds, allowing a single drop of fluid to form at the tip of the licking port. Additionally,  the bread board contains LEDS to signal to the researcher when the IR beam has been crossed.

Currently, a membrane keypad allows different protocols or modes to be selected. The system is powered through a 9V wall adapter, providing 3.3V to the LEDs and IR circuits and 9V to the solenoids.

Importantly, the entire system can be built for under 80€. In the future, Ballesteros hopes to add a screen and an SD card port, and to switch the keypad out for a wireless interface.


The full description may be found here, the Github page for the project may be found here,

and the sketch and arduino code may be found here.

Nose Poke Device

April 20, 2017 

Andre Chagas, creator of OpenNeuroscience, has generously shared the following with OpenBehavior regarding an arduino-based, 3D-printed nose poke device:


“This nose poke device was built as “proof-of-principle”. The idea was to show that scientists too can leverage from the open source philosophy and the knowledge built by the community that is developing around open source hardware. Moreover, the bill of materials was kept simple and affordable. One device can be built for ~25 dollars and should take 2-3 hours to build, including the time to print parts.

The device is organised as follows: The 3D printed frame (which can also be built with other materials when a printer is not available) contains a hole where the animals are expected to insert their snouts. At the front part of the hole, an infrared led is aligned with an infrared detector. This forms an “infrared curtain” at the hole’s entrance. If this curtain is interrupted, a signal is sent to a microcontroller (an Arduino in this case), and it can be used to trigger other electronic components, such as a water pump, or an led indicator, or in this case a Piezo buzzer. At the back of the hole, a white LED is placed to indicate that the system is active and ready for “nose pokes”.

The microcontroller, contains the code responsible for controlling the electronic parts, and can easily be changed, as it is written for Arduino and several code examples/tutorials (for begginners and experts) can be found online.”


Find more documentation on FigShare and Open Neuroscience.

Pixying Behavior

APril 3, 2017 

Robert Sachdev, from the Neurocure Cluster of Excellence, Humboldt Universität Zu BerlinGermany, has generously shared the following regarding automated optical tracking of animal movement: 


“We have developed a method for tracking the motion of whiskers, limbs and whole animals in real-time. We show how to use a plug and play Pixy camera to monitor the real-time motion of multiple colored objects and apply the same tools for post-hoc analysis of high-speed video. Our method has major advantages over currently available methods: we can track the motion of multiple adjacent whiskers in real-time, and apply the same methods post-hoc, to “recapture” the same motion at a high temporal resolution.  Our method is flexible; it can track objects that are similarly shaped like two adjacent whiskers, forepaws or even two freely moving animals. With this method it becomes possible to use the phase of movement of particular whiskers or a limb to perform closed-loop experiments.”