Re: [DIYbio] Re: $800 USB UV/VIS spec Ocean Optics knockoff (re: nanodrops)

It looks like global shutter camera chips are only just starting to
penetrate the mass consumer market:
Samsung Galaxy S III has "zero shutter lag" and BSI (back side
illumination) for increased sensitivity:
http://www.samsung.com/global/galaxys3/specifications.html

I think one of the iPhones has the same...

There's indiecam but I can't find pricing easily so it must be high
http://www.indiecam.com/index.php?option=com_content&view=article&id=99&Itemid=123

Aptina has a github account with global shutter camera drivers for the
beagleboard-xm!
https://github.com/Aptina/BeagleBoard-xM/blob/master/MT9V034/Angstrom/README_Beagleboard-xM_mt9v034.txt

And here is a dev board for that camera chip:
http://shop.leopardimaging.com/product.sc?productId=29

So $79-89 for the camera board depending on lens mount (m12 or cs),
plus $149 for the beagleboard-xm... and that's pretty pricey compared
to a Parallax Propeller and a single line CCD.


Plus to get UV you need to coat the CMOS/CCD with a fluorophore to get
decent signal, it would be harder to do that with something like a
DSLR... negating rolling shutter artifacts (that really shouldn't
matter if you just want DNA, or you're not looking at kinetics/stuff
that's actively changing)

On Tue, Aug 17, 2010 at 1:25 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
>
>
> On Mon, Aug 16, 2010 at 5:24 PM, Simon Quellen Field <sfield@scitoys.com>
> wrote:
>>
>> Since I joke that I teach physics to people with short attention spans,
>> most of
>> my designs can be built in about a half hour, including the spectroscope.
>> So
>> you can build one while waiting for the lab tech to set up the expensive
>> one, and
>> compare them. ;-) Kids in middle school are building these for their
>> science fair projects.
>>
>> If you only want a narrow range, that's really easy with a zoom lens.
>> Just zoom in on the part of the spectrum you want.
>> Building your own zoom lens for your low resolution sensor is just another
>> thing to
>> build, more servos or steppers, and more software. All that is already
>> built in to
>> the camera you already own.
>
>
> sure if you're aiming for hobbyists and school children that just want to
> have fun, or impoverished nations that just want to detect hemoglobin levels
> or something easy... but you're not getting a fancy piece of diagnostic
> equipment, especially one thats rigged with some big heavy camera, lossy
> optics that you have no clue about the lens coatings, etc.
>
>>
>> You have not said whether your "global shutter" can take a picture faster
>> than 1/64,000th
>> of a second.  But since my camera can do 3,000 lines in that time, the
>> line is shot in
>> 5.2 nanoseconds. So I think that your low resolution sensor might actually
>> be slower,
>> especially if you are using an off-the-shelf DSP board to capture it.
>
>
> nope, the global shutter sensor I was talking about is a 1/3 Mpixel camera
> for industrial/automotive applications... it was just an example... the sony
> CCD used in Ocean Optics USB specs is the equivalent of one row of a 4
> Mpixel matrix... that's pretty high-res... so I don't know why you keep
> referring to 'my' sensor as low-res
>
>>
>>
>> The Gumstix board you plan to use costs about what the camera costs,
>> assuming you
>> don't use your DSLR. But then you say you think you can build better
>> optics than Canon
>> sells for the DSLR, which seems unlikely. Much less likely is that you can
>> build those
>> optics for less than Canon can, when they have much better economies of
>> scale than
>> you have. Also, the assumption that the cheap low resolution sensor will
>> have better
>> noise specs than the camera is probably wrong as well.
>>
>
> I can build optics which I know the properties of, and can choose what the
> lenses are coated with, implement notch/holographic filters... you can't do
> this practically/easily with a bulky DSLR.
>
>>
>> A spectroscope is a pretty simple device. A slit and a grating. All the
>> rest of the device
>> is a camera. And instead of picking up the camera you already have, you
>> think you can
>> build a better one, and justify spending an extra $2,000 or more for it.
>> That seems suspect.
>> But you can build the one I built for $10 and a half hour's work, and
>> compare it to yours
>> when you finish it, and we can see if the extra cost and trouble was worth
>> it. We can also
>> see if yours stays calibrated (remember mine is self-calibrating), and
>> stays accurate to less
>> than a nanometer resolution.
>>
>>
>> If you spend the extra $2,000 on a really nice camera, you will most
>> likely blow away any
>> homebrew optical system you come up with, and you will have a really nice
>> camera when
>> you aren't doing spectrography.
>>
>> Since cost is not a concern for you, just buy a camera to build into the
>> device. It already
>> has a USB connector, and you can control it from your computer. So now to
>> use it, you
>> put the sample in front of the slit, and hit the ENTER key.
>>
>
> even RAW file formats don't output a truly raw image, there is always some
> processing that goes on other than the user-selectable options.
>
>>
>> Cathal wanted a reasonably priced spectrometer. It's hard to beat $10.
>> He wants to compare his output with his friends' output. It generates a
>> JPEG file, and
>> can easily generate a spreadsheet instead. And he can be confident that he
>> is comparing
>> apples to apples because both devices show the mercury vapor lines of the
>> calibration
>> graph, so he knows both his and his friends' devices are calibrated. As
>> for only being as
>> accurate as the builder, the self-calibration covers that concern as well.
>>
>>
>> I chose $2,000 as the price difference by looking up what people are
>> selling microplate
>> readers for, and choosing the cheapest one instead of the $30,000 one. But
>> if Nathan
>> is building one for the latter market, I think that's great. And if
>> someone on this list can
>> afford one for their home lab, that is even better.
>>
>> As for me, I take the 'DIY' part of the list seriously, but only because
>> it is fun. I can afford
>> the expensive devices (Google was very good to me), but I have a lot more
>> fun outdoing them
>> with a little sideways thinking.
>> ;-)
>
>
> I'm not exactly doing this myself... as I have a few friends helping out...
> but we're definitely doing it ourselves...
>
>>
>>
>>
>> On Sun, Aug 15, 2010 at 8:24 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
>>>
>>>
>>>
>>> On Sun, Aug 15, 2010 at 10:22 PM, Simon Quellen Field
>>> <sfield@scitoys.com> wrote:
>>>>
>>>> A little thought and you'll realize that is nonsense.
>>>> What you want is to spread the spectrum of interest across the available
>>>> width of the sensor. That is what a zoom lens does. If you want to read
>>>> from 200 nanometers to 1200 nanometers, zoom until the leftmost pixel
>>>> sees
>>>> the line at 200 nm and the rightmost pixel sees the line at 1200 nm.
>>>> With the 2048 sensor, you will get 2 pixels per nanometer, or 0.448 nm
>>>> resolution. With the 12 megapixel camera, the 4000 pixels across give
>>>> you 0.25 nm resolution.
>>>
>>>
>>> maybe you've got something there, but its different when you only want a
>>> span of 30-60nm range (common for Raman) and the global shutter is not the
>>> same as a 90 degree rotated progressive scan.
>>>>
>>>>
>>>> It does not matter how close the pixels are to one another.
>>>> In the camera, the microlenses butt up against one another anyway,
>>>> so effectively the pixels are touching. The microlenses focus the light
>>>> onto the
>>>> sensor transistor, so how close the transistors are to one another is
>>>> not
>>>> an issue.
>>>
>>>
>>> I'm not sure that's true with CMOS technology, but anyway, this would be
>>> considered a spatial integrator, so you might lose signal in some cases.
>>>
>>>>
>>>>
>>>> But the ease of building the device is a huge issue.
>>>> Building something from a raw linear sensor requires writing software
>>>> for
>>>> the microcontroller you choose, buying or building the microcontroller,
>>>> interfacing to the computer where you will actually be doing the
>>>> analysis,
>>>> and some amount of soldering, and uncertainty about whether your
>>>> software
>>>> actually works properly and isn't lying to you.
>>>>
>>>
>>> right I would only consider building a spectrometer with a DSP, to handle
>>> all the internals and "just giving an answer" with the push of a button. In
>>> my eyes I shouldn't waste my time looking for OK solutions, when I have the
>>> capability to produce great solutions... But that is where you seem to see
>>> things differently, which is good. I might not always have the right
>>> mindset, but my general idea is to make science easier for the folks that
>>> can't, or don't want to, build a damn thing.
>>>
>>>>
>>>> Taking a picture, however, is fairly simple, and almost everyone has
>>>> access to a cheap
>>>> digicam.
>>>>
>>>> My cheap digicam has a shutter speed of 1/64,000th of a second.
>>>> Try doing that with software on a microcontroller reading your 2048 bit
>>>> linear
>>>> sensor. Plus, if for some reason that isn't fast enough for you, and you
>>>> don't
>>>> like progressive reads, turn the camera 90 degrees.
>>>>
>>>
>>> again I'd consider nothing but a DSP... there are lots of
>>> open-source/DIY-friendly (friendly priced too) invocations of these:
>>> gumstix, beagle board (both TI processors, WOO... (we use TI at work) )
>>>
>>>>
>>>> Astrophotographers are familiar with cooling their cheap cameras (and
>>>> their expensive
>>>> ones) if noise is a problem. But I really doubt that the noise levels in
>>>> a cheap digicam
>>>> are above the noise threshold of the other parts of the device.
>>>>
>>>
>>> My mentor earlier this year was a breakthrough Astrophysicist that built
>>> the first scanning camera that assembled a megapixel image of the solar
>>> skies:
>>> http://www.sciencemag.org/cgi/content/abstract/242/4883/1264
>>> (if anyone can forward me this article, I'd appreciate it)
>>>
>>> And he got there by applying DIY attitude to a big budget.
>>>
>>>>
>>>> A commercial device with fiber optics and a liner sensor make a lot of
>>>> sense when
>>>> profit margins are the main objective. Why make the researcher use his
>>>> own camera
>>>> and take a picture and upload it when he is willing to pay thousands of
>>>> dollars more
>>>> for something he can just push a button to operate? But when someone on
>>>> this list
>>>> is asked whether they would go to the trouble to snap a picture if it
>>>> saved them $2,000,
>>>> they might give a different answer. These are people who actually want
>>>> to build things.
>>>>
>>>
>>> Better optics, a better/faster/less-noisy/more programmable detector and
>>> electronics can mean a lot in my opinion... maybe I am being too much of a
>>> perfectionist, when its not needed. These kind of systems can add to an
>>> unacceptable error budget when you try to scale up productivity past a
>>> weekend hobby. Its this scaling that I'm so cautious to develop myself, just
>>> yet.
>>>
>>>>
>>>>
>>>> On Fri, Aug 13, 2010 at 9:41 AM, Nathan McCorkle <nmz787@gmail.com>
>>>> wrote:
>>>>>
>>>>> The difference is in the backend electronics... you get better
>>>>> resolution with a CCD (which the sony chip is) because the pixels are closer
>>>>> to each other... also with components you can add thermoelectric cooling to
>>>>> physically minimize noise in your signal. You also have a lot less control
>>>>> over something like exposure time, as well as timing, which for fast
>>>>> application (say measuring enzyme kinetics, or DNA sequencing) you would
>>>>> want a chip with a global shutter rather than a progressive one. Global are
>>>>> generally more expensive, lower resolution, but you know all the data is
>>>>> aligned in time.
>>>>>
>>>>> I guess it depends on who you are and what your goals are... why would
>>>>> a microplate reader in industry use a digital camera for a sensor... its all
>>>>> focused into a fiber that goes through a grating onto a linear CCD array for
>>>>> spectroscopy.
>>>>>
>>>>>
>>>>> On Fri, Aug 13, 2010 at 12:11 PM, Simon Quellen Field
>>>>> <sfield@scitoys.com> wrote:
>>>>>>
>>>>>> Why use a low resolution pixel array when you already have a high
>>>>>> resolution
>>>>>> digital camera? And I'll bet that a 3 megapixel digital camera
>>>>>> (equivalent to the
>>>>>> 2048 array) is cheaper than $100.
>>>>>>
>>>>>> Build the device without the sensor.
>>>>>> Then have the user take a picture and run the image through some
>>>>>> software.
>>>>>>
>>>>>> On Fri, Aug 13, 2010 at 5:50 AM, Nathan McCorkle <nmz787@gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> 280nm is a general 'average' absorbance for amino acids... remember
>>>>>>> we commonly deal with 20 unique AAs, so each one's absorbance will actually
>>>>>>> be different, but 280nm was found in the old days (50-90 years ago) to work
>>>>>>> well as a general indicator.
>>>>>>>
>>>>>>> 260nm LEDs from a U.S. distributor run about $300(I'm checking with
>>>>>>> direct from manufacturers overseas, but I will have to have an agent acquire
>>>>>>> the parts in manufacturers country, as distribution agreements often
>>>>>>> prohibit them from selling direct to U.S.)... the NanoDrops 2048 pixel array
>>>>>>> is about $100 for the sensor, coupled with grating and a broad spectrum
>>>>>>> light source... you've got an instrument relatively priced, but with
>>>>>>> broadband acquisition capabilities, as well as potential ability for Raman.
>>>>>>>
>>>>>>> On Thu, Aug 12, 2010 at 6:53 PM, ben lipkowitz
>>>>>>> <fenn@sdf.lonestar.org> wrote:
>>>>>>>>
>>>>>>>> On Tue, 10 Aug 2010, Simon Quellen Field wrote:
>>>>>>>>>
>>>>>>>>> But it sounds like you don't need a spectroscope.  You just want to
>>>>>>>>> know
>>>>>>>>> how much your sample absorbs at 280 nm.  What you need is a 280 nm
>>>>>>>>> LED
>>>>>>>>> and a photocell, and a couple samples to use for calibration.
>>>>>>>>>
>>>>>>>>> You can use a simple multimeter for the readout.
>>>>>>>>
>>>>>>>>
>>>>>>>> good advice (260nm actually)
>>>>>>>>
>>>>>>>>
>>>>>>>>> It seems unlikely that your sample would have non-DNA/RNA
>>>>>>>>> contaminants that absorb strongly in the same range as the DNA or RNA for
>>>>>>>>> some chosen wavelength. So choose a wavelength that is convenient for you
>>>>>>>>> (maybe your green laser pointer or a cheap red one, or a blue LED) and do
>>>>>>>>> the calibration.  Then you simply adjust the protocol, so that if the
>>>>>>>>> protocol you are following calls for 10% absorbance at 280 nm, and a DNA
>>>>>>>>> sample that absorbs 10% at 280 absorbs 30% at 532 nm, then you look for 30%
>>>>>>>>> absorbance from your green laser pointer.
>>>>>>>>
>>>>>>>>
>>>>>>>> bad advice.
>>>>>>>> DNA is basically clear in the optical range, you can't tell by
>>>>>>>> looking at a sample whether it has any DNA in it or not.
>>>>>>>>
>>>>>>>> DNA absorbance spectrum, peak at 257nm:
>>>>>>>> http://www.cbs.dtu.dk/staff/dave/roanoke/bluescript.jpg
>>>>>>>>
>>>>>>>> since DNA absorbance at 405 or 700 is basically 0% then your
>>>>>>>> measurement will be pure noise.
>>>>>>>>
>>>>>>>> good spectrometers also measure the ratio of absorbance at 260nm to
>>>>>>>> absorbance at 280nm because amino acids absorb at 280 and might throw off
>>>>>>>> your measurement.
>>>>>>>>
>>>>>>>> more good info here
>>>>>>>> http://en.wikipedia.org/wiki/Nucleic_acids_analysis
>>>>>>>>
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Nathan McCorkle
>>>>>>> Rochester Institute of Technology
>>>>>>> College of Science, Biotechnology/Bioinformatics
>>>>>>>
>>>>>>> --
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
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>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Nathan McCorkle
>>>>> Rochester Institute of Technology
>>>>> College of Science, Biotechnology/Bioinformatics
>>>>>
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>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>>
>>> --
>>> Nathan McCorkle
>>> Rochester Institute of Technology
>>> College of Science, Biotechnology/Bioinformatics
>>>
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>>
>>
>>
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>
>
>
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> Nathan McCorkle
> Rochester Institute of Technology
> College of Science, Biotechnology/Bioinformatics



--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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