Category: Data Analysis

VASIC

September 19, 2018

In HardwareX, Brendan Drackley and colleagues share VASIC, an open source weight-bearing device for high-throughput and unbiased behavioral pain assessment in rodents.


The assessment of pain in animal models is a key component in understanding and developing treatments for chronic pain. Drackley and colleagues developed VASIC (Voluntary Access Static Incapacitance Chamber), a modified version of a weight-bearing test. A brief water deprivation encourages rats or mice to seek water in a test chamber, set up with a weighing platforms under the water spout, which can assess weight shifting to an unaffected side in animals with damage to nerves or inflammatory pain. The design incorporates a custom printed circuit board (available from the paper), infrared sensor, Arduino microcontroller, 3D printed parts, and open source software for analysis. A full parts list, links to files, and data from a validation study are available in their paper.

Read more here!


NeuroMatic

September 12, 2018

In Frontiers in Neuroinformatics, Jason Rothman and R. Angus Silver share NeuroMatic, an open-source toolkit for acquiring, analyzing and simulating electrophysiological data.


Data acquisition, analysis, and simulation are key components of understanding neural activity from electrophysiological recordings. Traditionally, these three components of ephys data have been handled by separate software tools. NeuroMatic was developed to merge these tools into a single package, capable of performing a variety of patch-clamp recordings, data analysis routines and simulations of neural activity. Additionally, due to its open-source, modular design in WaveMetrics Igor Pro, NeuroMatic allows users to develop their own analysis functions that can be easily incorporated into its framework. By integrating acquisition, analysis, and simulation together, researchers are able to conserve experimental metadata and track the analysis performed in real time, without involving separate softwares.

Read more about NeuroMatic here!

Or check out their website and GitHub.


Argus

September 5, 2018

In a recent Behavior Research Methods article, Soaleha Shams and colleagues share Argus, a data extraction and analysis tool built in the open-source R language for tracking zebrafish behavior.


Based on a formerly developed custom-software for zebrafish behavior tracking, Argus was developed with behavioral researchers in mind. It includes a  new, user-friendly, and efficient graphical user interface and offers simplicity and flexibility in measuring complex zebrafish behavior through customizable parameters set by the researcher. The program is validated against two commercially available programs for zebrafish behavior analysis, and measures up in its ability to track speed, freezing, erratic movement, and interindividual distance. In summary, Argus is shown to be a novel, cost- effective, and customizable method for the analysis and quantification of both single and socially interacting zebrafish.

Read more here!


An inexpensive, scalable Picamera system for tracking rats in large spaces

August 15, 2018

In the Journal of Neurophysiology, Sachin S. Deshmuhk and colleagues share their design for a Picamera system that allows for tracking of animals in large behavioral arenas.


Studies of spatial navigation and its neural correlates have been limited in the past by the reach of recording cables and tracking ability in small behavioral arenas. With the implementation of long-range, wireless neural recording systems, researchers are not able to expand the size of their behavioral arenas to study spatial navigation, but a way to accurately track animals in these larger arenas is necessary. The Picamera system is a low-cost, open-source scalable multi-camera tracking system that can be used to track behavior in combination with wireless recording systems. The design is comprised of 8 overhead Raspberry Pi cameras (capable of recording at a high frame rate in a large field of view) recording video independently in individual Raspberry Pi microcomputers and processed using the Picamera Python library. When compared with a commercial tracking software for the same purpose, the Picamera system reportedly performed better with improvements in inter-frame interval jitter and temporal accuracy, which improved the ability to establish relationships between recorded neural activity and video. The Picamera system is an affordable, efficient solution for tracking animals in large spaces.

Read more here!

Or check out their GitHub!


Saxena, R., Barde, W., and Deshmukh, S.S. An inexpensive, scalable camera system for tracking rats in large spaces (2018). Journal of Neurophysiology. https://doi.org/10.1152/jn.00215.2018

An opensource lickometer and microstructure analysis program

August 8, 2018

In HardwareX, an open access journal for designing, building and customizing opensource scientific hardware, Martin A. Raymond and colleagues share their design for a user-constructed, low-cost lickometer.


Researchers interested in ingestive behaviors of rodents commonly use licking behavior as a readout for the amount of fluid a subject consumes, as recorded by a lickometer. Commercially available lickometers are powerful tools to measure this behavior, but can be expensive and often require further customization. The authors offer their own design for an opensource lickometer that utilizes readily available or customizable components such as a PC sound card and 3D printed drinking bottle holder. The data from this device is collected by Audacity, and opensource audio program, which is then converted to a .csv format which can be analyzed using an R script made available by the authors to assess various features of licking microstructure. A full bill of materials, instructions for assembly and links to design files are available in the paper.

Check out the full publication here!


Raymond, M. A., Mast, T. G., & Breza, J. M. (2018). An open-source lickometer and microstructure analysis program. HardwareX, 4. doi:10.1016/j.ohx.2018.e00035

Collaboration between OpenBehavior and Hackaday.io

July 23, 2018

OpenBehavior has been covering open-source neuroscience projects for a few years, and we are always thrilled to see projects that are well documented and can be easily reproduced by others.  To further this goal, we have formed a collaboration with Hackaday.io, who have provided a home for OpenBehavior on their site.  This can be found at: https://hackaday.io/OpenBehavior, where we currently have 36 projects listed ranging from electrophysiology to robotics to behavior.  We are excited about this collaboration because it provides a straightforward way for people to document their projects with instructions, videos, images, data, etc.  Check it out, see what’s there, and if you want your project linked to the OpenBehavior page simply tag it as “OPENBEHAVIOR” or drop us a line at the Hackaday page.

Note: This collaboration between OpenBehavior and Hackaday.io is completely non-commercial, meaning that we don’t pay Hackaday.io for anything, nor do we receive any payments from them.  It’s simply a way to further our goal of promoting open-source neuroscience tools and their goal of growing their science and engineering community.


https://hackaday.io/OpenBehavior

 

NeRD: an open-source neural recording device

July 16, 2018

In a special issue of Journal of Neural Engineering, Dominique Martinez and colleagues their share design for NeRD, an open source neural recording device for wireless transmission of local field potential (LFP) data in in freely-behaving animals.


Electrophysiological recording of local field potentials in freely-behaving animals is a prominent tool used by researchers for assessing the neural basis of behavior. When performing these recordings, cables are commonly used to transmit data to the recording equipment, which tethers the animals and can interfere with natural behavior. Wireless transmission of LFP data has the advantage of removing the cable between the animal and the recording equipment, but is hampered by the large number of data to be transmitted at a relatively high rate.
To reduce transmission bandwidth, Martinez et al. propose an encoder/decoder algorithm based on adaptive non-uniform quantization. As proof-of- concept, they developed a NeRD prototype that digitally transmits eight channels encoded at 10 kHz with 2 bits per sample. This lightweight device occupies a small volume and is powered with a small battery allowing for 2h 40min of autonomy. The power dissipation is 59.4 mW for a communication range of 8 m and transmission losses below 0.1%. The small weight and low power consumption offer the possibility of mounting the entire device on the head of a rodent without resorting to a separate head-stage and battery backpack. The use of adaptive quantization in the wireless transmitting neural implant allows for lower transmission bandwidths, preservation of high signal fidelity, and preservation of fundamental frequencies in LFPs from a compact and lightweight device.
Read more here!

Github


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. http://dx.doi.org/10.1101/340141

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!

GitHub


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