January 2013 Newsletter

This is the third installment of the Open Ephys newsletter, which we plan to send out on a monthly basis. Since last time, we took a trip to Janelia Farm to discuss open-source standards for multichannel electrophysiology, updated our headstage designs for the new Intan chips, and fleshed out the documentation for both users and developers of the Open Ephys GUI.

Developing open-source standards

On December 11, Josh and Jakob traveled to Janelia Farm to talk with members of the Applied Physics and Instrumentation Group, other group leaders, and representatives from Blackrock Microsystems. Dr. Tim Harris initiated the meeting in order to reduce some of the redundancy in open-source tool development, a goal we could not be more enthusiastic about. We discussed the need to develop open-source standards for extracellular electrophysiology, which have been conspicuously absent until now. In communities such as the audio recording industry, standardized interfaces make it possible for hardware and software from different vendors to work together seamlessly.

In our discussions, we identified a few interfaces where standards would be especially useful to have:

• Connections between implanted electrodes and a detachable headstage
• Connector and cable type between headstage and acquisition board
• Communication protocol between Intan chips and an FPGA-based acquisition board
• Data transmission between an FPGA-based acquisition board and a computer
• Writing data to disk, including file types for raw and pre-processed data

We've been working closely with Reid Harrison of Intan to develop standards for each of these interfaces. As a result, our headstages and acquisition boards will be fully compatible with the next generation of Intan evaluation hardware. Whether or not these catch on, we hope our efforts will draw attention to the importance of standards for moving our field forward.

New headstages

We finished the first revision of our updated headstage design in December. If you have access to Eagle PCB software, you can check out the design files on GitHub: https://github.com/open-ephys/headstage. By incorporating the new RHD2132 Intan chips (as opposed to the older RHA2132 chips), these headstages will feature:

• 32 channels
• on-chip analog-to-digital conversion
• low-voltage differential signaling, which allows significantly longer cable lengths
• reduced size and weight
• 36-pin Omnetics connectors compatible with many current implants and probes (mates with Omnetics part #A79026-001)
• a built-in 3-axis accelerometer (for detecting head movements)

The printed circuit boards just arrived, and we're excited to test them out as soon as possible. We ordered a bunch of extras, so if you're interested in building your own headstages (instead of purchasing them through Intan), we might be able to send some bare boards your way.

Updated documentation

In the last month, we added a page to the GitHub wiki to orient new users to our cross-platform data acquisition package: https://github.com/open-ephys/GUI/wiki/User-documentation. If you've been using the Open Ephys GUI for data acquisition and any aspects of the software have been confusing, please let us know. We will gladly use your input to revise the documentation (which is still very much a work in progress).

We also posted some much-needed developer documentation: http://htmlpreview.github.com/?https://raw.github.com/open-ephys/GUI/master/Source/Docs/html/classes.html. We're using Doxygen to extract the documentation directly from the source code, which makes it trivial to keep everything up to date. As of last week, all of the major classes and methods are described. If you plan on changing the software yourself, we highly recommend browsing through these pages.

If you have any questions, or would like to get involved in our efforts, please get in touch with us through the contact page (http://open-ephys.org/contact) or by replying to this email.

December 2012 Newsletter

This is the second installment of the Open Ephys newsletter, which we plan to send out on a monthly basis. We reached an important milestone in November by carrying out the first neural recordings with our custom acquisition system. We've also made progress on updating our hardware and software.

Neural recordings

Over the past few weeks, we've been using the Open Ephys acquisition system to record data from awake, behaving mice. Previously, we'd only tested our acquisition board and headstages with signal generators and pre-recorded data. While our measurements indicated that the data quality would be excellent, we were obviously eager to see how it performed with actual neural signals. We're happy to report that everything looks great!

We implanted an array of low-impedance tungsten electrodes in mouse hippocampus and recorded with a skull screw reference. We see beautiful theta, gamma, and ripple oscillations, with barely detectable 60 Hz line noise. Since we're digitizing the signals directly on the headstage, movement artifacts are greatly attenuated. Saturating events are very infrequent, even in an animal actively running on a track. The next step is to implant an array of independently movable tetrodes. We'll keep you posted on our progress.

Upcoming hardware revisions

We're on schedule to have our hardware updated by the time the new Intan chips are available in early 2013. As described in the last email, the new chips will feature an onboard analog-to-digital converter, low-voltage differential signaling, and a number of other improvements. The new headstages will be a major upgrade in terms of size, weight, and performance. We already redesigned the circuit board, which now measures a mere 21 x 13 mm. We also added a 3-axis accelerometer to use as an alternate indicator of animal activity.

Another thing we're changing is the connector. Our current headstage design uses 0.4 mm pitch Molex connectors because of their compact size and low price point. Although these connectors can yield stable recordings in awake animals (as described above), they require additional reinforcement. We're also concerned about their long-term durability. Since Omnetics is the standard for the field (and many people have already requested Omnetics adapters for our hardware), our new headstages will use their 34-pin connectors.

Software improvements

The software interface we use for experimental control, visualization, and recording has received some significant upgrades. In order to collect real data, we made the recording capabilities more robust and updated the file format. We also added modules for real-time event detection, TTL-triggered recording, and digital referencing, all of which can be used in combination with data from any input source. We're making progress on fleshing out the documentation, with new wiki entries on data format (https://github.com/open-ephys/GUI/wiki/Data-format) and creating custom data-processing modules (https://github.com/open-ephys/GUI/wiki/Custom-processors).

That said, there are still a variety of ways in which the software could be made more reliable and user friendly. If you or anyone you know is interested in helping with C++ software development, please get in touch with us through our contact page (http://open-ephys.org/contact/) or by replying to this email. We'll make sure your message reaches the most appropriate recipient.

November 2012 Newsletter

Open Ephys is still in its infancy, but we've already made great strides toward our first major goal: a complete hardware and software solution for recording, visualization, and closed-loop feedback. At the recent Society for Neuroscience conference in New Orleans, we showed off a prototype system that could acquire 128 channels of data and respond to neural events in 20 milliseconds or less. Given that the plan for this system was hatched a little more than a year ago, we're optimistic that the production of a more polished system will happen in a matter of months, rather than years.

To learn more about the tools we're developing, check out our website (http://open-ephys.org) or download the poster we presented at SfN (bit.ly/RpxRim).

The road ahead

What's not currently on our website is our plan for moving forward, which became much clearer at the conference. As you may know, our hardware incorporates amplifier chips from Intan Technologies (http://www.intantech.com), which have allowed us to dramatically simplify and miniaturize our recording system. According to Reid Harrison, the founder of Intan, an updated version of the amplifier chips will be produced in December. The new chips will feature an analog-to-digital converter, low-voltage differential signaling, and a number of other improvements. If these chips pass the necessary tests, we will start using them in our system. We are already updating our designs so we can accommodate the new chips as soon as they're ready.

Besides revising our hardware, we also have clear-cut plans for manufacturing and distributing our recording systems. If our updated designs are sound, we will have our headstages and compatible cables available for purchase from the Intan website. Sometime in early 2013, we will mass-produce a round of about 50 acquisition boards and cases, which we will send to interested labs. The total cost of a 64-channel system will be around $1500, and there will be minimal assembly required. Of course, since the design is completely open-source, you could build your own system right away using the designs on GitHub (https://github.com/open-ephys/). But we recommend waiting for the next round of revisions to become available, as there are still a few updates we want to add.

How you can help

While our plans for improving the Open Ephys hardware are mainly settled, there's a lot of work to be done to make our software as flexible and user-friendly as possible. In parallel with our hardware, we've been developing a cross-platform application (called "the GUI") for experimental control (https://github.com/open-ephys/GUI). The major strength of the GUI is its modularity, which makes it easy to modify and extend. The software was designed from the start to be compatible with almost any input source, so it can also be used with hardware other than the Open Ephys acquisition system. It currently includes basic modules for filtering, spike detection, audio monitoring, recording, and LFP and spike visualization. But its functionality is very stripped down, and it still has more than a few bugs.

If you or anyone you know is interested in volunteering their time to improve our software, please get in touch with us. Possible projects range from the simple (adding a buffer to the audio monitor) to the complex (creating an OpenGL plotting library). Knowledge of C++ is required, but if you already have basic skills in another language, it's not very difficult to learn!

We'd also be thrilled to have full-time programmers helping with software development. If anyone has funding available for such a position, please let us know. We realize this is a major investment, but we feel strongly that easy-to-use, open-source data acquisition software would be an invaluable asset to the entire community. In the scheme of things, the cost of hiring a programmer for a year is much less than the price of a new commercial ephys system. Our software reached its current state through the efforts of two graduate students working in their spare time for one year. A more concerted effort to polish the software could generate substantial returns in even less time.

Channels of communication

We plan on using this mailing list to deliver updates on a monthly basis. If that's too much for you, feel free to unsubscribe using the link at the bottom of this message. But if you're craving up-to-the-minute information on our progress, we plan on using GitHub as our main channel of communication. Once you create a GitHub account (a very easy process), you'll be able to:

- subscribe to feeds that broadcast updates to all our repositories
- edit the wiki pages for each repository, which will eventually evolve into comprehensive online documentation (most likely hosted somewhere other than GitHub)
- use the "issues" system as a basic forum for solving problems and getting feedback

It's also fine to get in touch with the Open Ephys team directly through our contact page (http://open-ephys.org/contact/) or by replying to this email. We'll make sure your message reaches the most appropriate recipient.