Category: Data Analysis

Microwave-based Homecage Motion Detector

June 25, 2018

Andreas Genewsky and colleagues from the Max Planck Institute of Psychiatry have shared the design, construction and validation of a simplified, low-cost, radar-based motion detector for home cage activity monitoring in mice. This simple, open-source device allows for motion detection without visual contact to the animal and can be used with various cage types. It features a custom printed circuit board and motion detector shield for Arduino, which saves raw activity and timestamped data in CSV files onto an SD card; the authors also provide a Python script for data analysis and generation of actograms. This device offers a cost-effective, DIY alternative to optical imaging of home-cage activity.

Read more from the Journal of Biomedical Engineering publication!

Genewsky, A., Heinz, D. E., Kaplick, P. M., Kilonzo, K., & Wotjak, C. T. (2017). A simplified microwave-based motion detector for home cage activity monitoring in mice. Journal of Biological Engineering,11(1). doi:10.1186/s13036-017-0079-y

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

ToxTrac: A fast and robust software for tracking organisms

June 8, 2018

OpenBehavior has shared a variety of popular open-source tracking software, and there’s another to add to the list: ToxTrac!

Alvaro Rodriguez and colleagues from Umeå University in Umeå, Sweden, have developed ToxTrac, an open-source Windows program optimized for high-speed tracking of animals. It uses an advanced tracking algorithm that requires no specific knowledge of the geometry of tracked bodies and can therefore be used for a variety of species. ToxTrac can also track multiple bodies in multiple arenas simultaneously, while maintaining individual identification. The software is fast, operating at a rate >25 frames per second, and robust against false positives. ToxTrac generates useful statistics and heat maps in real scale that can be exported in image, text and excel formats to provide useful information about locomotor activity in rodents, insects, fish, etc.

Learn more about ToxTrac here:

Or Download ToxTrac software here:

Rodriguez A, Zhang H, Klaminder J, Brodin T, Andersson PL, Andersson M. ToxTrac: A fast and robust software for tracking organisms. Methods Ecol Evol. 2018;9:460–464.


June 6, 2018

This post is relevant for MedPC users who also use MatLab or Python for data analysis.

We recently became aware that many MedPC users are not saving precise times for behavioral events from their experiments. A method called time-event codes was worked out around 2000 by Russ Church and his group at Brown, working with MedAssociates. Marcelo Caetano, a former postdoc in the Laubach Lab at Yale, incorporated this approach into an existing MatLab function (MedParse, written by Kumar Narayanan during his PhD training in the Laubach Lab at Yale). More recently, the code was ported to Python by Kyra Swanson, a Phd student in the Laubach Lab at American University. It is available at MedPC code for saving precise times of behavioral events (example in MedPC Template) and MatLab and Python functions are provided that convert MedPC data (see the template) into “time-event codes,” i.e., a two-column matrix with times (column 1) and events (column 2).


LocoWhisk: Quantifying rodent exploration and locomotion behaviours

March 8, 2018

Robyn A. Grant, from Manchester Metropolitan University, has shared the following on Twitter regarding the development of the LocoWhisk arena:

“Come help me develop my new arena. Happy to hear from anyone looking to test it or help me develop it further.”

The LocoWhisk system is a new, portable behavioural set-up that incorporates both gait analysis (using a pedobarograph) and whisker movements (using high-speed video camera and infrared light source). The system has so far been successfully piloted on many rodent models, and would benefit from further validation and commercialisation opportunities.

Learn more here:

Article in Nature on monitoring behavior in rodents

An interesting summary of recent methods for monitoring behavior in rodents was published this week in Nature.The article mentions Lex Kravitz and his lab’s efforts on the Feeding Experimentation Device (FED) and also OpenBehavior. Check it out:


December 18, 2017

ZebraTrack is a cost-effective imaging setup for distraction-free behavioral acquisition with automated tracking using open-source ImageJ software and workflow for extraction of behavioral endpoints of zebrafish. This ImageJ algorithm is capable of providing control to users at key steps while maintaining automation in tracking without the need for the installation of external plugins.

Nema, S., Hasan, W., Bhargava, A., & Bhargava, Y. (2016). A novel method for automated tracking and quantification of adult zebrafish behaviour during anxiety. Journal of Neuroscience Methods, 271, 65-75. doi:10.1016/j.jneumeth.2016.07.004



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.