open-source electrophysiology

June 2014 Newsletter

Added on by Open Ephys.

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!

Recording simultaneous units in cortex with the flexDrive

Added on by Open Ephys.

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.

units_per_session.png

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

Added on by Open Ephys.

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

Added on by Open Ephys.

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.

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.

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).

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)

1390500780705.png

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):

image2014-1-21 9-52-47.png

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

Added on by Open Ephys.

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

Added on by Open Ephys.

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

Added on by Open Ephys.

We presented a poster outlining the Open Ephys system at the 2013 Society for Neuroscience meeting.
You can find the poster here (.pdf, ~15mb). If you are looking for more in-depth documentation, have a look at the wiki.

Thanks to everyone who stopped by for the great discussi

November 2013 Newsletter

Added on by Open Ephys.

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

Added on by Open Ephys.

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.

Manufacturing costs

Added on by Open Ephys.

Now that our first round of manufacturing is complete, it's time to take a look at our finances. We funded the construction of our first 50 acquisition boards solely through donations. A handful of labs chipped in to get the process up and running. We received generous gifts from the Meletis and Carlén Labs at the Karolinska Institute, the Jazayeri Lab at MIT, the Yizhar Lab at the Weizmann Institute, the Kemere Lab at Rice University, and the Goldberg Lab at Cornell. The Wilson and Moore Labs have continued to support us through miscellaneous small purchases.

A major contribution also came from Texas Instruments. Through their partnership with Rice University, we received over $17,000 worth of free components (around $7200 of which went toward our current manufacturing run). This included the auxiliary analog-to-digital and digital-to-analog converters, the most expensive parts on our boards. 

The final product was 50 acquisition boards with custom cases, not including the FPGA used for USB communication ($400 extra). The grand total for the parts, assembly, and cases was $19,294, or approximately $386 per board. This would have been $26,500 if we hadn't gotten the donation from Texas Instruments.

Here's the breakdown of what we spent it on: 

  • Printed circuit boards: $3064
  • Assembly and DigiKey parts for first 5 boards: $1600
  • Assembly and DigiKey parts for last 45 boards: $5319
  • Omnetics connectors: $2728
  • Samtec connectors: $388
  • LEDs: $248
  • Cast urethane cases: $4420
  • Acrylic tops: $349
  • Screws, rubber feet, and hex keys: $66
  • Spray paint and glue: $15
  • I/O boards: $1010
  • Boxes for shipping: $69
  • "5V DC ONLY" stickers: $18

Obviously these costs don't account for the time we spent orchestrating all of the orders, but this wasn't that much in the end. We only lost a few days of work, in return for spreading our tools to over 30 labs around the world.

To put this in more relatable terms, we just built fifty 256-channel data acquisition systems for a fraction of the cost of one commercial system. If you add $20k to account for the FPGAs purchased by individual labs, the cost remains lower. Of course, labs still need to purchase headstages and cables, but at around $1000 for 32 channels, this is still a bargain. 

For the average lab, will the incredibly low price justify the extra time investment needed to get an open-source system up and running? Perhaps not at the moment, but potentially it will in the future. Over the next few months, our beta testers will help us spot problems with our hardware and software, and hopefully add some useful features. If all goes well, we should reach a point at which the extra effort is negligible, but the price difference is substantial. 

Boards for Beta Testing

Added on by Open Ephys.

Last week we received 45 assembled acquisition boards from Advanced Circuits and placed each one in a cast urethane case. Needless to say, they're looking great! 

Recording 16 tetrodes in the GUI

Added on by Open Ephys.

After some bugfixing in the spike display, we are now using the software for our actual long recordings in mice implanted with the 64 channel flexDrive (see GitHub for the EIB design). The dual-screen interface works perfectly and the runtime-extracted spikes look as good as the one we extracted from the full voltage traces.

Screenshot of the GUI (shown here running on Windows), during a recording of spikes and LFPs on 16 tetrodes on a flexDrive.

Screenshot of the GUI (shown here running on Windows), during a recording of spikes and LFPs on 16 tetrodes on a flexDrive.

The first shipment arrives...

Added on by Open Ephys.

This week we received a shipment of five fully assembled Open Ephys acquisition boards from Advanced Circuits. Previously, all of our boards had been assembled by hand, a process that takes 2-3 hours per system. In order to spread our tools beyond our labs, we needed to outsource the manufacturing.

After running the boards through a battery of tests, we're happy to report that everything is working exactly as expected. We're now ready to order an additional 45 units, which we'll distribute to labs around the world for beta testing.

One of the assembled boards, exactly as it arrived (except for the handwritten serial number).

One of the assembled boards, exactly as it arrived (except for the handwritten serial number).

A stack of Open Ephys acquisition boards in cast-urethane cases. The next round of boards we make will have blue cases with translucent acrylic tops.

A stack of Open Ephys acquisition boards in cast-urethane cases. The next round of boards we make will have blue cases with translucent acrylic tops.

Open Ephys and Neuralynx: a head-to-head comparison

Added on by Open Ephys.

In our first blog post, we described the fantastic signal quality of the Open Ephys acquisition system. Today, we made our first direct comparison between signals recorded with Open Ephys and those recorded with a Neuralynx Digital Lynx system. The conclusion? The recordings are virtually indistinguishable. There's still more rigorous testing to be done, but to the trained eye of a seasoned electrophysiologist, the signal quality of the two systems is qualitatively identical. Read on to see for yourself.

We performed the test by recording from a mouse implanted with an eight tetrode flexDrive. The Omnetics connector on the electrode interface board was compatible with both the Open Ephys headstage and a special-ordered Neuralynx HS-36. 

Open Ephys headstage (left) and Neuralynx headstage (right) used for the test. The Open Ephys headstage is based on the Intan RHD2132 amplifier chip. It measures 25 x 13.5 mm and weighs 1.0 g. The Neuralynx headstage is based on the Analog Devices AD8643 chips (we think). It measures 27 x 21 mm and weighs 2.3 g.

Open Ephys headstage (left) and Neuralynx headstage (right) used for the test. The Open Ephys headstage is based on the Intan RHD2132 amplifier chip. It measures 25 x 13.5 mm and weighs 1.0 g. The Neuralynx headstage is based on the Analog Devices AD8643 chips (we think). It measures 27 x 21 mm and weighs 2.3 g.

The mouse was placed in a 1' x 1' arena, and attached to either recording system via a tether that was counter-balanced via a system of pulleys.

The tether used by the Open Ephys system (available for purchase from Intan Technologies) weighs 8.2 g/m, contains 12 conductors, and is 2.9 mm in diameter. The tether used by Neuralynx weighs 10.1 g/m, has 44 conductors, and is approximately 3 mm in diameter.

The tether used by the Open Ephys system (available for purchase from Intan Technologies) weighs 8.2 g/m, contains 12 conductors, and is 2.9 mm in diameter. The tether used by Neuralynx weighs 10.1 g/m, has 44 conductors, and is approximately 3 mm in diameter.

We made sure the settings on each system were the same (1 to 7500 Hz bandpass, ~30 kHz sampling rate), then recorded for 3 minutes with Open Ephys and 3 minutes with Neuralynx

The Open Ephys acquisition board (shown here in a special-edition yellow case) measures 16 x 16 x 4 cm, weighs 0.3 kg, and costs approximately $30 per channel. The Neuralynx Digital Lynx SX system measures 45 x 27 x 30 cm, weighs quite a bit more than 0.3 kg, and costs approximately $1000 per channel.

The Open Ephys acquisition board (shown here in a special-edition yellow case) measures 16 x 16 x 4 cm, weighs 0.3 kg, and costs approximately $30 per channel. The Neuralynx Digital Lynx SX system measures 45 x 27 x 30 cm, weighs quite a bit more than 0.3 kg, and costs approximately $1000 per channel.

The examples below all come from a single electrode, but the signals across all 32 channels are identical between the two systems, as far as we can tell. We hope to carry out a more detailed comparison in the near future, but we couldn't be happier with the initial results!

Several seconds of raw data from each system. If we can spot any difference, it's that the Neuralynx recording has slightly more high-frequency noise (but we haven't quantified this yet).

Several seconds of raw data from each system. If we can spot any difference, it's that the Neuralynx recording has slightly more high-frequency noise (but we haven't quantified this yet).

Zooming in, it's clear that the signal quality is basically identical.

Zooming in, it's clear that the signal quality is basically identical.

Spikes extracted from the continuous signals also look the same.

Spikes extracted from the continuous signals also look the same.

Since this was a hippocampal electrode, we could directly compare ripple oscillations recorded by the two systems. Again, we can't see any difference.

Since this was a hippocampal electrode, we could directly compare ripple oscillations recorded by the two systems. Again, we can't see any difference.

May 2013 Newsletter

Added on by Open Ephys.

In the last newsletter, we described the features of our new acquisition system based on the RHD2132 amplifier chips from Intan. Since then, we assembled that system and started using it in our experiments. We also set up a blog to document our progress.

Testing the new hardware

We now have fully functional designs for headstages and acquisition boards based on Intan's Rhythm interface and digital SPI cable standards. With four headstages connected to one acquisition board, it's possible to stream 128 channels of neural data over a USB cable. We've been testing the system using our 16-tetrode flexDrive in behaving mice and the signal quality looks fantastic.

Images of our new headstages and acquisition board are now available on our website. We'll add details and pictures of the complete system shortly.

Manufacturing

Now that our designs have been validated, we're ready to start the manufacturing process. We'll be sending the first round of boards to the 24 labs that have signed up to be beta testers. In return, we hope that they'll help us add features to the software by creating new plugins for online analysis and by reporting and fixing issues with the software. If each lab contributes only one plugin, the capabilities of our software will increase tremendously.

If you're interested in trying out our system but didn't sign up for beta testing, we're working on an instruction manual that describes how to build it from scratch. We've already built two complete systems ourselves, and each took us the lesser part of an afternoon. And if all goes well with the beta boards, there's a good chance we'll manufacture another round of boards in a few months, so stay tuned for more information.

Open Ephys blog

For more frequent and more technical updates than we provide in our newsletters, you should check out the new Open Ephys blog. So far, we've written posts on using our system for tetrode recordings, making Intan-compatible fine wire tethers, and configuring our system for closed-loop control. We hope the blog will become a place where all users can share their unique applications.

As always, feel free to get in touch if you have additional questions or want to know how you can contribute.

Closed-loop feedback

Added on by Open Ephys.

One of the key advantages of the Open Ephys acquisition system is its prioritization of closed-loop feedback. Our software makes it easy to mix and match modules for acquiring data, detecting events, and sending triggers to external devices. The figure below depicts the configuration we've been using for our own experiments. In the middle, the histogram shows the amount of time elapsed between an event occurring and the feedback being delivered (measured for 1000 events). The delay is never more than 20 ms, and it's around 11 ms on average (white dotted line). This is short enough to facilitate a wide range of closed-loop experiments.

  1. Electrical potentials are generated by the brain and detected by an array of electrodes.
  2. Analog electrical signals are digitized by our headstage and sent to the acquisition board.
  3. The acquisition board packages samples into a buffer, synchronizes them with auxiliary digital and analog inputs, and sends them to a computer via USB.
  4. A dedicated module in our GUI unpacks the incoming data, converts it to floating-point values, and places it into a separate buffer for analysis.
  5. Another software module analyzes the incoming data stream and looks for specific types of events. These can be simple, first-order characteristics of a continuous signal, such as phase or amplitude, or more complex features that are matched to a template. Other modules could be created to analyze the attributes of spike activity, such as multiunit firing rate or decoded sequences. When the event is detected, this module generates a signal that's passed to all the modules farther down the signal chain.
  6. In the final step in the software processing, we have a module that communicates with a Pulse Pal, an open-source stimulator designed by Josh Sanders in the Kepecs Lab at CSHL. This module receives the signal sent by the event generator and triggers the Pulse Pal via USB.
  7. The Pulse Pal is pre-programmed to generate pulses of a precise frequency and duration. Any of its four output channels can be triggered independently via software.
  8. A Plexon PlexBright LED is activated by the Pulse Pal, generating a brief pulse of light that activates channelrhodopsin in the brain.

At every step of the way, it's possible to swap out the hardware or software modules for ones with different functionality. For example, someone proficient in C++ could write a module in Step 4 that communicates with National Instruments hardware. The module in Step 6 could be programmed to deliver feedback via an Arduino. Feedback can also come directly from the Open Ephys acquisition board. The hardware in Step 8 could be a laser, a current source, or a mechanical actuator. Right now, the range of available software modules is limited. As more labs start using our system, we hope they will help us extend its functionality by contributing modules with new capabilities.

Digital fine wire tether

Added on by Open Ephys.

For recordings in freely behaving mice, it is important to minimize the weight and torque applied by the cables. This is especially important for experiments that require natural behavior and becomes a real issue for channel counts over 32 where even light wire tethers become bulky.

The standardized interface cable for Intan RHD chips we use is ideal for this application. Thanks to the digital LVDS signal, only 12 conductors are needed for transmitting up to 64 channels of neural data. Cables that conform to this standard can be purchased from the Intan website in 3- or 6-foot lengths.

If you want something even more lightweight and flexible, it's possible to build your own cables. We did this by soldering wires to two 12-pin Omnetics PZN-12 polarized nano connectors. Here, we've used Cooner CZ 1187 wire, FEP Insulation 38AWG with 0.012" diameter and 0.720Ω/foot. This is the standard wire for analog tethers because it is very flexible and light, but also durable. The cables sold by Intan are 0.423Ω/ft for the LVDS and 0.172Ω/ft for ground and power, so we're at the upper end of the possible resistance values, but it seems possible that the 40AWG version of the wire could work for the LVDS pairs. For the GND and VCC traces using two 38AWG wires or going to a thicker wire with <0.2Ω/foot is recommended unless the tether is pretty short.

The wiring diagram of the cable is simple: There are two rows, each with 6 conductors. Each pair consists of a 'top' and 'bottom' conductor which must be wired straight to the same pair, except with the top and bottom cables switched at the opposite end. If one connector is laid facing the other back-to-back and one connector is upside-down, each pin needs to be connected with its opposite pin (see illustration below).

Each tether will need 12 conductors total: 5 LVDS pairs, plus power and ground. To begin, securely clamp one of the connectors so there's enough space to lay out wires in front of it. Measure out 12 equal lengths of wire.

Now for each LVDS pair, de-insulate ~1 mm on one end of a wire (sharp forceps work well for the cooner wire), tin the wire, and solder it to one pin on the connector. Use plenty of flux when dealing with small wires like these and solder quickly to avoid heating up the plastic body of the connector.  Attach a label to one of the wires in each pair indicating the number (1-6) and which wire is top or bottom.

For each LVDS pair, twist the wires (top and bottom) until they maintain contact even when the tether is bent. Don't simply twist both wires together so they they remain under tension - instead move one wire around the other, without twisting each of the individual wires. Otherwise, the tether will twist around itself later. The ground and power wires don't need to be twisted.

Once all wires on one connector are soldered, fix the tether to the table with standard lab tape or Kapton tape about 1 cm from the connector. This way you can gently pull on the wires to ensure they are the same length, without the risk of breaking the solder joints. Next, lay out the tether so that the free end with the labelled wire ends can be soldered to the 2nd connector.

Make sure the tether is straight and that all wires are tightly twisted with no open loops. Fix the free end to the table with another piece of tape, so that its easy to cut individual wires to the same length, and solder them to the 2nd connector. Make sure that all LVDS pairs remain well-twisted, and add a few more twists on the free end where needed.

After soldering, carefully connect the tether to the acquisition system and headstage and verify that it's working. Use a 64 channel headstage or a 2-to-1 adapter to test both of the 32 channel data lines.

Remove the flux from the connectors with ethanol, and secure the solder joints with a thin coat of epoxy. Tie the wires together at the connectors, and at regular intervals throughout the cable. Add some more epoxy to the knot at each connector and to the sides of the connector to make a solid connection that can withstand handling.

For added strength, it might be useful to add a thin string in parallel with the wires.

Et voilà, 64 channels of neural data on a tether even lighter than those used for conventional 16-channel analog recordings.

March 2013 Newsletter

Added on by Open Ephys.

Since the last newsletter, we've made significant progress updating our hardware to incorporate the new digital chips from Intan. The design for our new acquisition board can be viewed on our GitHub site, with a full bill of materials on Google Docs. Read on to find out about our plans for distributing these boards.

Open Ephys RHD2132-based acquisition system

If you've been following the latest updates from Intan Technologies, you know that they've recently released an evaluation system for their RHD2000-series chips. We worked with Intan to come up with some of the specifications for these boards, and will also adopt those standards for our own hardware. Both the Intan RHD2000 Evaluation System and our new acquisition systems will feature:

  • compatibility between acquisition boards, headstages, and software
  • 32-channel headstages with 36-pin Omnetics connectors (available from Intan for $745 each)
  • 4 headstage connectors (for a total of 128 channels of data acquisition when using 32-channel headstages)
  • 12-wire cables that can be daisy-changed up to 10 meters (available from Intan for $175 per 3-foot length)
  • 8 analog-to-digital converters (separate from the converters on the headstages)
  • 8 digital-to-analog converters (for real-time audio monitoring and signal generation)

Both the Intan evaluation boards and our acquisition boards are powered by the Opal Kelly XEM6010 FPGA development board. This means they can both use the same firmware (Intan's "Rhythm" USB/FPGA interface), and that the same FPGA can be used with either system.

If you're eager to test out the new Intan chips as soon as possible, we encourage you to order the RHD2000 evaluation system, which is available now from Intan. Depending on your needs, however, it might be worth waiting for our boards to be released. Our acquisition system will include some changes that make it more user-friendly for neuroscientists:

  • 5V logic on the digital input and output channels (vs. 3.3V for the Intan evaluation system)
  •  +/-5V input range for the analog-to-digital converters (vs. 0 to 3.3V)
  • +/-5V output range for the digital-to-analog converters (vs. +/- 3.3V)
  • HDMI connectors to interface with peripheral BNCs (vs. screw terminals)
  • an injection-molded case
  • tricolor indicator LEDs

These changes make our boards slightly more complex, but, in return, they will be more convenient for experimenters.

Plan for distribution

When new tools come along in neuroscience, it's typical that the first and last step in propagating them is to publish a methods paper. It's up to the readers to figure out how to put the tools together (or to hassle the original authors for more information). We want to do things a little differently. In addition to posting the design files and complete assembly instructions online prior to publication, we'd also like to manufacture a small number of boards and give them away to interested labs for free. In return, we hope that those labs will contribute to improving our open-source data acquisition software.

This is our first time manufacturing anything at this scale, so we expect there to be some hiccups along the way. Our current plan is to test a few of the new boards by the end of this month, then place an order with Screaming Circuits to produce a larger run. If all goes according to plan, we should have the boards ready by the end of April. But there's always a chance that things will be pushed back if our prototypes don't work as expected.

This effort will be supported by generous donations from a few principal investigators. We only have enough funds to purchase the populated circuit boards and cases, not complete systems. If you receive one of our acquisition boards, you'll still have to buy headstages and cables from Intan, and an FPGA from Opal Kelly (a minimum investment of $1319). Considering that 32-channel systems from commercial vendors start at around $20k, this is not a bad deal.

How to sign up

If you'd like to test out our acquisition boards in your lab, please fill out this request form.

We will have a limited number of boards to give away, so signing up doesn't guarantee you'll receive one. If we've already talked about sending you a system or two, your chances are much better. But please fill out the form anyway, so we can keep track of everyone who's interested.

Keep in mind that we're a team of graduate students—not professional engineers—so there's a chance that the first round of boards will be buggy or won't work at all. We also can't guarantee there will be any technical support (beyond the online documentation) if things go wrong. We do know that, at the very least, this effort will teach us useful lessons about the best ways to distribute open-source hardware. At best, though, it will be an important step toward making multichannel electrophysiology more flexible and more affordable.