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Open-Source Hardware For Neuroscience

samzenpus posted about 5 months ago | from the freeing-things-up dept.

Medicine 41

the_newsbeagle (2532562) writes "The equipment that neuroscientists use to record brain signals is plenty expensive, with a single system costing upward of $60,000. But it turns out that it's not too complicated to build your own, for the cost of about $3000. Two MIT grad students figured out how to do just that, and are distributing both manufactured systems and their designs through their website, Open Ephys. Their goal is to launch an open-source hardware movement in neuroscience, so researchers can spend less time worrying about the gear they need and more time doing experiments."

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less money yes, less time no (4, Insightful)

Trepidity (597) | about 5 months ago | (#47227805)

Their goal is to launch an open-source hardware movement in neuroscience, so researchers can spend less time worrying about the gear they need and more time doing experiments.

My experiences with lab-built equipment in academia suggest that building your own equipment is not really a good way to "spend less time worrying about the gear". Usually you will spend quite a lot of your time worrying about DIY gear. The advantages are not in time saved, but in two other things: 1) you can build gear that would be prohibitively expensive to purchase; and 2) you can customize it in-house.

Re:less money yes, less time no (3, Insightful)

Thanshin (1188877) | about 5 months ago | (#47227865)

Based on the comparative nature of "less", I would guess it depends on how much time one spends worrying about how to get the money to buy the prohibitively expensive equipment.

Re:less money yes, less time no (2)

sirlark (1676276) | about 5 months ago | (#47229271)

Agreed! Firstly, as the P pointed out, a significant amount of time goes into getting grants to fund the experiments. This isn't going to go away, funding is still required, but it will mean that YOUR lab now has a chance of getting the grant, as opposed to the lab that already has the machine available for use because it was funded by the last grant. This means a wider variety of labs doing the science, which is a good thing. Also, having worked for a commercial science institute that really pushed the idea of 'brand name equipment saves you time and money', I can assure you, it's not the case. Our brand name equipment was ALWAYS down, waiting on a repair guy to be flown in from another continent, because the local guy didn't know how to fix it, or didn't have the parts. On top of that, we often had to run experiments multiple times because the results were suspect. The machine operator ended up with more repair skills than the first-level call out guy after about a year... that saved us time! So I'd say having in-house skills for maintaining your CORE equipment is a good thing. Open source design and hopefully some interchangeability in parts, a bonus!

Re:less money yes, less time no (1)

smaddox (928261) | about 5 months ago | (#47231173)

I tend to agree, but it does matter what the equipment is. I would hate to have to design, build, and maintain our own lock-in amplifier or x-ray diffractometer. I guess it depends how good the available products and companies are.

Re:less money yes, less time no (1)

LifesABeach (234436) | about 5 months ago | (#47230171)

I'm thinking one just goes over the Analog Engineering Department, and the Mechanical Engineering Department and says, "Pardon me, I have a question on how to build this..."

Re:less money yes, less time no (0)

Anonymous Coward | about 5 months ago | (#47227949)

Not even less money.
If you DIY, what are you going to use as a reference to prove the device works correctly?
You also need to buy reference equipment.

A company an amortise the reference equipment cost over sales; DIY can not.

Re:less money yes, less time no (4, Interesting)

mandginguero (1435161) | about 5 months ago | (#47227987)

you can use published results to validate your new equipment. if you can find the same trend in the data, same, and at least similar order of magnitude, then you are on the right path.

Re:less money yes, less time no (0)

Anonymous Coward | about 5 months ago | (#47229245)

you can use published results to validate your new equipment. if you can find the same trend in the data, same, and at least similar order of magnitude, then you are on the right path.

hahaha remember this is neuroscience we're talking about.

Re:less money yes, less time no (1)

mandginguero (1435161) | about 5 months ago | (#47239459)

you can use published results to validate your new equipment. if you can find the same trend in the data, same, and at least similar order of magnitude, then you are on the right path.

hahaha remember this is neuroscience we're talking about.

i am a neuroscientist who does electrophysiological recordings. i perform validation tests every time i get a hold of a new piece of equipment.

Re:less money yes, less time no (2)

gl4ss (559668) | about 5 months ago | (#47228173)

depends what you're trying to do.

if you're trying to prove that you can drive an rc car by reading inputs x123 and x124 and y984 and running them through such and such filter... then accomplishing that is the proof.

Re:less money yes, less time no (4, Interesting)

mandginguero (1435161) | about 5 months ago | (#47227953)

True, but imagine how bringing the cost down can lower the entry barrier for things such as teaching labs. My best course by far in undergrad was an electrophysiology course where we recorded action potentials in earthworms with just a couple electrodes and a differential amplifier hooked up to an old macintosh. Getting these technologies lower in cost may not alleviate quality concerns for high throughput research (which is what some of the quoted established company reps are saying in the article). But imagine how cheap the next iteration of these could be? An order of magnitude lower for the openBCI 8 channel EEG system http://www.openbci.com/ [openbci.com] . And with scalp potentials and a 512 hz sample rate you can measure muscle potentials too, not just brain. If you could find a way to increase the sample rate you could do things like galvanic skin response too.

Re:less money yes, less time no (1)

Anonymous Coward | about 5 months ago | (#47228835)

Speaking as a neuroscientist (who works at MIT's Picower Institute with the OpenEphys creators) I don't think it's really true that the average end-user will spend more time with worrying about this hardware than they would a commercial system. That's true if you're starting from scratch, but this is basically a complete solution already with little-to-no development needed for users interested in doing standard extracellular ephys. Once the board is populated (a day or two at most, with a good set of directions to follow), the system is no harder to use than any of the 60K solutions. And, it has the massive advantage that when you discover an error in the software you can just fix it yourself and keep going. I've personally seen a -LOT- of time wasted because Plexon (one of 2 or 3 big commercial solutions) didn't handle tetrode data correctly (google it). Weeks of time wasted trying to reverse engineer what was going wrong in a closed system sucks. Even worse, waiting weeks-months for a patch while you twiddle you thumbs. And, when they do fix things they don't alert existing users that there is a problem, so most in the community of users don't know there was a problem and that existing analysis might be wrong. And, if at any point you discover that you want to do something even subtly different from what the commercial system was built to do, you better start writing a new R01 because the commercial companies are willing to help only so far as you're willing to spend tens of thousands above and beyond what you're already invested. Or you want a part number for whatever flavor of edge connector they used so you can build a new $10 cable for yourself? Well, they can't tell you that but they'll sell you a cable for $250.

All in all, I think this system will actually save time for the average lab. And be much cheaper. And more capable.

Re:less money yes, less time no (1)

Trepidity (597) | about 5 months ago | (#47231043)

That's a good point, if this is more like a polished, well-tested kit solution, then it won't be nearly as time-consuming as a one-off DIY system to build and maintain.

Re:less money yes, less time no (1)

jvoigts (3693665) | about 5 months ago | (#47232751)

Just to clarify this, the current system can be put together without any assembly, everything is pretty much plug n play by now (windows, mac & linux). You can of course customize things as much as you like. As for the data quality, measuring quality for this type of system is not at all hard. It is well known what the data is supposed to look like, and if it doesn't, its usually pretty obvious. It's a bit like a microphone and a sound card, all you need is to play a known signal and then compare the result to see if there was any degradation. Pretty much any lab using the system has testing equipment for this. There is a pretty long list of labs that are currently using the system and are getting very good results. These are all labs that have a lot of experience with this kind of recording and in most cases are recording the same data with commercial systems and can compare the data. We're currently going through a bunch of in-depth measurements and will publish the results as soon as time allows. Here's a quick side-by-side for now: http://open-ephys.org/blog/201... [open-ephys.org] Finally, the Intan chips that we're using are already being used by a bunch of commercial vendors, which speaks to their quality and is a great opportunity for making equipment more inter-operable in the future.

Re:less money yes, less time no (1)

mandginguero (1435161) | about 5 months ago | (#47239465)

upmod the parent comment if you have the points....

MIT is pure evil (-1)

Anonymous Coward | about 5 months ago | (#47227835)

MIT murdered Aaron Schwartz! Boycott everything MIT produces!

Of course you can get cheaper equipment ... (0)

Anonymous Coward | about 5 months ago | (#47227851)

... if you don't have to jump through all the hoops (quality management, defect tracking, regulatory compliance, manufacturing yield, safety risk assessment/mitigation, customer support, liability, translation into three dozen languages, etc.) that a commercial manufacturer has to.

Re:Of course you can get cheaper equipment ... (1)

jellomizer (103300) | about 5 months ago | (#47228141)

But these companies do have the following.
Ability to buy in bulk, tax write off on all the parts they buy, vendor competition.

medical devices directive (0)

Anonymous Coward | about 5 months ago | (#47227919)

Is the reason medical devices are so expensive. The actual hardware of medical devices is normally fairly low cost. However the regulatory burden on companies to provide safe and effective medical devices is substantial and rightly so. I am extremely sceptical that these devices have the necessary certifications for use on patients and it would be an irresponsible doctor that allowed their use on their patients without these certifications.. they are there for a reason!

And its not just the devices that need the certifications, the companie that supplies them have to be audited to things like ISO 13485, 14971 as well as 9001/9002. This requires substantial investment, experience and knowledge to achieve, and again I seriously doubt that two grad students have that capability. Finally, these requirements are in place for patient safety.. that is the number one factor in designing these devices. And while it creates a high hurdle for small companies to overcome, it is fully justified and necessary

Re:medical devices directive (1)

CurryCamel (2265886) | about 5 months ago | (#47227961)

These are not doctors and patients, but researchers. And the device in question is a passive recorder of brain activity (AFAIK).
Also, I don't think that many people want to record the brain activity of mice, so the biggest cost here is that the equipment is pretty custom made causing big non-recurring expenses.
Furthermore, an IC subcontractor had made a miniturized four dedicated custom ICs into one, and from the article it sounds this device was the first to use the new chip. Expect all other manufacturers to jump to this new chip too, probably shaving off big % of the total price.
This is news only for the intersection of the sets "neuroscientists" and "nerd". The rest of us are happily unafected.

Re:medical devices directive (1)

Molt (116343) | about 5 months ago | (#47228325)

When a paper is published it should include the methodology used to gather the results, and if that includes a lot of untested and uncertified pieces of kit then it's going to cast serious doubts as to the validity of the findings. Have they actually found something of significance, or are they just prodding round some experimental error which wouldn't be there if they used tried and tested setups? It'll be fine for teaching, and that will help it to gain some credibility, but for a lot of research it's going to take a long time to gain acceptance without a large testing and certification budget behind it.

Re:medical devices directive (0)

Anonymous Coward | about 5 months ago | (#47228407)

Yea yea, FUD the shit out of open science. Only proprietary expensive instruments are valid. Keep it in the towers, can't have the masses doing science.

Fuck you.

Re:medical devices directive (1)

Ihlosi (895663) | about 5 months ago | (#47228467)

Yea yea, FUD the shit out of open science. Only proprietary expensive instruments are valid.

With all your rage, you missed the point.

And the point is not that self-built instruments are incapable of being validated, but that you'll have to include the effort for validating them (and documenting the validation) yourself. This costs a lot of time, and, unless your time doesn't cost anything, money.

Re:medical devices directive (1)

Stem_Cell_Brad (1847248) | about 5 months ago | (#47229463)

I don't think this is as big of a problem as you do.

Regardless of the instrument's origin (bought for big $ from company or open source built), scientists are going to run positive controls. It's a common practice for GOOD experiments. In this case, apply treatment X to a mouse, and you should see response Y as measured by the instrument. If you don't see response Y in the positive control, you cannot trust experimental results. If the positive control give expected results, then reviewers have little choice but to accept the experimental result.

You need to do the same thing for fancypants commercial instruments to make certain they are working properly, operated properly, and the rest of the experimental variables (the mice, the treatment) are as expected.

Bottom line is that if the homebrew instruments work reliably for the positive controls, they will be easily accepted.

Re:medical devices directive (0)

Anonymous Coward | about 5 months ago | (#47229933)

Because you can just trust that your off-the-$helf proprietary hardware is working as designed and certified.

Re:medical devices directive (0)

Anonymous Coward | about 5 months ago | (#47231815)

You don't work in CNS. Even for FDA drug studies it's not uncommon to have biomarkers that are not FDA-approved as secondary endpoints. Every paper (regardless of whether they use a swanky commercial tool kit or not) has to demonstrate that their data is significant. Using a "tried and true" solution often does nothing to advance the field.

Re:medical devices directive (0)

Anonymous Coward | about 5 months ago | (#47228503)

These are not doctors and patients, but researchers. And the device in question is a passive recorder of brain activity (AFAIK).

Also, I don't think that many people want to record the brain activity of mice, so the biggest cost here is that the equipment is pretty custom made causing big non-recurring expenses.

Furthermore, an IC subcontractor had made a miniturized four dedicated custom ICs into one, and from the article it sounds this device was the first to use the new chip. Expect all other manufacturers to jump to this new chip too, probably shaving off big % of the total price.

This is news only for the intersection of the sets "neuroscientists" and "nerd". The rest of us are happily unafected.

Regardless of whether it is used for treatment or research, it must be safe and compliant. Does it meet basic electrical safety for example? as its designed to make an electrical connection to the skin, it is a type BF applied part and must meet the leakage current, isolation requirements for safety.

Even if an IC manufacturer has made a dedicated chip for this, the power supply to the system must meet the above requirements and it often means using secondary isolation as very few off the shelf PSU's (even medical rated power supplies) meet the type BF requirements. And that's just the tip of the iceberg in terms of safety..

As I said, its not the hardware costs that drive medical device prices, its the large R&D investment to ensure the devices are safe, effective and compliant to safety standards

Re:medical devices directive (2, Informative)

Anonymous Coward | about 5 months ago | (#47228571)

In fact I just checked their schematics.. no secondary isolation, and power taken from the USB or from an external PSU (not supplied or specified)

computer power supplies provide less isolation and allow higher leakage currents than a medical grade PSU, let alone one rated for BF. So it doesn't even meet basic electrical safety, let alone any other parts of IEC60601. I personally woun't want this used on me..

Re:medical devices directive (1)

Stem_Cell_Brad (1847248) | about 5 months ago | (#47229499)

Good thing you're not a mouse.

Re:medical devices directive (0)

Anonymous Coward | about 5 months ago | (#47229909)

Their February newsletter states they've already used it on humans, and they've released an adapter for connecting to a standard electrode cap

OpenEEG? (1)

h5inz (1284916) | about 5 months ago | (#47228077)

So how does it differ from OpenEEG project? I read the summary and I read a couple of paragraphs from their site, but it was all some round talk. You can get fully assembled 2 channel (uses smt components - it's small) OpenEEG device from Olimex for 99 euros (+electrodes and shipping costs), if you are not into soldering.

Re:OpenEEG? (1)

jvoigts (3693665) | about 5 months ago | (#47232595)

The main difference is that the open ephys system is designed for recording neurons, not just scalp potentials and scales to very high channel numbers >128 channels at rates of 30kHz, which is fast enough to do extracellular electrophysiology. That being said, a few labs are starting to use open ephys for EEG ( https://open-ephys.atlassian.n... [atlassian.net] ).

Laudable, but there are scientific risks (0)

Anonymous Coward | about 5 months ago | (#47228655)

I'm a bio-electrical engineer from MIT, course 6-1b, back when that was the number for the department. I used to design neuroscience equipment: built the highest frequency, fastest pulse stimulators on the planet fand tested on humans in a functional MRI. *MAN*, I miss that work. The pay was horrible, but getting to do genuinely new science was fascinating.

Anyway: there were hard-learned lessons that new designers are unlikely to have learned, so I'd be concerned about amateurish efforts. They include:

1) The ground plain is not actually at ground voltage. It never is: making it bigger will not solve all your problems, capacitive coupling to ground is *localized* and can spread signals via paths you'd never see in a circuit diagram.
2) That line on the diagram that says parts are tied together and the same voltage at the same time is a *lie*. Signals take time to go down wires and can couple to all sorts of things.
3) Really good measurement equipment, low noise, calibrated, used correctly, is worth its weight in gold, and certainly its weight in intern organs. (Which organ depends on the intern.) It can detect subtleties that you never realized were there until you measured them correctly.
4) 60 cycle creeps in *EVERYWHERE*. So do various high frequencies on the power lines from other equipment. I don't care if the "power line filter" vendors say it blocks "95% of all transients", it does not block 60 cycle. Mu metal and magnetic shielding do not block 60 cycle. Running off of clean batteries on an isolated power supply, with a wooden desk and no conductive surfaces blocks 60 cycle. A good motor generator can also block 60 cycles, but make damn sure the coupling between them is wood, not metal.
5) Capacitors leak DC. You cannot completely block DC voltage to nerve electrodes by putting a blocking capacitor on it, and if you do use that as a safety issue, use a *ceramic* capacitor, not a *polarized* capacitor, even if those do come in bigger values for the same size, Make damn sure your stimulators run at a zero DC output *before* the capacitor, or as close as you can get to it, or the leaked DC current can screw up all your results and may cause neurological damage. (This discovery caused a lot of adventures in my lab, I freaked out when I found that some twit had used "polarized" capacitors in a 10 year old design, which do not treat positive voltages the same way they treat negative voltages.)
6) Rebuilding the equipment effectively guarantees somewhat different results, even if you followed the specs exactly.

These kind of hard-won lessons are why I'd be really cautious about student built hardware. Some of those lessons took a long time to learn, and were never really taught in design courses.

Re:Laudable, but there are scientific risks (1)

Ihlosi (895663) | about 5 months ago | (#47235471)

1) The ground plain is not actually at ground voltage. It never is: making it bigger will not solve all your problems, capacitive coupling to ground is *localized* and can spread signals via paths you'd never see in a circuit diagram.

Looking over the analog guys' shoulders at work, I've seen a nifty little piece of software that takes the geometry of your ground plane and its connections, and tells you where exactly you'll need to put your Cs to minimize ground plane effects.

This is neat since it shows you that just placing Cs next to your components connections doesn't work the way you thought it would.

60 cycle creeps in *EVERYWHERE*.

You mean 60 Hz line frequency? Well, wait until you design devices for an international market. You'll have environments completely free of 60 Hz line stuff there, unfortunately, that usually means you'll have to deal with 50 Hz. Have fun testing your device for behavior with 60 Hz line frequency in a 50 Hz line frequency country. Oh .. and be sure to keep those harmonics in mind.

Oh, and debugging these devices is its own kind of hell, since connecting your microcontrollers emulator breaks any kind of isolation and makes the device behave differently. Ugh.

Capacitors leak DC.

More generalized, it should be: There are no resistors, capacitors or coils. Anything that claims to be one of the three is actually an RLC circuit, and you will see them behaving as one at the worst possible moment. Yes, your resistor has capacity and inductance; yes, your capacitor leaks DC, etc.

WOOT 7p (-1)

Anonymous Coward | about 5 months ago | (#47228731)

expulsion of IPF surveys show that us the courtesy NNigers everywhere

"Brain signals" (3, Interesting)

RyanFenton (230700) | about 5 months ago | (#47228911)

This has always bothered me with the current state of neuroscience: The whole point of nerves/brain matter is to communicate/remember/transform information, but we're still relying on crude external cues like heat/bloodflow/electrical activity to tell us "somethings happening around...here", and that's pretty much it. It always bothers me when I hear the term "brain signals".

Nerves should be able to query their neighbors about their state, and the state of other nerves - otherwise, they wouldn't really be able to form something like a mind (as in, "the mind is what the brain does"). Why still can't we find a way to just "ask" the nerves what their state is?

Even in our simulations, we just represent nerves as nodes that grow associations - but those associations are useless, unless they can be traversed in queries by the system, to gather inputs, and send outputs at all levels.

Are we getting anywhere close to a stage where we can communicate with nerves to use that same communication system that logically must exist for it to function? Seems like even with limitations, that would be a LOT more useful than analogously inferring from traffic levels what the function of buildings in a city are, like we're doing now.

Ryan Fenton

Re:"Brain signals" (1)

ziggystarsky (3586525) | about 5 months ago | (#47229425)

You noticed that the described project is used to implant electrodes into the brain of live animals (mostly rodents)? The aim is to measure an electrical signal that can be associated with a small cluster of neurons.

This indeed sounds cruel (and I think it is), and for such research the ethical cost has to be related to the scientific gain in a reasonable ratio.

Btw, I know researchers that say you can pull out the electrodes after the experiment and the animal could live on without much impediment. But the laws here in Germany demand that the animals are killed.

Re:"Brain signals" (1)

jeffb (2.718) (1189693) | about 5 months ago | (#47230895)

Sure, but there are a few issues:

1) Nerve signals aren't purely electrical, but electrochemical. You can do brute-force stimulation or detection by purely electrical means, but it's hard on the nerves (literally).

2) Nerves are tiny, and there are lots and lots of them, and they aren't arranged in a regular, predictable fashion. You can't build a standard module that plugs into any random individual human's nervous system and just works.

3) The most interesting nerves in the brain are hard to get to, because they're surrounded by several centimeters of, well, more brain -- not to mention dura, skull, skin, hair, and so on.

4) Even if we do invasively get to the nerves we want, higher-level activity seems to be encoded as a vast phase space. We're better equipped than ever to find patterns in that kind of information, but we're still closer to the beginning of the process than its end.

And so on...

Re:"Brain signals" (0)

Anonymous Coward | about 5 months ago | (#47232377)

The brain has ~85,000,000,000 neurons and ~500,000,000,000,000 synapses. "Let's just query..."

Circuit Cellar (1)

kallen3 (171792) | about 5 months ago | (#47230061)

I seem to recall that years and years ago Steve Ciarcia wrote a series of article in his Circuit Cellar magazine about making sensors and a home built EEG. If I recall correctly it used relatively inexpensive parts and off the shelf sensors when necessary. All designed for the hobbyist and much lower in cost. Of course I may be wrong. But still wondering, whats the big hoo haw about something this expensive?

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