October 24, 2018
Qingchun Guo and colleagues share their cost-effective, multi-channel fiber photometry system in Biomedical Optics Express.
Fiber photometry is a viable tool for recording in vivo calcium activity in freely behaving animals. In combination with genetically encoded calcium indicators, this tool can be used to measure neuronal and population activity from a genetically defined subset of neurons. Guo and colleagues have developed a set-up to allow for recording from multiple brain regions, or multiple animals, simultaneously with the use of a galvano-mirror system. This creative and simple solution reduces the number of detectors necessary for multi-channel data collection. This expands the ability of researchers to collect calcium imaging data from many subjects in a cost-effective way.
Read more here!
Guo, Q., Zhou, J., Feng, Q., Lin, R., Gong, H., Luo, Q., … Fu, L. (2015). Multi-channel fiber photometry for population neuronal activity recording. Biomedical Optics Express, 6(10), 3919–3931. https://doi.org/10.1364/BOE.6.003919
We are looking for your feedback to understand how we can better serve the community! We’re also interested to know if/how you’ve implemented some of the open-source tools from our site in your own research.
We would greatly appreciate it if you could fill out a short survey (~5 minutes to complete) about your experiences with OpenBehavior.
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.
August 29, 2018
In a recent bioRxiv preprint, Scott Owen and Anatol Kreitzer share PhotometryBox, an open-source solution for electronic control of fiber-based fluorescence measurements.
Fluorescence measurements from deep-brain structures through optical fibers (fiber photometry) represent a versatile, powerful, and rapidly growing neuroscience technique. A typical fiber photometry system consists of three
parts: (1) an implant with an optical fiber that is cemented to the skull, (2) optical components for generation of fluorescence excitation light and detection of emission light, and (3) electronic components for controlling light sources and acquiring signals. Excellent technical solutions are available for implants and optical components; however, currently available electronic control systems are not optimized for these experiments. The most commonly used electronic components are either over-engineered or unnecessarily inflexible. To address these issues, Owen et al have developed an open-source, low-cost solution for the electronic components. This system is based on a programmable microcontroller (MBED LPC1768) and can be assembled in ~1 hour (less than a day for an inexperienced user with limited soldering experience). The total estimated cost is about $650, less than one tenth the price of the most commonly used commercially available systems.
The design, development and implementation of this project is described in a manuscript now available on bioRxiv, while details regarding parts, construction and use are available on Hackaday.
Read more on bioRxiv
or check out the Hackaday page.
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 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.
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
July 2, 2018
In Current Protocols in Neuroscience, Alexander Jacob and colleagues share their open source compact head-mounted endoscope (CHEndoscope) for imaging in the awake behaving mouse.
This miniature microscope device is designed to provide an accessible set of calcium imaging tools to investigate the relationship between behavior and population neuronal activity for in vivo rodents. The CHEndoscope is open source, flexible, and consists of only 4 plastic components that can be 3D printed. It uses an implanted gradient index (GRIN) lens in conjunction with the genetically encoded calcium indicator GCaMP6 to image calcium transients from hundreds of neurons simultaneously in awake behaving mice. The aim of the open source model is to provide an accessible and flexible set of calcium imaging tools for the neuroscience research community. The linked article describes in depth the assembly, surgical implantation, data collection, and processing of calcium signals using the CHEndoscope.
Link to paper: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpns.51
Jacob, A. D., Ramsaran, A. I., Mocle, A. J., Tran, L. M., Yan, C., Frankland, P. W., & Josselyn, S. A. (2018). A compact head‐mounted endoscope for in vivo calcium imaging in freely behaving mice. Current Protocols in Neuroscience, 84, e51. doi: 10.1002/cpns.51
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