Opgen Argus DNA Optical mapping system part 2

Shaking the fiber is all about bending it sligtly in random directions so that the light gets distributed randomly in the different fiber modes, and utimately the speckle that results from the interference of the light that traveled through the different modes changes so fast that it appears blurred on a "slow" detector

I recently had a chance to pull apart a $0.5 M AUD genetics instrument in a 2 cubic meter size enclosure. Aside from the incredible build quality and over-engineering, the most incredible thing is how quickly these kind of equipment go out of relevance. The unit was only 5 years old an no longer supported (critical consumables no longer manufactured) and practically obsolete in terms of performance.

Hi Mike! 3:40 The technical term for these is 'flexures'. They are designed in such a way to only couple through the degrees of freedom intended, and release other mechanical degrees of freedom. Currently I am working/doing research in a group specialized in flexural mechanisms. Most important in flexure design, is figuring out what constraints you want. This particular configuration is quite common, and only allows for a single degree of freedom, namely translation 'out of plane' (towards/away from the camera). It is stiff in all other degrees of freedom. They do this to minimize over-constraints in the system. You are right that indeed it is meant to resolve the alignment problem between screw and sled. Personally I am a bit confused why they only care about releasing that 'out of plane' translation alignment axis, but not for example the vertical translational alignment. Ideally you would only want to couple the translation along the screw axis to the slide, and a flexure that would do just that isn't that much more complicated. Seeing the non conventional construction of that flexure, I am doubting whether it was designed by someone that is very familiar with flexures, but I digress. Flexures are very common in high precision mechanisms (think wafer stepper machines like ASML, spacecraft etc). They have a couple of advantages over 'traditional' mechanisms with bearings: - No relative movement between parts, and thus no friction. Friction (combined with limited stiffness) causes a phenomena called 'virtual play' which limits machine precision, thus eliminating this is very important. - No lubrication required (very important for space applications, where bearing grease can cause major headaches with vacuum and temperature fluctuations) - Can be relatively cheap (depending on the materials used). - More flexible in the allowable degrees of freedom (bigger design space). Although this can be mitigated with more complicated designs. If you would like, I have some good recommendations to learn more about them. In particular I would recommend 'Exact constraint: Machine design using kinematic principles' by Blanding. It is not flexure specific, but more on the topic of constraint design, but it has transformed the way I am looking at mechanisms in general (and is quite a fun and light read!). 11:55 I doubt that they would add weight for damping. I would expect that the weight would only shift a mechanical resonance to a lower frequency. Perhaps without the weight it has a resonance peak at the same frequency as another part of the system, thus amplifying each other? Still in such a case, such a massive weight is quite overkill. Generally adding damping to precision mechanisms is avoided, as doing damping without friction is quite hard/expensive (you want viscous damping without friction, most viscous dampers have internal friction).

That unbalanced motor fiber jiggler thing just blew my mind. I've never seen that implementation for despeckling done before! It's such an elegant and parsimonious solution! The lengths we have to go to in order to suppress speckle on inertial confinement fusion targets is insane: distributed phase plates, smoothing by spectral dispersion, distributed polarization rotators... all to the tune of many tens of millions of dollars. Of course, we also have to do it on picosecond timescales, so there's that little caveat too.

Fiber is multimode, so by shaking it - you mix modes by physically bending the fiber. So it's nothing fancy. You can test it yourself - project fiber to a wall, bend the fiber - and observe that speckle pattern change as you bend it.

I think the principle of operation of the fiber shaker is just to continuously shuffle the internal incidences of reflection to avoid hot spots. I think it's mostly just a geometry problem rather than relativistic problem.

This expensive piece of kit is used to map the dna. It relaxes the whole dna molecule that is fluorescent dye tagged, loads it into a microfluidics chamber stretching it further, and finally cuts the dna in pieces. Dunno if the samples deteriorated, but 18:21 is what it should look like, a unique visible map of the whole dna stretched, cut at various specific positions, with each piece length specific to a cell type, organism, specie.

Might be just me but the birds improved the already fascinating video.

Had to pause the video early on once I started hearing the Parakeets, I thought the fan was playing up on my air frier 😂

Jboss.. of course. Gotta get that oldschool java monolith energy.

The shaker on the optical cable operates in much the same way as a galvanometer in that it changes the angle of reflection in the optical cable thereby effectively blurring the speckle effect.

Where do you keep getting these unusual teardown items? Is the UK eBay that much better than here in Germany? I might need to relocate. 😅

I used to work on imagesetters which require very precise beam positioning; the moving mirror carriage assembly had lead weights stuck to it to move the resonant frequency much lower than the excitation frequency from the mirror motor and fans.

You get that speckle reduction in laser cinema projectors (with vastly higher powered lasers). It works by changing the path lengths by altering the number of bounces it takes to get around the coils.

That is a mode scrambler. Used for making it a pure color of light like a very bright led. These units generally have a 488nm and 635nm laser as well as the 532nm laser. If this one only had a 532nm in it, it was uses for an extremely specific kind of test. That photometrics camera is what was inside a Coherent laser beam mode analyzer with a heavy duty attenuator, they cost a fortune back then. 562nm is the emission peak of florescent green 🪼 protein. 😂

I'm guessing that the custom stepper motor driver was an attempt at implementing something like the new sine wave "silent" TMC drivers which are now commonplace, perhaps. The relays on the output feel like some form of a solution added to ease compliance with some form of certification, since perhaps then they wouldn't have to certify all of the complex electronics as "functionally safe" or something. Definitely feels like there was no shortage of "not invented here" syndrome in this machine, which appears to be common in lab equipment

Yeah that display is perfect perfect. The shaker device would change bounce angles for the light, shifting interference pasterns continously, enabling averaging of interference patterns at high resolution.

8:00 No, there are many conditions that must be followed with medtech equipment and one of them is that if fex a lid is opened so you can access moving parts the moving parts must be stopped immediately, so there is a reason those relays are there.

Despeckling fiber jiggler. Only on uncle Mike's youtube corner.

You should sell the objective with the corresponding tube lens. Even more useful would be the whole assembly with laser, dichroics and possibly camera. I was once in a microscopy course in plymouth. A good way to test a fluorescent microscope with a 60x immersion objective is to place pollen (from flowers) below. You'll need slides, coverslips (0.17mm thickness), immersion oil, embedding medium (you could use the oil as well) and nail polish to seal the coverslip on the microscope slides.