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.
open-source electrophysiology
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
Figure 1 from Siegle et al. (2015) "Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology." Current Opinion in Neurobiology 32: 53-59.
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!
Open Ephys on Wired.com
Wired.com just posted an article on Open Ephys, as part of their "Out in the Open" column. It does a great job of capturing the motivations behind our initiative:
Recording simultaneous units in cortex with the flexDrive
We've been using the flexDrive (wiki) for over a year now in the Moore lab, recording almost 100 sessions in 5 mice. I'm just now starting to analyze neural ensemble statistics that require simultaneously recorded neurons.
Here's the real-world distribution of how many simultaneous neurons in primary somatosensory cortex (with some thalamic electrodes) I could sort over a total of 75 sessions in awake mice with 16 nichrome tetrodes.
The mean unit yield was 25.8, with a minimum of 8 and a maximum of 46 units. These numbers include some not so great recordings, and bad tetrodes hat got damaged etc., but only very few sessions were outright discarded, mostly in the beginning of the drive lowering process where it looked like some electrodes were not in cortex yet.
All in all, these numbers should be good enough to do some interesting assembly-analysis, though the relatively low density of the tetrode array (250 micron pitch) results in a relatively low occurrence of strong fast-timescale correlations between spike trains.
February 2014 Newsletter
Official incorporation
Open Ephys recently registered as a nonprofit corporation in the state of Massachusetts. This makes us an official entity, separate from any individual lab. Having nonprofit status will allow us to accept donations and sell supplies through our website. We plan to redistribute custom components, such as electrode interface boards, to cut down on wasted time and manufacturing costs. We'll send out an update when that's up and running.
Our founding board of directors is Josh Siegle, Jakob Voigts, Christopher Moore, Matt Wilson, and Caleb Kemere. Our mission statement (as written in our Articles of Organization) is:
"To promote tool-sharing among members of the worldwide systems neuroscience community. Open Ephys will support the development, distribution, and maintenance of open-source hardware and software for collecting and analyzing neuroscientific data. Special focus will be given to tools with expensive or inflexible commercial alternatives, and which serve the needs of a broad user base. Open Ephys strives to make it easier for investigators to share the tools they develop by establishing a centralized tool repository and by coordinating distributed support networks."
We think this represents an important unmet need in our field, and we hope Open Ephys can grow to fill this niche. Our ultimate goal is to not to create an open-source electrophysiology platform, but to change the way tools for neuroscience are developed and shared.
Open Ephys in new species
The initial testing of our data acquisition system was carried out in mice. Now we're happy to report that Open Ephys has been used to collect data from a number of other species. We've received reports of successful recordings from rat, zebra finch, and primate subjects. We also have some fresh data from human EEG. Our design for an EEG adapter board makes it possible to connect our headstages to a standard electrode cap.
Software, hardware, and firmware updates
The latest release of our GUI (version 0.2.5) includes some interface upgrades that make Open Ephys more convenient to use. We now have a "Graph Viewer" component that allows you to visualize your entire signal chain at once, making it easier to navigate between modules. Users now have the option to automatically load the last-used configuration upon launch, so it takes less time to start experiments. And minor tweaks, like ensuring the buttons inside the control panel collapse gracefully (instead of overlapping as they did previously), make the overall user experience more enjoyable.
You can download pre-compiled binaries for the GUI from our website. If you're a new user, we recommend starting with this tutorial.
Our acquisition board has been updated for the most recent round of manufacturing. It includes two useful new features: (1) a port that makes it possible to synchronize timestamps across boards connected to different computers and (2) protective circuitry in case the wrong power supply is used.
To view the design files, browse through our repository on GitHub.
Finally, the firmware for our acquisition boards now allows digital input channels to trigger an amplifier reset. This makes it possible to minimize electrical artifacts, for example when doing antidromic stimulation. Thanks to Reid Harrison at Intan Technologies and Shay Ohayon at Caltech for their help with implementing and testing this feature.
The FPGA firmware is also available on GitHub.
First recording in NHP & real time analysis
Shay Ohayon at Caltech just conducted an experiment that makes use of the numerous new modules that he developed for the Open Ephys system over just the last two months. He recorded neurons from the Middle Face Patch and verified the recording by analyzing the data in real time. Here's what he had to say:
When I first heard about Open Ephys, I got very excited. The system is extremely cheap and everything is open source. However, after I got my hands on the hardware and software, I was initially disappointed. The initial software release lacked many basic features one would need to run a full-blown acute monkey electrophysiology experiment. There wasn't an option to do real-time spike sorting, or to display real-time firing rates. Furthermore, it lacked the ability to connect to external sources of information, like events arriving from a machine which presents stimuli. Nevertheless, I saw a great potential in the design and decided it would be worthwhile to program all the missing components.
Two months have passed since. With a lot of help from Josh Siegle and the rest of the Open Ephys community, we are now close to releasing a new stable version with many new features that make the system much more useful for acute experiments. In many ways, it has surpassed the capabilities of my old recording system (MAP by Plexon).
Last week I finally found the time to test Open Ephys on my monkey. Below are some notes on my configuration and the new features that I have added:
Summary of the experiment and configuration
My first goal was to try and recreate the standard way signals are processed in Plexon. Josh was extremely helpful in debugging bugs related to split & merge modules, and recently Josh added this great feature that permits the visualization of the entire signal chain:
As you can see, the initial signal is split into two, a high pass version that goes into a spike detector, and a low pass version that computes LFPs. Furthermore, there is another input, called "Network Events", that can receive strings over TCP/IP with various information coming from other machines. An Eye Tracking module is capable of communicating with standard ISCAN system and adds eye position information to the signal chain.
The advancers module is used to keep a record on where each electrode was placed in the recording chamber, and also records information about the depth of each probe that changes during the experiment. This makes post-processing analysis much easier!
The new spike detector module gives the user the ability to isolate units in real time, either by the box method, or polygons in true PCA space:
There is no limit on the number of units that the user can add. In this example, I have a yellow unit defined with two boxes (spike wave form must intersect both boxes), one green unit that is defined in PCA space, and a cyan unit that is defined with a single box.
Finally, the PSTH module can display firing rates, averaged relative to trial onset, and aggregated across similar trial types (junk data, just for demonstration purposes):
Here, each curves corresponds to a different category (think trial types that all have something in common).
Both trial and category information is sent over TCP/IP. High accuracy trial alignment can also be achieved by sending a single TTL pulse. However, software timestamps are quite accurate as well (~3-4 ms jitter, when sent from a different machine). Software timestamp taken in the machine running HUI scan be easily converted into hardware timestamps with very good accuracy using robust linear regression:
For my actual experiment, I recorded with a single electrode (1 MOhm), targeting the so called "Middle Face Patch" (image generated with Planner)
At depth 52mm, I was able to isolate a noisy unit (data shown below is from the real time spike sorting):
Trials were sent from our behavioral machine, which displays images to the monkey. The behavioral machine sent information about which image was displayed. This information was acquired in GUI using the Network Events source (see Spike sorting & PSTH). I could determine in real time that unit 2 was face selective by looking at the PSTH curves (unfortunately, I didn't take a snapshot). In post-processing, it is quite easy to read out the trial information that was sent and build an average raster plot (smoothed with a 3 ms gaussian kernel):
Here, you can see the average responses relative to image onset (approximated onset, photodiode information still not taken into account). First 16 images are face images, and the rest are non-face images.
The PSTH, averaged across the six image categories is:
which looks very very similar to what the PSTH module showed in real time.
Conclusion
The new spike sorting branch seems to be ready for action! It can be used in acute experiments in which real time characterization of isolated units is required.
Minor issues still remain, but all will be addressed in the upcoming weeks.
To view the code Shay used for these experiments, check out the "spikesorting" branch of the GUI on GitHub.
Software version 0.2.4 released
The latest version of the Open Ephys GUI includes several important upgrades. We've now made it possible to construct more complex signal chains. For example, you can split the signal chain, do separate analyses on each branch, then combine the branches with a merger. This is useful for analyzing spikes and LFP simultaneously, then integrating the results for visualization or closed-loop feedback.
To make it easier to navigate through your signal chain once it's constructed, we've added a Graph Viewer that allows you to visualize the connections between all your processors. Clicking on any one of the nodes will take you directly to its editor interface, so you no longer have to search through splitters and mergers to find it. Everything can be seen at a glance:
We've also made it possible to collapse and expand editors by double-clicking on their name. This will make it easier to construct long signal chains without taking up more screen real estate:
There are a variety of other useful features and bug fixes in this release, so we recommend upgrading as soon as possible. You can either download precompiled binaries from our GUI page, or download the source code from GitHub.
Thanks to Shay Ohayon for his input on these features! The next major release will incorporate some awesome new modules he developed, such as an Advancer Node to track electrode position, a PSTH node to display stimulus-locked firing rates, and a Spike Sorter (incorporated into the Spike Detector) to identify units in real time. Stay tuned for more info...
Open Ephys at UT Austin
Jenni Siegel from the Cellular Mechanisms of Working Memory group at UT Austin recently sent us some screenshots from her latest experiments. She's been using the Open Ephys acquisition board and GUI to record from M2 and anterior cingulate in awake, head-fixed mice. The tetrode projections (right side of the screen) show some beautiful units! So far she's been really happy with the data quality—the noise floor is greatly reduced compared to her previous recording system.
SfN 2013 Poster
November 2013 Newsletter
There are a variety of opportunities to check out the latest from Open Ephys at the Society for Neuroscience conference in San Diego next week. Whether you're already using our tools, or just want to find out more about what we've been up to, we'd love to chat with you!
Open Ephys acquisition boards are now being evaluated by over 30 labs as part of our beta testing round. So far, we've received great feedback from these users. Everyone that's tried it has reported that the system is easy to set up and yields high-quality neural signals. They've also pointed out software bugs and feature requests that have made our system more user-friendly and robust.
Now it's time to spread the word about our tools, and hopefully recruit some new developers. Over the past two months, we've visited labs at the Karolinska Institute, UCL, NYU, Princeton, Harvard, and Cold Spring Harbor to discuss potential collaborations. But we expect to gain even more exposure at this year's Society for Neuroscience conference, which takes place in San Diego from November 9th through 13th.
At last year's SfN, we presented a working prototype system that was very well-received. Many of you signed up for this newsletter after seeing our tools in New Orleans. This year, we have an acquisition system that we've already mass-produced, and that's being used by labs around the world. We're excited to show it off at our poster presentation, which takes place on Wednesday morning. It's poster number NNN33—we hope to see you there!
This is the first year that Intan Technologies will have an exhibition booth at SfN. The Open Ephys system wouldn't be possible without the chips that Intan manufactures, and we're especially grateful for all the technical advice provided by Reid Harrison, the president of Intan. We encourage everyone to stop by booth #920, where our acquisition board will be on display.
We're also organizing an informal meetup, which will take place on Monday from 5:00-6:30 pm at Neighborhood in San Diego. Anyone is welcome to join. We'll be discussing ways to grow our initiative in the short term, and how to sustain it over the long term.
Finally, we're currently working out the details of the next round of manufacturing, which will take place in December. We'll make some small tweaks to the hardware (such as adding a port for synchronizing multiple acquisition systems), then have 50-100 boards assembled by Advanced Circuits. Stay tuned for more information...we'll send out a request form after the conference.
September 2013 Newsletter
Open Ephys recently reached an important milestone: our hardware has spread beyond the labs that developed it. Over the next few months, we'll get lots of feedback from our new users. We also hope they'll help us improve the software by fixing bugs and adding new modules. A list of the labs that volunteered as beta testers can be found on our people page.
If you didn't receive one of our acquisition boards but are interested in testing one out, we now have a wiki page with instructions on how to build one from scratch. We've built a number of systems by hand with great success.
We'd love to kick off another round of manufacturing, but we don't know exactly when that will happen. Keep an eye on upcoming newsletters for more details. The timing will depend on both how quickly things progress with our beta testing phase, and how long it takes to secure funding for manufacturing. The first 50 boards cost around $20,000 to produce, and we expect the next 50 will be the same. We still haven't figured out the best financing model, but donations have worked well so far. If you might be interested in funding our efforts, definitely get in touch. Eight labs contributed to the first round of manufacturing, in addition to the generous donation of parts by Texas Instruments. We don't feel comfortable selling our hardware without some mechanism for providing support, but perhaps this will become a possibility in the future.
We're also looking for people to help with software development. Our platform is already at the point where it has all the functionality needed to carry out basic electrophysiology experiments and observe data in real time. We've been using the Open Ephys system on a daily basis for the past few months, and we're very happy with its usability. But there's plenty of room for improvement, especially when it comes to making the software easy to modify. The fact that it's open source already represents an advantage over the commercial alternatives, but we'd like to make it simpler to add new processing modules, even for those with limited development experience. If you work with a programmer that might be able to contribute some of his or her time, or have access to funds that could be used to hire one, please get in touch. We've been amazed by how liberating it feels to collect all of our data with open-source tools, and we'd like others to experience the same thing.
For more information on what we've been working on, check out our blog and wiki.