open-source electrophysiology

November 2017 Newsletter

Added on by Josh Siegle.

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

Added on by Josh Siegle.

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

Added on by Josh Siegle.

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

Added on by Josh Siegle.

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

Added on by Open Ephys.

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

Added on by Open Ephys.

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

Added on by Open Ephys.

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:

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

October 2014 Newsletter

Added on by Open Ephys.

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