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

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.

May 2015 Newsletter

Hardware distribution

As a small, volunteer-run organization, one of Open Ephys' primary challenges is putting the hardware we’ve designed into the hands of everyone that wants to use it. A few intrepid souls have successfully built our tools from scratch, but most of our users prefer to have something that’s plug and play. To streamline the hardware manufacturing and distribution process, we’ve partnered with CircuitHub, a manufacturing startup, and the Champalimaud Institute in Lisbon. Over the past few months, they've assembled and shipped our acquisition boards, I/O boards, and electrode interface boards to dozens of labs around the world. Almost all of the components were sold before the manufacturing process was finished, so we're currently holding off on accepting orders for most items through our online store. The electrode interface boards, especially, were more popular than expected. We apologize to everyone who requested boards we haven’t delivered yet.

Moving forward, plans are already underway for CircuitHub and Champalimaud to produce additional hardware. As usual, the bottleneck is Omnetics connectors. The 12-pin connectors for the acquisition boards should arrive at the end of May, while the 36-pin connectors for the electrode interface boards are expected in 10 weeks. Announcements about product availability will be sent via our newsletter as soon as we have more precise shipping dates.

In the future, we'll try to keep some backup stock of all the items featured on our store, and to have product availability reflect our ability to ship right away. While pre-orders have been useful for gauging interest levels and financing production runs, our current goal is reducing lead times. We’d like to have the experience of ordering from Open Ephys be as simple as making purchases from any commercial retailer, and we realize that hasn’t always been the case. Now that we have a better sense of demand, we'll work with both CircuitHub and the Champalimaud Institute to keep the supply more consistent.

Panel Discussion on “Making in Science”

On May 12, Josh Siegle and Jon Newman took part in a panel discussion at MakerCon in San Francisco. Josh is the co-founder of Open Ephys, and Jon is the engineer behind the Cyclops LED driver and the NeuroRighter data acquisition system, as well as a key contributor to Open Ephys. MakerCon is a semi-annual meeting of entrepreneurs, engineers, and designers with an interest in growing communities around novel hardware platforms. Open Ephys has benefitted tremendously from the rise of tools for prototyping and manufacturing on a small scale, while the community of makers is always excited to learn how open-source hardware can facilitate scientific discoveries. Our session, titled "Making In Science," was organized by Steve Potter of Georgia Tech, an ardent advocate of the benefits of open-source tools in neuroscience. Other panelists included Conor Russomanno of Open BCI, Ariel Garten of InteraXon, Greg Gage of Backyard Brains, and Jamie Tyler of Thync. Both the panelists and the audience were highly enthusiastic about our progress and goals. There is huge potential for applying our tools for human EEG research, with only minor modifications.

Our first tax return

This month, Open Ephys filed its first tax return as a nonprofit corporation. Although we don’t have to pay income tax, we’re required to disclose our finances to the IRS, and to make our tax forms available upon request. In 2014, we coordinated the distribution of acquisition boards ourselves, earning $137,406 worth of revenue in the process. We spent $97,318 on manufacturing at Advanced Circuits, American Precision Prototyping, and Ponoko. The remaining funds covered the stipend of Aarón Cuevas López, our official support person. Having Aarón’s help has been essential for the growth of Open Ephys over the past year. Not only has he handled bug fixes and general support requests, but he’s also made key upgrades to the software, such as adding HDF5 recording capabilities and 64-channel headstage support. We’re happy to report that we just extended his contract for at least another year.

January 2015 Newsletter

Open Ephys Store

One of the central goals of Open Ephys is to make it simpler for neuroscientists to access open-source tools. With the launch of the Open Ephys store, we are further lowering the barrier to entry for getting the tools we're sharing up and running in your lab. The store is still in beta, so we can't guarantee everything will be in stock, and the volunteers who run it will only be sending shipments out once or twice a week. Still, we will try our best to fulfill your orders in a timely manner.

The first round of acquisition boards we're selling through the store have been manufactured by the Champalimaud Neuroscience Program. They have the same design as the boards distributed through our previous CircuitHub campaign. In addition to the acquisition boards, our partners in Lisbon have built fully assembled I/O boards (for interfacing with auxiliary analog signals or digital triggers) and electrode interface boards (EIBs, for building drive implants), which will also be available through the store. We're taking orders now which we expect to fulfill in early February.

Software update (version 0.3.4)

There's a new version of the Open Ephys GUI available for download through our website (pre-compiled binaries) or via GitHub (source code). As a major under-the-hood upgrade, we added the ability for processing modules to simultaneously handle data with different sample rates and timestamps. Previously, all data traveling through the signal chain had to use the same clock. This change will make it possible to merge continuous data from different types of sources, and to process down-sampled LFP data in parallel with the spike band, which can speed up analysis and reduce file sizes.

In addition, the updated GUI includes four new processing modules:

• A Common Average Referencing module, which takes the average signal of a subset of the incoming channels and subtracts it from the output. This can be useful for extracting spikes from noisy data.

• A Network Events module, which allows other computers (or another piece of software running on the same machine) to control the behavior of the GUI.

• A PSTH module, which creates average firing rate plots aligned to particular events, either triggered by TTL inputs or incoming network messages.

• An Arduino Output module, which makes it possible for events within the GUI to control the state of digital output pins of an Arduino. This is a simple way to set up experiments involving closed-loop feedback.

Documentation for these processors can be found on the Open Ephys Wiki.

Goals for 2015

We have a lot of exciting developments planned for 2015. Here are some of the most important ones:

• We will become an official 501(c)(3) nonprofit. We just finished the application and will send it out in the next few days.

• We will expand our manufacturing partnership with CircuitHub. We'd like to be able to reduce lead times for acquisition boards and other hardware from a few months to a few weeks. We want to have our tools available year-round, and with less time between placing the order and receiving a package in the mail.

• We will implement a "feature freeze" on the Open Ephys GUI and limit the development on the GitHub master branch to bug fixes and performance upgrades. This will ensure that our users always know where to go to find the most stable version of our software, and will never have to worry that an upgrade will change the functionality in a major way. As more people start using the GUI for their day-to-day data collection, it's important to balance our eagerness to add features with the need to provide a robust platform for performing experiments. The development of new processors will continue, but it will take place in a separate, plugin-based repository.

If you'd like to know more about where Open Ephys is headed, or would like to help out in any way, don't hesitate to send an email to info@open-ephys.org.

Until next time,
The Open Ephys Team

Current Opinion in Neurobiology Publication

Josh Siegle and Jakob Voigts (the co-founders of Open Ephys), along with Jon Newman (developer of NeuroRighter, Puggle, and Cyclops) and Greg Hale (developer of ArtE), have written an opinion piece describing the past, present, and future of open-source hardware for multichannel electrophysiology. The article, titled "Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology," will appear in a special issue of Current Opinion in Neurobiology on large-scale recording technology, edited by Francesco Battaglia and Mark Schnitzer.

If you don't have access to the article and would like a copy, send an email info@open-ephys.org.

Open Ephys at SfN

The Open Ephys SfN meetup is exactly one month away! We hope to see you all there!
Room Change: We got moved to Room 155, time is still 6:30 on Monday.

October 2014 Newsletter

The new Open Ephys website is live

We recommend that everyone check out the latest iteration of open-ephys.org, which has been public since Sunday night. Almost every element of the site has been rewritten and redesigned. We wanted to make the site as informative as possible with respect to the goals of our initiative. In addition to the tools we showcased on the original site, we now include pages on hardware and software designed outside of MIT: the Array Drive from the University of Maryland, the Puggle from Georgia Tech, the Pulse Pal from Cold Spring Harbor Laboratory, and Bonsai software from the Champalimaud Institute. We hope to turn open-ephys.org into a hub for promoting and distributing tools for electrophysiology. With the new site design, it's easier for visitors to browse through the range of tools that we feature.

If you have any suggestions about improving the site, or if you made a contribution and we haven't added your name to the "People" page yet, please get in touch! We've also made it even simpler to sign up for our newsletter, so be sure to spread the word to your friends and colleagues.

A new software update has been released

We recently released version 0.3.2 of the Open Ephys GUI. We've added a number of useful features:

• Online spike sorting. Using the "Spike Sorter" module to detect spike events allows you to extract clusters online using manual box-based or PCA-based sorting. Cluster labels will be saved to disk along with the spike waveforms, and other processing modules can take advantage of this information when responding to incoming spikes. The Spike Sorter updates the functionality of the "Spike Detector" module, but the latter module remains in the software so people can continue using it. Many thanks to Shay Ohayon, now at MIT, who contributed most of the code for the Spike Sorter module.

• Recording in HDF5-based Kwik format. We've been wanting to switch over to an HDF5-based data format for a long time. HDF5 offers many advantages over simple binary formats, the most important being dramatically reduced delays and more efficient memory use when loading data for analysis. When we found out that the Harris Lab at UCL was developing a general-purpose HDF5 format to use with their KlustaSuite of spike-sorting software, we decided to adopt this for Open Ephys as well. We want to support the proliferation of open standards for neuroscience, and many people will find it useful to save data that be immediately loaded into the KlustaSuite pipeline. Users still have the option to save their data in the original Open Ephys binary format if they like. As an added bonus, the source code for saving data has been modularized to make it easier to add new formats in the future. Thanks to Aarón Cuevas López, our core technical support person, for implementing this update.

• Saving timestamped strings. Often, it's useful to be able to annotate your recordings with messages that a human can read. This is now possible in the GUI, using the new widget at the bottom of the acquisition window. Just type your message and hit "save," and your text will be saved along with a corresponding timestamp.

These are just a few examples of the upgrades we've implemented in the latest version of the software. We recommend that everyone either download the binaries or compile their own version from source. If you find any bugs, or have additional feature requests, don't hesitate to open a new issue on GitHub.

Society for Neuroscience meetup

If you'll be at the Society for Neuroscience conference next month, we encourage you to attend the official Open Ephys meetup on Monday the 17th. It's happening between 6:30 and 8:00 pm in Room 209A in the convention center. We'll talk a bit about the future directions of our initiative, but we mainly want to take the opportunity to bring together users and developers that may have only interacted virtually thus far. We are not presenting a poster this year, so this will be the best chance to meet the people behind Open Ephys and hear about what we've been up to. Of course, if you can't make it to the meetup, we're happy to set up a meeting at another time.

Other updates

We now have a mailing list/forum to help our users better access the community knowledge base. Sign up here to subscribe to emails sent to open-ephys@googlegroups.com. If you're a regular user of our software or hardware, we strongly encourage you to sign up.

We've added the first Python modules to our analysis-tools repository, as well as code for converting Open Ephys data to files that can be used by Plexon's Offline Sorter. This code has yet to be thoroughly tested, so we'd love for any users familiar with Python or Offline Sorter to download it and try it out.

Finally, many of you have asked about when we'll be selling the next round of Open Ephys acquisition boards. We're eager to get the store up and running, but we're still waiting for more stock to arrive. We'll send out an update via this newsletter as soon as they become available (hopefully by the end of next month). The good news is that our test run of manufacturing with CircuitHub went really well. If you want to get your hands on a board as soon as possible, you can now order fully assembled acquisition board PCBs via this link. You'll have to order an FPGA separately, and some simple assembly is required, but all the necessary instructions can be found on our wiki.

Until next time,
The Open Ephys Team

The new site is live!

As of October 12, 2014, the new Open Ephys site is open to the public. Not only does it look a lot nicer and contain a lot more information than the previous iteration, but we now feature a variety of projects developed outside of MIT. We hope you like it!

First publication using the Open Ephys system

Josh Siegle and Matt Wilson have authored the first paper based on data collected with the Open Ephys system. "Enhancement of encoding and retrieval functions through theta phase-specific manipulation of hippocampus" appeared in eLife in July 2014. In their experiments, Siegle & Wilson used closed-loop optogenetic feedback to alter behavior in mice performing a spatial navigation task. The Open Ephys software and hardware were designed with this type of experiment in mind. The lightweight headstage and cable did not impinge animals' movement, while the modular software made it simple to incorporate algorithms for triggering stimulation at specific phases of the theta rhythm. The experiments also incorporated a dual-site flexDrive capable of simultaneously targeting both sides of the hippocampus. We're looking forward to many more papers based on Open Ephys data in the future!

SparkFun article

A Q&A with Jakob and Josh was just published in a blog post on SparkFun.com, as part of their "Enginursday" series. This is a real honor, since SparkFun was an essential resource for us during the formative years of Open Ephys. Our first engineering project, the Twister, consisted of parts from the SparkFun Inventor's Kit before we turned it into a polished product. SparkFun's tutorials taught us a great deal about soldering, designing circuit boards, and general electronics know-how. We're proud to be featured on their site!

Thanks to Toni Klopfenstein for making this happen!

Open Ephys at TENSS 2014

Open Ephys recently donated equipment and a teaching assistant to the Transylvanian Experimental Neuroscience Summer School near Cluj-Napoca, Romania. For the past 3 years, TENSS has taught students from around the world how to build their own cutting-edge rigs for two-photon imaging, in vivo whole cell recordings, behavior tracking, and chronic electrophysiology. It's organized by Florin Albeanu of Cold Spring Harbor Laboratory, Adam Kampff of the Champalimaud Neuroscience Programme, and Raul Muresan of Coneural Cluj-Napoca.

The course takes place in an isolated pension on the shore of Pike Lake in the Transylvanian countryside.

For seventeen days, students participate in modules that teach the theory behind techniques in systems neuroscience and provide hands-on experience with data collection. The venue is basically a bed and breakfast when it's not being used by the course, so everything had to be built from scratch. Since the focus is on DIY rigs and open-source tools, Open Ephys was the perfect choice for the electrophysiology module.

"Open" Josh puts the finishing touches on one of six flexDrives that were used in the course.

Within a few days of arrival, we had two Open Ephys data acquisition systems up and running, which allowed us to monitor single units from tetrodes in the prefrontal cortex and striatum of freely moving mice. We also recorded data from a mouse navigating in virtual reality, thanks to the help of Georg Keller from the Friedrich Miescher Institute in Basel. During the final days of the course, the students applied their new knowledge to design and carry out experiments that combined behavior, optogenetics, and electrophysiology.

A mouse navigates along a virtual track while the Open Ephys system records from tetrodes implanted in the striatum and cortex.

Participating in TENSS was an extremely rewarding experience. If you're looking to gain firsthand exposure to the latest techniques for recording neural data, we'd definitely recommend applying next year!

IEEE Spectrum article

Eliza Strickland from recently wrote an article about Open Ephys for IEEE Spectrum. It includes quotations from Josh and Jakob, the Open Ephys co-founders, as well as Reid Harrison of Intan Technologies, Keith Stengel of Neuralynx, and Andy Gotshalk of Blackrock Microsystems.

Here's one choice excerpt, courtesy of Reid:

"The existing tools are like the PCs and the Macs of the neuroscience world, but now we also have this Linux."

June 2014 Newsletter

Successful Distribution of 100 Additional Acquisition Boards

In the summer of 2013, Open Ephys kicked off its beta testing program by paying Advanced Circuits to assemble 50 of our acquisition boards. Generous donations allowed us to distribute most of these boards for free, which lowered the barrier to entry for those interested in trying out our platform. Based on the feedback we got from our beta testers, we made some improvements to the boards, then initiated a second round of manufacturing in spring 2014. Advanced Circuits produced 100 more boards for us, to meet the increased demand following our presentation at the Society for Neuroscience conference in San Diego. As of last week, all of these boards have been sent to their final destinations.

Assembling 100 boards cost approximately $32,000, which included the price of the completed circuit boards, cases, and power supplies. Thanks to a donation of key components from Texas Instruments, we saved around $14,000 on parts.

We shipped these boards to over 50 labs around the world, adding China, Korea, Belgium, Switzerland, and Finland to the list of countries using Open Ephys. In this round of distribution, there were three institutes that requested 10 or more acquisition boards each: University College London, the Champalimaud Centre for the Unknown in Lisbon, and the Donders Institute in Nijmegen. Along with MIT, where Open Ephys was launched, there are now four "hubs" in which our acquisition systems are concentrated. Having hubs like these will be important for increasing adoption, since scientists are more likely to try out new hardware that their neighbors are already familiar with.

In total, we have now delivered over 38,000 channels of ephys recording capacity to the field. The first two basic science publications that include data collected with our platform are now in submission. We're looking forward to seeing many more in the future!

Open Ephys Hires Its First Support Person

When choosing an ephys system to buy, the availability of support is a crucial factor. Having a guarantee that faulty hardware will be replaced, or that someone will be available to help troubleshoot problems, often makes it worth the price of investing in a commercial platform. Since its inception, Open Ephys has successfully served its small user base entirely through volunteer efforts. But with the number of new systems about to come online, we decided it was time to hire an official support person.

Leftover donations from the last round of manufacturing will fund a contract with Miguel Hernández University in Alicante, Spain to provide technical support for Open Ephys. The point person will be Aarón Cuevas López, a PhD student who has already contributed substantially to developing and testing our platform. Having Aarón as an official support person will make it easier for everyone to use our system. We'll continue to rely on the constantly growing community for adding new features, but it will be hugely helpful to have Aarón available for fixing bugs and responding to technical questions.

Manufacturing Partnerships

We recently established an official partnership with the Champalimaud Neuroscience Program in Lisbon to manufacture Open Ephys acquisition hardware. This is the first time anyone outside of MIT will build our designs for distribution. Investigators at the Champalimaud—including Alfonso Renart, Adam Kampff, Leopoldo Petreanu, Megan Carey, and Zach Mainen—have been some of the most enthusiastic supporters of Open Ephys. We plan to produce 100 boards in Portugal in the next few months. Once these become available, we'll send out a newsletter with detailed information about how to purchase them.

Another avenue for getting your hands on an Open Ephys acquisition board is through CircuitHub, a startup aimed at lowering the barrier to entry for obtaining custom hardware. If you order a board using this link, CircuitHub will purchase all the parts and assemble the circuit board for you. You'll still have to find a way to 3D print or machine the case; instructions for that can be found on our wiki. We haven't ordered anything from CircuitHub yet, but it could become the easiest way to order acquisition boards in the future. If you're interested in testing this out, please get in touch with us—we may be able to coordinate a group order.

Stay tuned for more information about updates to the wiki and website, as well as the launch of the official Open Ephys store!