April 17, 2019
In a recent Nature Protocol’s article, Edoardo Balzani and colleagues from Valter Tucci’s lab have developed and shared Phenopy, a Python-based open-source analytical platform for behavioral phenotyping.
Behavioral phenotyping of mice using classic methods can be a long process and is susceptible to high variability, leading to inconsistent results. To reduce variance and speed up to process of behavioral analysis, Balzani et al. developed Phenopy, an open-source software for recording and analyzing behavioral data for phenotyping. The software allows for recording components of a behavioral task in combination with electrophysiology data. It is capable of performing online analysis as well as analysis of recorded data on a large scale, all within a user-friendly interface. Information about the software is available in their publication, available from Nature Protocols.*
Check out the full article from Nature Protocols!
(*alternatively available on ResearchGate)
March 29, 2019
In a 2011 Journal of Neuroscience Methods article, Pishan Chang and colleagues shared their design for an open-source, novel telemetry system for recording EEG in small animals.
EEG monitoring in freely-behaving small animals is a useful technique for observing natural fluctuations in neural activity over time. Monitoring frequencies above 80 Hz continuously over a period of weeks can be a challenge. Chang et al. have shared their design for a system that combines an implantable telemetric sensor, radio-frequency transmission, and an open-source data acquisition software to collect EEG data over a span of up to 8 weeks. Various modifications to the system have increased the longevity of the device and reduced transmission noise to provide continuous and reliable data. Schematics of the device, transmission system, and validation results in a population of epileptic rodents are available in their publication.
Learn more from the Journal of Neuroscience Methods!
August 1, 2018
In a 2014 PLoS ONE article, Shaun R. Patel and colleagues share their design for PriED, an easy to assemble modular micro-drive system for acute primate neurophysiology.
Electrode micro-drives are a great tool that allow for independent positioning of multiple electrodes in primate neurophysiology, however, commercially available micro-drives are often expensive. Printed Electronic Device (PriED) is designed to advance existing micro-drive technology while staying inexpensive and requiring minimal skill and effort to assemble. The device combines 3D printed parts and affordable, commercially available steel and brass components which can then be controlled manually, or automatically with the addition of an optional motor. Using 3D printing technology researchers have the flexibility to be able to modify part designs and create custom solutions to specific recording needs. A public repository of drive designs has been made available where researchers can download PriED components to print for assembly. Additionally, researchers can upload modified designs with annotations for others to use. PriED is an innovative, inexpensive, and user friendly micro-drive solution for flexible multi-site cortical and subcortical recordings in non-human primates.
Read more here!
Or check out the repository here!
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.
Martinez, D., Clément, M., Messaoudi, B., Gervasoni, D., Litaudon, P., & Buonviso, N. (2018). Adaptive quantization of local field potentials for wireless implants in freely moving animals: An open-source neural recording device. Journal of Neural Engineering, 15(2), 025001. doi:10.1088/1741-2552/aaa041
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
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