open-source electrophysiology

July 2017 Newsletter

Added on by Open Ephys.

Open Ephys methods paper is out!

We're excited to announce the publication of the first methods paper describing the Open Ephys data acquisition platform. "Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology" is now available as an open-access article through the Journal of Neural Engineering website. The article describes the modular plugin architecture that makes the Open Ephys GUI so flexible, with a focus on how this facilitates the design and implementation of closed-loop feedback experiments. It also provides an overview of the low-cost hardware that has made such experiments accessible to a wide range of scientists. If you've been using the Open Ephys GUI or acquisition board for your experiments, please cite this article in any future publications or presentations.

The article is part of a special issue on Open-Source Tools in Systems Neuroscience, edited by Caleb Kemere. We encourage everyone to check out the other tools covered in this issue, including Falcon software for closed-loop processing and a head-mounted fluorescence microscope optimized for songbirds.

Our manufacturing partnership with OEPS

Since Open Ephys was founded, one of our biggest challenges has been keeping up with the demand for our hardware. As a volunteer-run organization with no external funding, once a batch of our tools sold out, it could take many months before the items were back in stock. Now, thanks to our ongoing partnership with Open Ephys Production Site (OEPS), our most popular piece of hardware—the acquisition board—has been continuously available throughout the year. OEPS is currently manufacturing a batch of Cyclops LED drivers, which are undergoing a final round of testing to make sure the production run performs as well as the prototypes. Stay tuned to our newsletter for an announcement when these will be available for purchase.

In addition to handling the manufacturing and distribution of our hardware, OEPS is now paying the stipend of our technical support person, Aarón Cuevas López. Therefore, all hardware purchases from OEPS will fund the ongoing development and support of our software. We recently released version 0.4.2 of the Open Ephys GUI, available for download here. The new version adds support for the "binary" recording format, a compact data format used by spike-sorting packages such as Kilosort.

OEPS has also worked with Gonçalo Lopes of the Sainsbury Wellcome Centre to make Bonsai software compatible with the USB 3.0 version of the acquisition board. Check out the example inside Bonsai's gallery (Bonsai - Ephys Example) to learn how to interface with the USB 3.0 hardware, which increases the maximum number of simultaneously recorded channels from 128 to 512. For questions and support, please visit the Bonsai user forum.

Open Ephys Summer Internship

When we weren't allocated any slots for this year's Google Summer of Code, we decided to pilot our own summer internship program. We selected Clayton Barnes of Indiana University as the first participant, given his previous work creating a real-time statistics plugin for the Open Ephys GUI. For his summer project, Clayton will combine his stats module with graphs that allow the user to visualize and quantify the neural response to specific events, both in terms of spike rate and LFP. Clayton's plugin can be applied to wide range of use cases, including optogenetics or sensory physiology experiments where the online neural response is used to guide stimulus selection or electrode placement.

Until next time, The Open Ephys Team