Josh - do you have more information on the monochromatic qPCR machine ? I need one!
On Monday, May 20, 2013 1:33:34 AM UTC-5, Josh W Perfetto wrote:
Hey Matt,--
My upcoming monochromatic qPCR machine is photodiode based, and Nathan
has been doing a lot of work with CCD linear arrays for his open
spectrometer project. We're starting R&D on a multichannel
multichromatic (500-750nm) qPCR project though, which will likely
require a 2D 12-bit camera. I would love to know what is "back to
basics" on such a device, as I am not an EE, and the off the shelf
solutions are pricey.
-Josh
On Sun, May 19, 2013 at 9:50 PM, matt harbowy <hberg...@gmail.com> wrote:
> One of the things that I think is being missed is too much of a reliance on
> off-the-shelf webcams. I'd really encourage everyone to "get back to
> basics".
>
> The model piece that I've been using is the AMS linear array.
> http://www.mouser.com/ProductDetail/ams/TSL1402R/? qs=sKasJQfA%252bi5t6//qMqmpuA= =
> It's a 16 dollar chip that if you spend some time actually playing with it,
> youll begin to realize that many of the arguments being made here are moot,
> or mootable.
>
> By controlling the signalling to the chip, you can control the integration
> time- the amount of time the chip spends "counting photons". Similar (or
> exactly the same thing) to exposure on a camera, you control the mantissa at
> the upper end of the range by reducing the amount of time the capacitors
> have to store the charge, the electrons being released by photons. If you
> need to resolve at the lower end, you can increase the exposure time to
> capture more events.
>
> To the point of "physics intensive"- you waste more time dealing with people
> who "cant do math" than just doing the math. What we need to do is start
> breaking apart the jargon. It annoys me when people talk about 16 bit ADC on
> a 8 bit camera. There's no such thing as an 8 bit camera- there's just
> capacitors storing charge off a diode, analog doesnt have bits, thats why it
> is analog. If you're hooking the ADC up right, its the physics of the
> underlying chip, the diode and capacitor, that really matters: the choice of
> wavelength (green is usually better), the tolerance and noise and things
> like "dark current" that dictate how well a 8-, 10-, 24-, 1000- bit chip are
> going to read that charge.
>
> 256 px doesn't seem like a lot, but it's all about controlling not just
> things like slit width, but also integration time and averaging, as well as
> all of the components of Beers law. A cheap ADC (Arduino supplies 10 bit)
> can cover way more range if you have control over exposure time, and attempt
> to adjust or autorange as best as possible. It would seem that for DIY qPCR,
> sinking all of your money into pricey detectors is wasted if your optics are
> crappy, and that sample averaging and exposure control can squeeze whatever
> resolution you need provided that you have decent control over the optics of
> the system.
>
> I think part of the problem I'm having engaging the DIY community is that
> there's a willingness to salvage parts but not as much attempt to document
> and share what people learn along the way. Taking apart $$$k equipment is
> fun and all, but it seems like we're losing the basic skills that were state
> of the art 20 years ago, like the power of what you can do with a single,
> crappy cheap ass photodiode or photomultiplier. Yes, "its been done", and
> it's not what the cool kids at Illumina or BioRad are doing, but often
> simple can force you to think of new ways of looking at the problem. There's
> no reason why these kind of experiments aren't open sourced and repeated to
> death so that everyone, no matter what their experience level, can begin to
> communicate and share with others.
>
> lets teach the physics, the math, the basic science, and not just gloss over
> it. do, don't debate. Grab an arduino and a photodiode and capacitor and do
> the experiment. mess around!
>
> -matt
>
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