Looking at single motor units during behavior with our Acquisition Board

We just wrapped another fantastic workshop, this time about using high-resolution EMG recordings to untangle single motor unit contributions to behavior! The workshop was focused around the new high-density muscle electrode arrays called myomatrix, and it turns out these are really easy to use with the Open Ephys Acquisition Board to record single-unit EMG activity. Let’s dive into how…

Flexible high-density myomatrix arrays for EMG single-unit recordings in freely-behaving animals.

The myomatrix arrays are planar, flexible multielectrode arrays for subcutaneous surface or intramuscular EMG recordings produced by the Center for Advanced Motor BioEngineering Research (CAMBER). In their current form, they contain 4 threads each with 8 contacts of 100 x 200 μm of < 1MOhm impedance, and a ground pad. They interface with a 32 channel (36 pins, 4 guide posts) Omnetics connector which makes them compatible with most headstages used in modern digital extracellular electrophysiology acquisition systems. The arrays come in different lengths for different target muscle groups, and users can request custom adaptations. They have been tested on a wide variety of species including rodents, songbirds, and even humans. You can read about their specifications and applications in detail in this research article, and find more about CAMBER’s work in fabricating and distributing these devices on their website.

Since these arrays uniquely allow single spike EMG resolution, researchers can look at individual motor unit contributions to muscle activity during behavior. The multichannel configuration can be used with a local referencing scheme to yield 16 channel bipolar input, or 32 channel monopolar input recordings using post-hoc digital referencing. The high channel counts and single unit resolution was previously inaccessible with traditional wire bulk EMGs. The ease of access to pre-fabricated electrodes with standard connectors also enables researchers to get started with common digital extracellular electrophysiology acquisition systems based on the Intan RHD2000 series bioamplifier chip such as the Open Ephys Acquisition Board.

The implant procedure is straightforward for experienced surgeons, and consists of making a headcap to cement the device connector to the head, running the array subcutaneously and suturing the array electrode contacts into place either intramuscularly or on the muscle surface. Arrays implanted chronically or intramuscularly are not reusable, while surface arrays used acutely can be reused around 4 times. After animal recovery, behavioral testing can start and units are best isolated during 1-2 weeks after implantation, while bulk EMG can still be recorded for several more weeks.

The array is then connected to a headstage for signal amplification and digitization, and the Open Ephys Acquisition Board is used for acquisition of headstage data and any additional analog and digital inputs you may need for data from other sensors or synchronization with behavior. You can take advantage of all the Open Ephys GUI functionality for signal visualization and online processing, or use the Bonsai programming language for integrated acquisition and behavioral arena control with hundreds of options for third-party cameras, lickometers, nose-poke detectors, etc. This makes it possible to dream up experiments during naturalistic behavior such as perturbations at specific gait phases based on muscle activity. And for sub-ms closed-loop latencies, a bipolar ONI-compliant coaxial headstage to hook up the array to our multimodal ONIX system would be all you need. With creative implantation techniques, the myomatrix arrays could even be used simultaneously with ephys headstages and miniscopes!

We taught about these approaches at the single unit EMG workshop organized by Graziana Gatto in collaboration with CAMBER (Sam Sober, Amanda Jacob), Open Ephys, Büschges Lab and the CRC1451 on Motor Control that took place in Cologne, Germany in March 2024, and plan to continue next year!

Amanda Jacob, Graziana Gatto, Cecilia Herbert and Sam Sober teaching at the single-unit EMG Workshop in Cologne.

Workshop participants learnt about the myomatrix arrays, neural data acquisition in the Open Ephys ecosystem and synchronization with behavioral tools, surgical techniques, spike sorting, and discussed the use of muscle activity as readout for behavior that provides more dimensions to traditional video based analysis of movement.

Single-unit resolution EMG recordings in the Open Ephys GUI with the Open Ephys Acquisition Board, and workshop participants deep at work!

The Gatto lab at Uniklinik Köln studies sensorimotor adaptation, characterizing the spinal circuits underlying reflexive movements in physiological, adaptive and disease conditions. They have spearheaded user testing of the myomatrix arrays, working with the CAMBER team to improve their development from the start, and increase adoption thanks to training opportunities such as this workshop. Thank you Graziana and the Gatto lab for being fantastic hosts.

CAMBER is based at Emory University and Georgia Tech in Atlanta, Georgia, USA. Their purpose is to develop and disseminate next-generation tools for investigating motor control. They have supply list, tutorials and example protocols to help you get started. They are currently providing myomatrix arrays free of charge - get in touch with them!

Open Ephys Starter Kit

€6,985.00

You can get an acquisition board and myomatrix-compatible headstages from the Open Ephys Store.

If you would like extra help, we can provide remote personalized Training to get you started using our systems.

Until next time!

Recent workshops

May was an exciting time for the Training team at Open Ephys. Read more about the two awesome events we participated in…

In early May we participated in a workshop during NeuroDoWo (Konstanz, Germany) with activities to learn about closed-loop behavior and electrophysiology. The week after, we gave lectures about Open Ephys and UCLA Miniscopes and contributed to the practical sessions of the Paris Neuro Course (Paris, France).

At NeuroDoWo, we talked about what events in a neural signal or in behavior can serve as triggers of effects on the subject or the behavioral arena. We looked at how to acquire and detect events with the Open Ephys GUI using our classic acquistion system, as well as in Bonsai using a behavioral camera for these closed-loop applications.

Open Ephys GUI working with the Acquisition Board in a closed-loop example that outputs a TTL pulse when a peak in the phase is detected.

Detecting animal entry intro a region of interest using a webcam and Bonsai in order to trigger subsequent events.

Participants then experienced these concepts first hand as they tracked insects and lit an LED based on their location, tried some online spike sorting on neuronal data, and used real-time pose estimation on themselves to make different body part positions modulate sound. They had lots of fun moving through the different activity stations and learnt a lot.

“It was fun and interesting to ask questions directly to an expert about the possibility and limits of using the GUI for ephys data analysis”

“It was a very interactive workshop and we could experience a wide variety of tools in a short amount of time”

Students learning about online spike detection and sorting in the Open Ephys GUI.

Students tracking robot insects in the Bonsai software.

At the Paris Neuro Course, we presented the UCLA Miniscope system, sharing insights about how user feedback shapes iterations of the tools we produce. The students also got to work with our new coaxial commutator and had a glimpse of how miniscopes can be used in Bonsai and synchronized with external hardware to integrate calcium imaging acquisition with behavioral paradigms.

The UCLA Miniscope is assembled from three 3D printed modules, lenses, a filter set and a PCB with all the electronics. It is straightforward and can be built in a couple of hours without the need for soldering or specialized tools.

During the practicals, students were led through an in-vivo imaging experiment from start to finish. They built their own scopes using our UCLA Miniscope assembly kits, observed the surgery, imaged animals during navigation in a complex arena and analyzed their data. Unreal, huh?

Inserting the lenses into the miniscope body.

Removing burrs from the 3D print of the body.

Checking that everything is spotless before assembly to ensure a clear field of view.

We often find that Neuroscientists that have not heard of us before are impressed with the straightforward implementation and low entry price of the system, and this was no exception. This makes us happy. They also got to hear about Open Ephys as a whole from one of the co-founders, Josh Siegle, who is responsible for most of the Open Ephys GUI (a founder that gets their hands dirty👷!).

Our educational and showcase activities strive to be interactive and open-ended so participants can experience challenges directly and attempt to answer their own questions. The goal is to provide general concepts that can be applied to different scenarios, using our open-source tools as examples to understand them. We also highlight features of open projects such as how they can be customized and how to contribute to expand them. This approach helps identify knowledge and need gaps so we can improve our training services and our tools to better serve users.

We want to extend a huge thanks to the course organizers and the rest of the teaching team for making such rewarding events for discussion and learning. Feel free to reach out to training[at]oeps.tech if you are interested in setting up similar activities with us.

You can find resources to learn more below. Until next time!

• Slides from the NeuroDoWo workshop on closed-loop behavioral neuroscience focusing on electrophysiology.

• Slides from the Paris Neuro Course on Miniscopes at Open Ephys

• Neurokit course on Extracellular Electrophysiology Acquisition

  Synchronous course application, Kit for the self-paced course and Open-source course materials

• Our Training services for the Open Ephys Acquisition Board and UCLA Miniscopes

• Documentation for using our Acquisition Board and GUI.

• The Open Ephys GUI includes sample data and you can stream it to try online signal processing without an acquisition board.

• The activities in Bonsai can be recreated following their video tracking tutorial and by using our real-time pose estimation activity.

Thank you to both course organizations for the course pictures. Please use other materials in accordance to the CC-BY-SA license.

Want to join the team? Check out our open positions and apply!

February 2020 Newsletter

We’re now accepting orders for open-source devices that expand the range of tools offered through our store. 

The Wire-Free Miniscope, developed by Daniel Aharoni & the UCLA Miniscope team, makes it possible to image cell populations deep inside the brain without the need for a tether. It was featured in this paper that recently appeared in Nature Neuroscience. The components required to transform the Miniscope V3 into the wire-free version can now be ordered through our online store. Since we ran the Open Ephys x Miniscope booth at SfN, we've been working on ways for both initiatives to collaborate, and this is one of the first examples of how these efforts are bearing fruit.

FED3, developed by Lex Kravitz, Mohamed Ali, Katrina Nguyen, and Filipe Carvalho, is a portable, hackable device that can be used to train mice on a variety of operant conditioning tasks. It's battery powered and completely wire-free, so it can be used for up to one week of home-cage training on a single charge. We hope to make it accessible to a wider audience by selling it through the Open Ephys store.

In addition, Twister3, a dramatically improved tetrode twister developed by Jon Newman and Jakob Voigts, in collaboration with SpikeGadgets, will be available for purchase soon. Stay tuned for more info on how to place an order!

Announcing StimJim

You may have seen the preprint for StimJim, an open-source electrical stimulator designed by Nate Cermak. Similar to Cyclops, its LED-driver cousin, StimJim outperforms all of the substantially more expensive closed-source alternatives based on a variety of metrics. We’re currently gauging interest from the community to decide whether we should manufacture and sell these devices. If you think StimJim would help your research, please fill out out the survey on this page!

OEPS is going green

Our manufacturing partner, Open Ephys Production Site (OEPS), has recently overhauled their shipping materials to lighten their environmental impact. They’re now using recycled packaging wherever possible, so keep an eye out for new green bags on your next order! They’ve also replaced all styrofoam with a biodegradable, antistatic filling material to protect your products during shipping. This effort is a work in progress, so advice is always welcome. OEPS will continue to explore the most sustainable ways to keep delicate equipment safe during transit.

Neurophotometrics is going open source

Neurophotometrics, a scientist-run company that sells state-of-the-art fiber photometry equipment, announced that their next round of devices will be fully open source. According to their recent blog post, "our firmware, software, analysis scripts, and optical designs will be freely available to everyone that wishes to access it. [...] Our hope is to strengthen our bond with labs that use our fiber photometry system by allowing everyone to look under the hood and have control over all aspects of their instrument."

Open Ephys was founded to promote open-source tools because we believe they are essential for carrying out cutting-edge science. They allow new methods to propagate further, evolve faster, and be applied in more creative ways. Most importantly, they respect the fact that the shortcomings of existing tools force neuroscientists to become engineers out of necessity, and flexible open-source platforms help ensure that their innovations are not wasted. Therefore, we were thrilled to learn that Neurophotometrics recognizes they can run a sustainable business based on open-source tools, and we look forward to other companies making the same decision!

Bonsai Mini-Hackathon

Gonçalo Lopes, the creator of Bonsai, spent 8 days at the Allen Institute last month, teaching software engineers about Bonsai and working together to prototype new features. Bonsai is a powerful visual programming language designed to handle the diverse needs of systems neuroscience experiments—from tracking behavior to controlling stimuli to triggering closed-loop neural feedback. Our next-generation PCIe-based acquisition system has been optimized for use with Bonsai, and we’re planning much tighter integration between Bonsai and the Open Ephys GUI.

During this “mini-hackathon,” the team successfully ran Bonsai on Mac and Linux machines (thanks to the recently open-sourced .NET Core platform), tested out an interface for configuring Bonsai from other software, and built a Bonsai source module for the Neuropixels PXI acquisition system. We believe that Bonsai is one of the most under-appreciated applications in neuroscience, and we'll be working hard to help it reach a wider audience in the near future.


Until next time,
The Open Ephys Team

October 2019 Newsletter

Open Ephys at SfN 2019

It's going to be a busy week for us at this year's conference! We're organizing our first-ever booth (in collaboration with the UCLA Miniscope team), as well as putting together a number of posters, satellite events, and a DJ set. Read on to find out all the details...

The best place to find us this year will be at the Open Ephys x Miniscope Booth (#1766). We'll be showcasing oni, or "open neural interface," a new data acquisition system that will work seamlessly with our next-generation tetrode headstages, Neuropixels, and the latest Miniscopes. This will be an incredibly versatile tool, no matter where your science takes you. It comes in PCIe and USB versions, and has a whole host of features you'll want to explore. If you won't be at the meeting, be sure to check out our "virtual booth" by following this link.

Open-Source Technology Social

Jakob Voigts and Denise Cai are organizing a social for people using open-source tools and those curious to learn more about them. Come say hello on Monday evening from 6:45-8:45 pm in room N135 of McCormick Place.

Tools & Tech: A BRAIN Initiative Alliance Social

Open Ephys will have a table at this event, along with numerous other toolmakers in the field. It's happening Sunday evening from 6:30 - 8:30 pm at the Hyatt Regency McCormick Place Ballroom CD. More info can be found on the event website.

Poster sessions

Our main focus this year is on our booth, but there are also a few key posters that highlight the open-source tools we're using and developing:

Gonçalo Lopes - “BonVision - An open-source software to create and control visual environments” (Monday morning, L14)

Pavel Kulik – “Real-time processing and visualization of high-channel-count electrophysiology data with the Open Ephys GUI” (Tuesday morning, CC52)

Aarón Cuevas López – “A low-power wireless transmission system of neural data by hardware compression” (Tuesday morning, CC53)

Ephys data acquisition software survey

We're launching a new survey to help guide our software development over the next year. If you regularly carry out experiments with extracellular electrodes (regardless of whether or not you use Open Ephys tools), you are highly encouraged to respond! One randomly selected participant will receive a $100 Newegg gift card. Please visit survey.open-ephys.org to fill it out; it should only take 5-10 minutes.

"Meet the Experts" at the Neuropixels Booth

If you're currently using Neuropixels—or thinking about starting—there will be plenty of opportunities to ask questions at the Neuropixels booth (#2037). Josh Siegle will be there discussing Open Ephys/Neuropixels integration Sunday from 4-5 pm, Monday from 1-2 pm, Tuesday from 4-5 pm, and Wednesday from 9:30-10:30 am. Josh will also be at the Allen Institute booth (#401) answering questions between 10:30 and 12:30 on Sunday.

Neurolabware Party

Our friends at Neurolabware have consistently thrown THE party to attend at SfN, and this year is no different. The event is happening on Tuesday night from 9 pm - 2 am at PRYSM Nightclub. They aren't giving out wristbands this year, so be sure to arrive early! In any case, you'll want to get there to catch Josh Siegle's DJ set, which starts right at 9.

Compact, Open Ephys compatible headstages

At their booth this year (#1669), Cambridge NeuroTech will be showcasing *very tiny* 64-channel headstages that are plug-and-play compatible with the Open Ephys acquisition board. We are huge proponents of open interfaces, and we're glad that Cambridge Neuro decided to adopt Intan's SPI standard for these, which only weigh 0.38 g.

Open Ephys GUI updates

There's a new version of the Open Ephys GUI available for download (version 0.4.5). The major updates include improved support for Neuropixels (Windows only) and migrating the build system to CMake, which will allow us to use continuous integration for application testing and distribution. A big change on the developer side is that all plugins that rely on external libraries (e.g. ZeroMQ, HDF5) have been moved to separate repositories, so you can build the GUI with Juce as the only dependency. If you have any questions about the changes, don't hesitate to write to info@open-ephys.org!


Until next time,
The Open Ephys Team

September 2019 Newsletter

Pre-prints describing two new tools

A key objective of Open Ephys has always been to make extracellular electrophysiology more accessible. This not only entails making hardware that costs less, but also designing tools that are easy to use. As anyone who does ephys experiments is well aware, there are still many time-consuming steps involved in preparing for each experiment. So we are excited to announce two new tools that will allow you to spend less time building things and more time Doing Science. 

The shuttleDrive, developed by Jakob Voigts and Jon Newman at MIT, makes it possible to assemble a 64-channel tetrode implant for a mouse in under a day. The shuttleDrive can be built quickly without sacrificing robustness—the preprint includes quantification of the screw-turn-to-tetrode-depth ratio, which is extremely linear. Most importantly, the components are readily available. Everything you need to get started building mouse shuttleDrives can be purchased through the Open Ephys store.

Twister3, developed by Jon Newman and Jakob Voigts in collaboration with SpikeGadgets, lays to rest the assumption that making tetrodes needs to be a time-consuming process. By eliminating the need to fold wires by hand, and reducing twisting times to a matter of seconds, the Twister3 takes the pain out of tetrode fabrication. Instructions for building Twister3 can be found in the pre-print on bioRxiv, with usage instructions in this handy video. We’re considering selling partially or fully assembled devices through our store, so if you’re at all interested in purchasing one, please fill out the survey on this page to let us know how much you’d be willing to pay for one.


Beta-testing our next-generation system (Open Ephys++)

We are almost ready to roll out our next-generation data acquisition system, which we will be demonstrating at SfN next month. This system, developed by Jon Newman, Jack Zhang, and Jakob Voigts at MIT, can stream thousands of channels of ephys data with sub-millisecond latency through a standard PCIe slot. It was designed to work with novel ultra-compact and fully kitted-out headstages for mice and rats, but it can also interface with the standard Intan headstages you know and love. The system is being used routinely for ephys experiments in the Wilson Lab, and now we’re looking for beta testers to give us feedback on the first round of devices. If you’re interested in becoming a beta tester, please send an email to info@open-ephys.org. Beta testers will be able to purchase the system early, and will receive an updated version free of charge if it improves significantly prior to general public release. We will have the system on display at our inaugural booth at SfN, which we’re organizing in collaboration with the UCLA Miniscope team. Our next newsletter will include more information about the booth, poster presentations, and other opportunities to meet with the Open Ephys team in Chicago.


New USB-based acquisition boards with over-voltage protection

All acquisition boards purchased through the Open Ephys store will now include over-voltage protection on the power jack. The device still only works with a 5V supply, but now you won’t fry the board if you accidentally plug in a different type of adapter. Over the past two years, OEPS has repaired 15 boards damaged by an incorrect voltage source. Hopefully this update will help make the acquisition board even more user-friendly.


Welcome Pavel and Anjal to the Open Ephys team

Back in April, the Allen Institute received a BRAIN Initiative U24 award to improve the accessibility of software for Neuropixels probes. The award will provide funding for two software engineers to work on Open Ephys, both of whom have now been hired. Pavel Kulik started working in April, and has already made significant contributions to the code base, including building a NIDAQ plugin for streaming auxiliary analog and digital data from National Instruments devices. Anjal Doshi was hired this month after finishing his CS master’s degree with a specialization in computer graphics. We are excited to have them on our team—be on the lookout for @medengineer or @anjaldoshi responding to your GitHub support requests!


Jon Newman joins the board of directors

We are pleased to have Jon Newman become a member of the Open Ephys board of directors. Jon has been a stalwart supporter of open-source tools throughout his career. His NeuroRighter system was a major source of inspiration for the original Open Ephys acquisition system, and his Cyclops LED driver has become an invaluable component of our optogenetics rigs. More recently, his designs for the shuttleDrive, Twister3, and Open Ephys++, among plenty of other work, have raised the standard for neuroscientific tools—open-source or otherwise. Along with Matt Wilson, Caleb Kemere, Chris Moore, Jakob Voigts, and Josh Siegle, Jon will help guide the overall vision of our organization, and ensure that, as a Massachusetts-based nonprofit, we continue to uphold our mission of promoting “tool-sharing among members of the worldwide systems neuroscience community.”


Until next time,
The Open Ephys Team

November 2018 Newsletter

Open Ephys at SfN 2018

For those of you going to San Diego this year, here are the opportunities to hear more about what we've been up to lately:

At the Monday afternoon session, Jon Newman will be presenting a poster on a PCIe-based platform for real-time feedback experiments. The specs on this thing are pretty incredible—it's easily the most advanced system for high-density tetrode recordings in freely moving rodents. Furthermore, the design includes a general-purpose API for low-latency data transmission, which will facilitate closed-loop experiments with all types of hardware.

We'd love to hear your thoughts on how this system should evolve. Please fill out this survey, and come talk to us on Monday!

431.24 / LLL59: Open Ephys++: High performance open-source firmware, APIs, and hardware for closed-loop neuroscience experiments
November 5
1 - 5 pm
Poster hall
https://abstractsonline.com/pp8/#!/4649/presentation/24889

On Tuesday evening, we'll be at the Open-Source Technology Social along with a host of other people developing and disseminating open tools for neuroscience.

SS29: Open-Source Technology Social
November 6
6:45 - 8:45 pm
Marriott Marquis - Grand Ballroom 10
https://abstractsonline.com/pp8/#!/4649/session/272

We also recommend checking out this list of posters and presentations about open-source tools compiled by the folks from Open Behavior.

Neuropixels: 384-channel silicon probes for multi-area recordings

This week saw the official public release of Neuropixels, a new type of silicon probe that is poised to have a major impact on the field of electrophysiology. These probes, which were developed by imec in collaboration with scientists at the Allen Institute, HHMI Janelia Research Campus, and UCL, contain more recording sites per shank than any other implantable neural recording device. Their high channel count makes it possible to record from many structures along the length of the probe, while their compact size makes it easy to insert multiple Neuropixels into the brain at once. They have already facilitated experiments that would have seemed like pipe dreams just a few years ago. For example, the Allen Institute is using Neuropixels to simultaneously record spiking activity from 9 nodes in the mouse visual system, including V1, LGN, superior colliculus, pulvinar, and 5 higher visual areas.

We expect that many members of the Open Ephys community will want to use Neuropixels, so we've tried to make it as easy as possible to integrate them into existing workflows. The Open Ephys GUI can stream data from any type of Neuropixels hardware, so you can take advantage of existing GUI plugins or develop your own.

To obtain probes, you’ll have to fill out the form available at neuropixels.org. There’s a minimum order size of 20 probes in 2018, with the first 30 orders filled by lottery. In 2019, imec expects to ship 2,400 probes, with the minimum order quantity reduced to five.

If you'll be at SfN, you can learn more about Neuropixels at the Allen Institute booth or check out one of over a dozen posters that include Neuropixels data.

Until next time,
The Open Ephys Team

September 2018 Newsletter

New product: pyControl

We are pleased to announce that a new open-source device is now available to be purchased through the Open Ephys Store. pyControl is a software/hardware package for implementing rodent behavior experiments, based on the Micropython microcontroller. The USB-based pyControl interface can be hooked up to nose pokes, LEDs, solenoids, audio drivers, and other devices used for behavioral training. A single computer can control many pyControl setups, allowing high-throughput experiments to be implemented at low cost.

From the pyControl documentation:

“pyControl makes it easy to program complex behavioural tasks using a clean, intuitive, and flexible syntax for specifying tasks as state machines. User created task definition files, written in Python, run directly on the microcontroller, supported by pyControl framework code. This gives users the power and simplicity of Python for specifying task behaviour, while allowing advanced users low-level access to the microcontroller hardware.”

pyControl is in daily use in a number of laboratories and has run many thousands of hours of behavior experiments. It's also a great tool for courses, given how easy it is to get started using it.

The system is being actively developed by researchers at the Champalimaud Foundation and Oxford University. Profits from the sale of pyControl will support the continued development of the system. For any questions please contact the pyControl Google Group.

New version of the GUI

Version 0.4.4 of the Open Ephys GUI is now available for download from our website and GitHub. This version includes a number of bug fixes and user interface improvements, including:

• A new plugin for streaming data from Intan's 1024-channel Recording Controller

• An improved Pulse Pal plugin that allows the user to configure the device from software

• An updated FrontPanel DLL that improves performance of our acquisition board on Linux machines

We recommend that all users upgrade to this version. As always, be sure to carefully test any features you need before using this software in your experiments.

This version has been improved by collaborative development more than any previous release. We’d like to thank Alessio Buccino, Ethan Blackwood, Iryna Yavorska, Kevin Boergens, Ben Acland, Martin Spacek, Jon Newman, Evan Matteson, Ronny Eichler, Clayton Barnes, and Chuck Holmes for their invaluable help with testing and bug fixes. And of course, this release would not have been possible without the hard work of our lead support person, Aarón Cuevas López.

Preprints from the Open Ephys community

In the last 2 months, there have been at least four new bioRxiv preprints based on data collected with Open Ephys tools:

A team from the Allen Institute led by Corbett Bennett and Sam Gale has posted a preprint describing their detailed characterization of the lateral posterior thalamic nucleus of mice. They found that this nucleus contains three sub-regions, each with its own distinct anatomical connections, cellular tuning properties, and maps of visual space. All of the data was collected with “Phase 2” Neuropixels probes using the Open Ephys acquisition board.
https://www.biorxiv.org/content/early/2018/08/18/395244

Nikolaos Karalis and Anton Sirota from Ludwig-Maximilian University Munich have shown that long-range coordination between the components of the limbic system is orchestrated by respiratory rhythms. Breathing creates an oscillatory scaffold that may facilitate information transmission between disparate regions of the rodent brain. They used chronically implanted tungsten electrodes and silicon probes streaming data through the Open Ephys acquisition board.
https://www.biorxiv.org/content/early/2018/08/16/392530

Michael Okun (now at University of Leicester) and his colleagues at UCL have released a preprint characterizing the dynamics of prefrontal neurons across a wide range of timescales. They find that coordination between individual units and their neighbors can be quite distinct, depending on the timescale under investigation. Much of the data was collected with chronically implanted silicon probes using the Open Ephys acquisition board.
https://www.biorxiv.org/content/early/2018/08/18/395251

Hyeyoung Shin and Chris Moore at Brown University have posted their recent findings on gamma oscillations in somatosensory cortex. They describe a class of fast-spiking interneurons that fire at gamma frequencies but are not strongly driven by sensory inputs. The precision with which these neurons are time-locked to gamma on a given trial is correlated with detection performance in mice trained to respond to whisker deflections. The authors used flexDrives and Open Ephys acquisition boards to collect all the data in this study.
https://www.biorxiv.org/content/early/2018/07/25/374314

We are happy to see so many exciting results coming out of the Open Ephys community. If you are aware of other preprints or publications using Open Ephys, please let us know!

Until next time, 
The Open Ephys Team

November 2017 Newsletter

Open Ephys at SfN

We're not hosting an info session this year, but there are a number of other opportunities to meet with us next week in DC:

On Monday at 9:35 am in room 145B, Jakob Voigts will be giving a presentation on Open Ephys as part of a Minisymposium on Open-Source Hardware for Neuroscience. Other presenters in this session include Josh Sanders of Sanworks and Gonçalo Lopes of UCL, two scientists/engineers that have worked closely with Open Ephys in the past. We highly recommend attending if you can!

In the Tuesday morning session (VV58), Jon Newman will be presenting a poster on a versatile 64- and 256-channel headstage optimized for closed-loop feedback experiments in freely behaving animals. The headstage plugs directly into a PCIe card, meaning no external acquisition system is required. We plan on manufacturing and selling these headstages via our partnership with OEPS, in order to make them more accessible to the community.

On Monday evening from 7-8:30 pm in room 147A, you can find Josh Siegle at the Neuropixels satellite event. Neuropixels probes, which were funded and tested by HHMI Janelia, Allen Institute, Wellcome Trust, the Gatsby Foundation, and imec, make it possible to record spikes from thousands of cells distributed across dozens of brain regions. They are likely to become a new standard for systems neuroscience research. Neuropixels probes can already be used with the Open Ephys GUI, and we're currently building new plugins to efficiently visualize the data they generate.

After the Neuropixels event, Josh will be DJing the Neurolabware party from 9-10 pm. Stop by the Neurolabware booth at the convention center to pick up your wristband and find out directions to the venue!

Cyclops version 3.6 on sale next week

A new and improved Cyclops LED driver will be available for anyone to order through the Open Ephys store beginning on Monday, November 13th. It's been a long time since we've had this in stock, so we're very excited to start selling it again. These units come fully assembled by OEPS—we're no longer selling kits. The base price is 450 euros, with the option to add an M8 connector (required to interface with LEDs from Thorlabs and Doric Lenses) for an additional 50 euros. This is an incredibly low cost, given how the Cyclops' specifications compare to LED drivers from commercial manufacturers.

GUI version 0.4.3 coming soon

A new version of the GUI is currently in the "testing" phase, meaning updated binaries will be available soon.

Some of the most important upgrades include:

• The ability to record in 4 different data formats. The "binary" format now uses numpy and JSON files for all data except for continuous signals, which are saved as flat arrays of 16-bit integers.
• A redesigned backend for defining and accessing information about particular channels. This provides greater transparency and flexibility for developers building new plugins.
• An overhauled LFP Viewer, which includes a built-in spike raster display and new color schemes.
• An Event Triggered Averaging module, which can display spike histograms time-locked to digital inputs for both multi-unit activity and single units.

Because this version includes so many new features, it would be extremely helpful if users could proivde some feedback prior to the official release. We'd like people to download the code from the testing branch on GitHub and make sure it works with their preferred experimental signal chain. If you're having trouble getting the code to compile, don't hesitate to email info@open-ephys.org for guidance!

Until next time,

The Open Ephys Team

October 2016 Newsletter

Announcing Open Ephys Production Site

We’re excited to announce our partnership with Open Ephys Production Site (OEPS), an independent company that will manufacture and distribute the tools featured on the Open Ephys website. In the past, we’ve produced hardware on an ad hoc basis, and it’s been difficult to keep products in stock. Having a dedicated company in charge of hardware distribution should reduce lead times dramatically. For the next two years, OEPS will be handling orders from our online store, and a portion of the profits will be donated to Open Ephys. By purchasing hardware from OEPS, you will help sustain our work in developing and supporting open-source tools for the neuroscience community.

At the beginning of November, OEPS will begin making Acquisition Boards and shipping them worldwide. Soon thereafter, they will begin manufacturing electrode interface boards for the flexDrive, as well as Cyclops LED drivers.

To place a reservation for one or more Acquisition Boards from OEPS, please send an email to info@oeps.tech indicating the quantity you'd like to order. The boards will cost 2250€ ($2500) each, and will include USB 3.0 data transmission by default. Orders can be placed through our existing store, or via purchase order. If you're at all interested, please get in touch. The number of reservations will be used to determine the quantity of boards in the first manufacturing run, to ensure that they don't run out.

The creation of OEPS is being led by Filipe Carvalho, who has spearheaded several previous acquisition board manufacturing runs, and who has extensive experience assembling and using our tools. We're thrilled to have his help in making it easier for neuroscientists to access open-source hardware!

Google Summer of Code

Our participation in the 2016 Google Summer of Code wrapped up in August. We had two students complete projects:

Kirill Abramov (Zaporizhzhya State Engineering Academy, Ukraine) built a Plugin Generator to simplify the process of creating new data processing plugins for the Open Ephys GUI. Instead of copying and pasting example code, there's now an intuitive graphical application for selecting the type of plugin you want to create (Source, Filter, Sink, File Reader, or Record Engine). You can also use the Plugin Generator to add parameters and lay out your plugin's interface. This will lower the barrier to entry for users wishing to add new features to the GUI, allowing them to focus on the functionality, rather than getting their code to run in the first place.

Ananya Bahadur (Amrita University, India) integrated the Cyclops LED driver into the Open Ephys GUI. On the hardware side, he upgraded the microcontroller on the Cyclops from an 8-bit Atmel AVR (Arduino Leonardo) to a more powerful 32-bit Freescale Cortex-M4 (Teensy 3.2). On the software side, he built a CyclopsStimulator plugin for the GUI that provides a simple way to use neural events (such as spikes or LFP features) to trigger LED-based optogenetic stimulation. These additions will improve the stimulation capabilities of the Open Ephys platform. We hope they will facilitate the next generation of experiments involving closed-loop optogenetics.

Ordering Cyclops LED Driver Kits

The most recent updates to Cyclops have been now incorporated into the hardware design, and the final prototypes are currently being tested by Jon Newman. We're planning to manufacture and distribute another round of Cyclops kits for $250 each. Before we place the order for all the components, we'd like to to gauge the level of community interest. If your lab would like to purchase one or more Cyclops kits, please add your name, email, and quantity requested to this Google spreadsheet. This does not constitute the actual order. We will have a separate ordering process once the kits are available.

Until next time,

The Open Ephys Team

June 2016 Newsletter

More acquisition boards are on the way

The last round of Open Ephys acquisition boards sold out in less than 10 minutes, much faster than we expected. Fortunately, CircuitHub is currently manufacturing additional boards, which will be ready to ship sometime in July. If you were hoping to purchase boards but weren't able to submit an order in time, you can place a reservation for the next round by sending an email to info@open-ephys.org.

The CircuitHub acquisition board packages will include USB 3.0 data transmission (up to 512 channels), and will ship with two assembled I/O boards. You'll have to purchase headstages and cables separately from Intan Technologies.

Next-generation system development

We've been working on a set of standards that will hopefully form the backbone for the next generation of data acquisition systems. We are optimistic that a very simple common standard for hardware and software interconnects can make future data sources highly inter-operable without sacrificing any performance or flexibility. This means that engineers in academia and industry could focus on making better tools rather than re-inventing the data acquisition interface for each new system. The standard is still being developed, so any and all input is welcome. We encourage everyone to read through the latest white paper and get in touch with suggestions and opinions.

Open Ephys at SWC and TENSS

Four members of the Open Ephys team recently traveled to London to take part in a workshop on next-generation electrode technologies organized by Adam Kampff of the Sainsbury Wellcome Centre for Neural Circuits and Behavior. Following the workshop, we headed to Romania to visit the Transylvanian Experimental Neuroscience Summer School (TENSS). TENSS provides a unique opportunity for students from around the world to learn how to build cutting-edge neuroscience rigs in an idyllic, isolated setting. Over the past 3 years, much of the extracellular electrophysiology data in the course has been collected with the Open Ephys acquisition board.

In the days before the course began, we set up a prototype data acquisition system that transfers data via the PCIe bus. PCIe data transmission can greatly reduce the amount of time it takes for neural signals to reach a computer, compared to either USB or Ethernet. By the time the students arrived at the course, we had a demonstration up and running in which spikes occurring in visual cortex were used to trigger optogenetic activation of neurons in motor cortex, with a delay of less than 100 microseconds. The details of the recording system we used (which is a prototype of the next-generation system mentioned above) can be found in this repository.

New software available for download

A new release of the Open Ephys GUI is now available as pre-compiled binaries for Windows, Mac, and Linux. This release (v0.4.1) includes major performance improvements related to visualization and recording, as well as a greatly simplified installation process on OS X. For even more new features currently under development, check out the plugin-GUI development branch (which needs to be compiled from source).

We'd also like to remind everyone to be diligent about using the GUI's Issues page on GitHub. The more information we have about bugs and crashes, the faster they can get fixed!

Until next time,

The Open Ephys Team

April 2016 Newsletter

Acquisition board pre-orders

CircuitHub is currently manufacturing 20 Open Ephys acquisition boards, which will be ready to ship in mid-May. We will start taking pre-orders through the Open Ephys web store at 12 pm Eastern time on Thursday, April 28th. We expect there to be high demand, so please place your order as soon as possible and limit your order to 2 boards per lab.

The new acquisition boards will come with USB 3.0 connectivity, which allows up to 512 channels of neural data to be acquired simultaneously. They will also ship with two assembled I/O boards, so you won't need to order those separately. The price will be $2500 per package. Headstages and cables can be purchased from Intan Technologies.

For this round, we can only accept payment via credit card. If you need to pay via purchase order, or you don't place your order in time, the Champalimaud Institute will be manufacturing more acquisition boards later this year. We'll send out an update via our newsletter once we know more about when those will be available.

GUI upgrades

We recently migrated our data acquisition software over to a true plugin architecture, which will make it much simpler to add and share new processing modules. Since that update, we've seen a flurry of changes that will considerably improve performance and enhance the user experience: Click-and-drag channel selection (added by Kirill Abramov, @sept-en) String-based channel selection via Matlab-like array syntax, e.g. "1:2:10" (added by Priyanjit Dey, @priyanjitdey94) Disk writing in a separate thread, to reduce CPU usage when recording many channels simultaneously (added by Aarón Cuevas López, @aacuevas) Faster LFP display (added by Jakob Voigts, @jvoigts) Streamlined build process on OS X (added by Christopher Stawartz, @cstawarz) Software icon (added by Josh Siegle, @jsiegle) All of these upgrades are now available in the "testing" branch of the plugin-GUI repository. If you have experience building the GUI from source, we would love help looking for bugs. After at least 2 weeks of testing, we'll move the changes to the "master" branch and make the upgrades available in the pre-compiled binaries.

If you haven't done so already, you should begin merging any changes you've made to the GUI into the plugin-based version. We will no longer be supporting the non-plugin GUI, although we'll leave the repository up if you need to refer to it. If you have any questions about migrating, don't hesitate to email info@open-ephys.org or send a message to our mailing list (open-ephys@google-groups.com).

Google Summer of Code 2016

We'd like to welcome three new members to the Open Ephys team: Kirill Abramov, Jonathan Sieber, and Ananya Bahadur. We selected these three students out of an outstanding pool of GSoC applicants. Between May and August, they will help us improve the Open Ephys GUI. Kirill will create a graphical interface for generating new plugins, which will lower the barriers to adding new functionality to the software. Jonathan will make it possible to write real-time data processing algorithms in Julia, as well as interface the GUI with EEG hardware from OpenBCI. Ananya will create a module for interfacing the GUI with the Cyclops LED driver, to simplify the process of setting up closed-loop experiments. These are features we've been hoping to add for a long time, so we're excited to see what Kirill, Jonathan, and Ananya come up with.

Until next time,

The Open Ephys Team

SfN2016 Poster

At SfN 2016 in San Diego, some of us at open ephys, together with many collaborators that helped shape the system, presented a rough outline of a proposed next generation data acquisition system based on the PCIe standard.

The poster can be viewed and downloaded on the next-gen-system Github repository.

The project is still a work in progress, and more information can be found in the whitepapers and specifications.