Nanodrop Spectrophotometer Take Apart?

[Tito Jankowski]

Hi all,
I'm wondering what the insides of a Nanodrop spec looks like. The
patents cover the measurement area, which is the size of a fingernail.
I would like to know what else is in that box! Anyone care to help
out, maybe take the cover off a nanodrop and snag a few pictures?

Thanks!

Tito

[Michael Gross]

I might be able to help out. We just got a NanoDrop in a few months ago. Could you give me more details of what you are looking for?

> Date: Sun, 17 Jan 2010 10:45:05 -0800
> Subject: Nanodrop Spectrophotometer Take Apart?
> From: titoja...@gmail.com
> To: diy...@googlegroups.com

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[Tito Jankowski]

Hey Michael,

I want to understand how the device works and also entertain the idea
of a pocket spectrophotometer. I took apart an old 25 pound PCR
machine to learn how it functioned, and discovered it was just a few
components (heat sink, transformer, metal block), though each
component was very big.

I'm looking for video or pictures of the Nanodrop with the (blue)
cover removed, front, top, bottom, sides, and back. Labeling of major
components like power supply, mechanism for clamping the arm, logic
board, heat sink as well would be great. I'm not sure what you'll be
able to see at that point, but if you're comfortable disassembling it
further, more is better!

Thanks, Michael!

Tito

[Nathan McCorkle]

I might be able to take it apart, undercover... :) ninja style

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[Tito Jankowski]

Awesome -- keep me posted, Nathan :)

Tito

[Mackenzie Cowell]

I had a conversation about this with Tom Knight a while back and he
seemed to have an idea about where to buy the light source and sensor
used in a nanodrop wholesale. He would be a good person to ask. If I
see him I'll ask.

What happened to the El Cheapo 6-LED spec idea? Or Simon's digital
camera spectrophotometer hack?

Mac

On Mon, Jan 18, 2010 at 1:51 PM, Tito Jankowski <titoja...@gmail.com> wrote:
> Awesome -- keep me posted, Nathan :)
>
> Tito
>

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---- Mackenzie Cowell <m...@diybio.org> wrote:
> I had a conversation about this with Tom Knight a while back and he
> seemed to have an idea about where to buy the light source and sensor
> used in a nanodrop wholesale. He would be a good person to ask. If I
> see him I'll ask.
>
> What happened to the El Cheapo 6-LED spec idea? Or Simon's digital
> camera spectrophotometer hack?

Most of the use that I would have for an LED spec (because of the fixed frequency) is as the old style "colorimeter". As such it would be nice if the LED spec had socketed LED units that could be changed out so that different frequencies could be used (rather than the color filter approach of the colorimeter).

[Simon Quellen Field]

My spectrometer is being published in issue 22 of Make magazine, probably

out in March.

[Tito Jankowski]

Congrats, Simon!

Tito

[Cathal Garvey]

Can't wait to see that!

[Nathan McCorkle]

On Tue, Jan 19, 2010 at 8:32 PM, Mackenzie Cowell <m...@diybio.org> wrote:
> I had a conversation about this with Tom Knight a while back and he
> seemed to have an idea about where to buy the light source and sensor
> used in a nanodrop wholesale.  He would be a good person to ask.  If I
> see him I'll ask.
>
> What happened to the El Cheapo 6-LED spec idea?  Or Simon's digital
> camera spectrophotometer hack?

I think for the 6-LED spec, for a lot of us that just isn't wide
enough of a spectrum... using laser ablation making a grism (grated
prism) might be possible in PDMS, which coupled to a camera matrix or
linear photodiode array would be quite useful.

>
> Mac
>
> On Mon, Jan 18, 2010 at 1:51 PM, Tito Jankowski <titoja...@gmail.com> wrote:
>> Awesome -- keep me posted, Nathan :)
>>
>> Tito
>>
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[Mackenzie Cowell]

On your site (http://sci-toys.com/scitoys/scitoys/light/spectrograph/spectrograph.html),
you describe how your analysis tool works:

"The computer program looks at each column of pixels in the photo, and
adds them up to get a value for how much light of that color entered
the camera. It then plots this value for each column, forming the
graph."

Neat. So it's based on the assumption that the diffraction grating
tube and camera optics spread the diffraction pattern uniformly across
the camera's CCD? By my understanding, this would work even if the
camera was in grayscale mode, correct?

Mac

[Simon Quellen Field]

The software is more complex than you might think.

Since different lenses, focal lengths, aiming points, and subtle differences

in construction can change where the spectrum shows up in the focal

plane.  Plus, I can't guarantee the kid building it actually has a mercury

vapor spectrum to calibrate it.

To cover that last point, the software looks for peaks in two colors, red

and green.  It then uses these peaks to calculate the wavelengths, the

resolution, the tilt of the spectrum on the focal plane, and the F stop of

the lens.  Many cheap digital cameras can't turn off autofocus, and so

we can't know that the camera keeps the same focus from time to time,

and we can't tell if the camera is focusing on the red peak, the green peak,

or some artifact it sees in the image plane.

So, yes, grayscale would work, but the software uses the red and green

signals as part of the calibration.  If you are thinking that using grayscale

would provide some advantage, that is not the case.  The software combines

thousands of pixels in the vertical dimension to get excellent resolution in

the value domain (brightness), and so the presence of the RGB filters in the

camera itself is completely offset.

[Nathan McCorkle]

So I'm waiting to get the pics from my friend, but I took it apart
tonight! Who will correctly guess how stupid it is??? One screw on top
(1/8th inch allen) gets the cover to raise off, and underneath is OMG
how stupidly simple... c'mon, I want to hear some guesses as to what
is monitoring this unit (I won't be explicit, but look at the spec
sheet for it)

I'll try to get the pics tomorrow!

On Mon, Jan 18, 2010 at 1:51 PM, Tito Jankowski <titoja...@gmail.com> wrote:
> Awesome -- keep me posted, Nathan :)
>
> Tito
>

[Ben Gadoua]

    I just wanted to emphasize a point here, if you're using your nano-drop for protein and dna/rna concentrations, there are only 3 or 4 frequencies you need to be concerned with. 230nm, 260nm, 280nm, everything you do for purity and concentration is a ratio of those or an absorbence. You'll need to calibrate your machine with known samples, it's not very hard to do in the world of software. To make a nano drop you need a light source, what sounds like a servo, an arm, two well machined parts, some filtered phototransistors or three light sources, a adc, a pic, and some kimwipes (have you ever been in a lab without kimwipes?!). Everything else is just wanking for those three types of measurements.

Ben

[Tito Jankowski]

Judging by the spec sheet, here's my guess. There is a xenon lamp (I
think these are the size of your pinkie finger) and a CCD hooked up to
a optical cable (I imagine this would be no bigger than 2"x3"x1"),
plus a microcontroller for the raw data, a little motor for the jaw/
arm and a power supply for it all. My guess is this takes up most of
the casing. Lastly, there are patents on the sample retention system,
which really does rock.

Wonder why they used a xenon lamp?

http://www.nanodrop.com/Productnd2000specs.aspx

[Michael Gross]

Sorry I haven't been moving fast on this request, Tito. My ninja skills aren't quite up to snuff, but I can get it done if the need is still there.

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[Nathan McCorkle]

Ok, so I took apart the 1000ND, not the 2000... so there is no motor,
and for a hint on how they literally "hacked" this together, compare
the CCD specs between your link and this one:
http://www.oceanoptics.com/products/usb2000.asp

Isn't the Nanodrop USB out??? :P

Editing the pics now, will post soon!

On Sun, Jan 24, 2010 at 11:39 AM, Tito Jankowski
<titoja...@gmail.com> wrote:
> Judging by the spec sheet, here's my guess. There is a xenon lamp (I think
> these are the size of your pinkie finger) and a CCD hooked up to a optical
> cable (I imagine this would be no bigger than 2"x3"x1"), plus a

> microcontroller for the raw data, a little motor for the jaw/arm and a power

> supply for it all. My guess is this takes up most of the casing. Lastly,
> there are patents on the sample retention system, which really does rock.
>
> Wonder why they used a xenon lamp?
>
> http://www.nanodrop.com/Productnd2000specs.aspx
>

[Nathan McCorkle]

http://diybioforum.org/takeItApart/

Enjoy!

[Cathal Garvey]

Yea, judging by the sounds our nanodrop makes in the lab I believe the arm is moved by a small electromagnet against a spring, rather than a servo.

I reckon if you can find LEDs of the three wavelengths required, you could actually hack one of these together using just your LEDs and an arduino. LEDs can be used as sensors of their own wavelength and below, so with some basic subtractive math and careful tuning, you shouldn't need much more than that, right?

2010/1/24 Nathan McCorkle <nmz...@gmail.com>

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[Tito Jankowski]

Beautiful, Nathan. Thanks for following through on this and getting
the pictures!

I'm excited to wonder what the development process was like for
nanodrop. I imagine they came up with an elegant solution for working
with a sample, and were able to use pre-built components (the ocean
spec and perkin elmer xenon lamp) to make it a reality. Remember,
making a useful innovation like the Nanodrop can be as simple as using
existing technologies in a new way.

Cathal, maybe LEDs can serve to fill a gap for "simpler" devices?
Anyone know if there are less powerful specs available, or a simple
cell culture spectrophotometer are available independently for those
of us who have specific applications, and don't need for a massively
powerful spec.

Tito

[Mackenzie Cowell]

Nathan: BRAVO!

So, a < $100 spec might consist of:

* two-layer stage/arms that brings together optical fibers into a gap in which most liquids will hang via surface tension

* light source: xenon lamp unit or several LEDs

* arduino, or a more powerful clone

* filtered photodiodes or a CCD 

* optical fiber couplers for light source and the detector

* a chassis for the stage and other components

Really cool.

So what could we try building first that would be doable in an afternoon and demonstrate the viability of one of the above modules?

Mac

Tito

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[Nathan McCorkle]

Yeah I forgot to get a good photo of the magnet device, but that is
what pulls the ND1000 arm down...

[Mackenzie Cowell]

Probably just a cheap solenoid, right?

Man, I can't believe that commodity spectrophotometer is $2639 (maybe nanodrop gets a deal?).  Nathan included a link to it.  From the description, it sounds like it uses basically the same principle Simon uses with his DIY-spectrograph setup: A linear CCD in which different frequencies correspond to different columns of pixels.  So it gives me hope we could build a similar spec with the guts of an off-the-shelf digital camera.

Their description: http://www.oceanoptics.com/products/usb2000.asp

"The USB2000 couples a low-cost, high-performance 2048-element linear CCD-array detector with an optical bench that's small enough to fit into the palm of your hand -- the same detector and optical bench that have provided superior performance to the users of our 15,000 systems out in the field. The USB2000 also works the same way as other Ocean Optics spectrometers in that it accepts light energy transmitted through single-strand optical fiber and disperses it via a fixed grating across the linear CCD array detector, which is responsive from 200-1100 nm."

Mac

[Nathan McCorkle]

It would probably be better to use an actual linear array, coupled
with a grating or prism. Add a peltier below the sensor for cooling
and you'd have a fine piece of equipment... mind the optics, good
optics especially for UV (even the upper range) can be expensive. And
then you have to focus everything...

I'm down to lend my mind to such a cause

[Nathan McCorkle]

Here's an updated link to the pics! (please feel free to browse the
site otherwise and give me feedback on it, my friends and I just
launched it)
https://www.takeitapart.com/guide/66


(p.s. in case anyone wants to author a disassembly guide, use this
sign-up code to get in (good for 50 users:
carefully-press-its-right-panel-QJCND-diybio)

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