Category: Stimuli

Open source modules for tracking animal behavior and closed-loop stimulation based on Open Ephys and Bonsai

June 15, 2018

In a recent preprint on BioRxiv, Alessio Buccino and colleagues from the University of Oslo provide a step-by-step guide for setting up an open source, low cost, and adaptable system for combined behavioral tracking, electrophysiology, and closed-loop stimulation. Their setup integrates Bonsai and Open Ephys with multiple modules they have developed for robust real-time tracking and behavior-based closed-loop stimulation. In the preprint, they describe using the system to record place cell activity in the hippocampus and medial entorhinal cortex, and present a case where they used the system for closed-loop optogenetic stimulation of grid cells in the entorhinal cortex as examples of what the system is capable of. Expanding the Open Ephys system to include animal tracking and behavior-based closed-loop stimulation extends the availability of high-quality, low-cost experimental setup within standardized data formats.

Read more on BioRxiv, or on GitHub!

Buccino A, Lepperød M, Dragly S, Häfliger P, Fyhn M, Hafting T (2018). Open Source Modules for Tracking Animal Behavior and Closed-loop Stimulation Based on Open Ephys and Bonsai. BioRxiv.

Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics

June 12, 2018

In a recent publication in the Frontiers in Systems Neuroscience, Solari and colleagues of the Hungarian Academy of Sciences and Semmelweis University have shared the following about a behavioral setup for temporally controlled rodent behavior. This arrangement allows for training of head-fixed animals with calibrated sound stimuli, precisely timed fluid and air puff presentations as reinforcers. It combines microcontroller-based behavior control with a sound delivery system for acoustic stimuli, fast solenoid valves for reinforcement delivery and a custom-built sound attenuated chamber, and is shown to be suitable for combined behavior, electrophysiology and optogenetics experiments. This system utilizes an optimal open source setup of both hardware and software through using Bonsai, Bpod and OpenEphys.

Read more here!


Solari N, Sviatkó K, Laszlovszky T, Hegedüs P and Hangya B (2018). Open Source Tools for Temporally Controlled Rodent Behavior Suitable for Electrophysiology and Optogenetic Manipulations. Front. Syst. Neurosci. 12:18. doi: 10.3389/fnsys.2018.00018

Open-source touch-screen for rodent behavioral testing

March 9, 2018

O’Leary and colleagues describe an open-source touch-screen for rodent behavioral testing. The manuscript is well documented and includes all of the parts needed to build the system on your own. Very useful methods for testing cognitive function and relating findings across species (rodents, primates, humans). Congrats to the authors on setting a high standard for open-source neuroscience!

O’Leary, J.D., O’Leary, O.F., Cryan, J.F. et al. Behav Res (2018).

DIY Rodent Running Disk

February 6, 2018 

Brian Isett, who is now at Carnegie Mellon, has kindly shared the following tutorial regarding the creation and implementation of a Rodent Running Disk he designed while at University of California, Berkeley.

“Awake, naturalistic behavior is the gold standard for many neuroscience experiments.  Increasingly, researchers using the mouse model system strive to achieve this standard while also having more control than a freely moving animal. Using head-fixation, a mouse can be positioned very precisely relative to ongoing stimuli, but often at the cost of naturalism. One way to overcome this problem is to use the natural running of the mouse to control stimulus presentation in a closed-loop “virtual navigation” environment. This combination allows for awake, naturalistic behavior, with the added control of head-fixation. A key element of this paradigm is to have a very fast way of decoding mouse locomotion.
In this tutorial, we describe using an acrylic disk mounted to an optical encoder to achieve fast locomotion decoding. Using an Arduino to decode the TTL pulses coming from the optical encoder, real-time, closed-loop stimuli can be easily presented to a head-fixed mouse. This ultimately allowed us to present tactile gratings to a mouse performing a whisker-mediated texture discrimination task as a “virtual foraging task” — tactile stimuli moved past the whiskers synchronously with mouse locomotion. But the design is equally useful for measuring mouse running position and speed in a very precise way.”

The tutorial may be found here.

Isett, B.R., Feasel, S.H., Lane, M.A., and Feldman, D.E. (2018). Slip-Based Coding of Local Shape and Texture in Mouse S1. Neuron 97, 418–433.e5.

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




December 20, 2017

StimDuino, an inexpensive Arduino-controlled stimulus isolator that allows for highly accurate, reproducible automated setting of stimulation currents. The automatic stimulation patterns are software-controlled and the parameters are set from Matlab-coded simple, intuitive and user-friendly graphical user interface. StimDuino-generated automation of the input-output relationship assessment eliminates need for the current intensity manually adjusting, improves stimulation reproducibility, accuracy and allows on-site and remote control of the stimulation parameters for both in vivo and in vitro applications.

Sheinin, A., Lavi, A., & Michaelevski, I. (2015). StimDuino: An Arduino-based electrophysiological stimulus isolator. Journal of Neuroscience Methods, 243, 8-17. doi:10.1016/j.jneumeth.2015.01.016

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.”

Pulse Pal

July 12, 2017

Josh Sanders has also shared the following with OpenBehavior regarding Pulse Pal, an open source pulse train generator. Pulse Pal and Bpod, featured earlier, were both created by Sanworks.

Pulse Pal is an Arduino-powered device that generates precise sequences of voltage pulses for neural stimulation and stimulus control. It is controlled either through its APIs in MATLAB, Python and C++, or as a stand-alone instrument using its oLED screen and a clickable thumb joystick. Pulse Pal can play independent stimulus trains on its output channels. These trains are either defined parametrically, or pulse-wise by specifying each pulse’s onset time and voltage. Two optically isolated TTL trigger channels can each be mapped to any subset of the output channels, which can range between -10V and +10V, and deliver pulses as short as 100µs. This feature set allows Pulse Pal to serve as an open-source alternative to commercial stimulation timing devices, i.e. Master 8 (AMPI), PSG-2 (ISSI), Pulsemaster A300 (WPI), BPG-1 (Bak Electronics), StimPulse PGM (FHC Inc.) and Multistim 3800 (A-M Systems).

Because Pulse Pal is an Arduino-powered device, modifying its firmware for custom applications is within the capabilities of most modern Neuroscience research labs. As an example, the Pulse Pal’s Github repository provides an alternative firmware for the device, that entirely repurposes it as a waveform generator. In this configuration, a user can specify a waveform, frequency, amplitude and max playback duration, and toggle playback by TTL pulse with ~100µs latency. The firmware can also loop custom waveforms up to 40,000 samples long.

Pulse Pal was first published in 2014, by Josh Sanders while he was a student in Kepecs Lab at Cold Spring Harbor Laboratory. A significantly improved second-generation stimulator (Pulse Pal 2) became available in early 2016, coincident with the opening of Sanworks LLC. Over the past year, >125 Pulse Pal 2 devices were sold at $545 each by the Sanworks assembly service, while several labs elected to build their own. The initial success of this product demonstrates that fully open-source hardware can make headway against closed-source competitors in the Neuroscience instrumentation niche market.

Sanworks Github page for Pulse Pal may be found here.

The Wiki page for Pulse Pal, including assembly instructions, may be found here.


July 10, 2017

Josh Sanders has shared the following with OpenBehavior regarding Bpod, an open platform for precision animal behavior measurement created by Sanworks.

Bpod is a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. Its software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller. Atop the heiarchy is a “state machine” module that accepts an abstract trial definition, relating detected behavioral events to progression through user-defined hardware states. On trial start, the module serves as a real-time controller in parallel with the non-real-time computer, reading inputs and updating outputs in 100µs cycles until it reaches an exit state. Measured events are then returned to the computer, where software updates user-defined online plots, and loads the next trial’s state machine.

The Bpod state machine has on-board hardware interfaces for TTL logic and behavior ports (a.k.a. nosepokes) containing a photogate to detect snout entry, a miniature solenoid valve for liquid reward, and a visible LED to deliver cues and feedback. Modules under state machine control specialize in larger solenoids, analog input and output, direct digital synthesis, and a gamepad interface (for human research). An Arduino shield is provided, for users to interface new sensors and actuators with the state machine.

By handling the time-critical logic relating measurements to environment control in an open-source embedded computing environment, the Bpod system provides experimenters with a powerful family of tools for rigor and automation in behavioral research.

Sanworks’ GitHub may be found here.

The Wiki page for Bpod, including assembly instructions and Bill of Materials may be found here.