Deep Discounts Yield Deep Reverse Engineering of Biotech Hardware

Hitting the electronic surplus shop is probably old hat to most of our readership. Somewhere, everyone’s got that little festering pile of hardware they’re definitely going to use some day. An old fax is one thing, but how would your partner feel if you took home an entire pallet-sized gene sequencing rig? Our friend [kaspar] sent along an interesting note that the folks at Swiss hackerspace Hackteria got their hands on an Illumina HiSeq 2000 last year (see funny “look what we got!” photo at top) and have generated a huge amount of open documentation about whats inside and how to use it.

Okay first off, what the heck is this machine anyway? The HiSeq is designed to automatically perform the sequencing step of Illumina’s proprietary multi step gene sequencing process (see manufacturer’s glossy for more), and to do so with minimal human intervention. That means that the unit contains a microfluidics system to manipulate samples, an extremely high performance optical scan system complete with controllable stage, imager, fluorescence modes, etc, and lots of other things this author isn’t sufficiently trained to guess at.

The folks at Hackteria have done a pretty thorough teardown of the system and produced block diagrams of most of its modules. They’ve also run some of the tools and recorded logs of what they were up to, including the serial commands sent to and from the machine to control certain subsystems. Of course a tool like this was meant to be driven by Illumina’s specific software, but unusually those are available and surprisingly usable which is how the aforementioned logs were captured. Right now it looks like Hackteria has put together tools to use the system as a fluorescent microscope.

Oddly the most interesting thing here might be how available these systems are. It appears that they’re being replaced en masse and have become easily available in the range of thousands of dollars on the secondary market. At that price point they’re almost worth snapping up for the enclosure and parts! But we prefer Hackteria’s goal of enabling the Citizen Scientist to make use of these incredible machines for their intended purpose. Who knows what exciting projects we’ll find when hackers start sequencing their cats!

Thanks for the tip [kaspar]!

See Cells In A New Light With A DIY Fluorescence Microscope

Ever since a Dutch businessman peered into the microscopic world through his brass and glass contraption in the 1600s, microscopy has had a long, rich history of DIY innovation. This DIY fluorescence microscope is another step along that DIY path that might just open up a powerful imaging technique to amateur scientists and biohackers.

In fluorescence microscopy, cells are treated with various fluorescent dyes that can be excited with light at one wavelength and emit light at another. But as [Jonathan Bumstead] points out, fluorescence microscopes are generally priced out of the range of biohackers. His homebrew scope levels the playing field a bit. The trick is to use 3D-printed parts to kit out commonly available digital cameras – a USB microscope, a DSLR, or even a smartphone camera. Excitation is provided by a ring of Nexopixel LEDs, while a movable rack holds a filter that blocks the excitation wavelength but allows the emission wavelength to pass through to the camera. He demonstrates the technique by staining some threads with fluorescent ink from a highlighter marker and placing them on a sheet of tissue paper; in conventional bright-field mode, the threads all but disappear into the background, but jump right out under fluorescence.

Ith’s true that the optics are not exactly lab quality, and the microscope is currently only set up to do reflectance imaging as opposed to the more typical transmissive mode where the light passes through the sample. That’s an easy fix, though, and reflectance mode is still useful. We’ve seen fluorescence microscopy get quite complex before, but this simple scope might be enough to get a biohacker started.

Continue reading “See Cells In A New Light With A DIY Fluorescence Microscope”

Arduino Provides Hands-Free Focus for Digital Inspection Scope

With surface-mount technology pushing the size of components ever smaller, even the most eagle-eyed among us needs some kind of optical assistance to do PCB work. Lots of microscopes have digital cameras too, which can be a big help – unless the camera fights you.

Faced with a camera whose idea of autofocus targets on didn’t quite coincide with his, [Scott M. Baker] took matters into his own hands – foot, actually – by replacing mouse inputs to the camera with an outboard controller. His particular camera’s autofocus can be turned off, but only via mouse clicks on the camera’s GUI. That’s disruptive while soldering, so [Scott] used an Arduino Pro Micro and a small keypad to mimic the mouse movements needed to control the camera.

At the press of a key, the Arduino forces the mouse cursor up to the top left corner of the screen, pulls down the camera menu, and steps down the proper distance to toggle autofocus. The controller can also run the manual focus in and out or to take a screenshot. There’s even a footswitch that forces the camera to refocus if the field of view changes. It looks really handy, and as usual [Scott] provides a great walkthrough in the video below.

Like it or not, if shrinking technology doesn’t force you into the microscope market, entropy will. If you’re looking for a buyer’s guide to microscopes, you could do worse than [Shahriar]’s roundup of digital USB scopes. Or perhaps you’d prefer to dumpster dive for yours.

Continue reading “Arduino Provides Hands-Free Focus for Digital Inspection Scope”

Replace your Calipers with a Microscope and Image Analysis

Getting a good measurement is a matter of using the right tool for the job. A tape measure and a caliper are both useful tools, but they’re hardly interchangeable for every task. Some jobs call for a hands-off, indirect way to measure small distances, which is where this image analysis measuring technique can come in handy.

Although it appears [Saulius Lukse] purpose-built this rig, which consists of a microscopic lens on a digital camera mounted to the Z-axis of a small CNC machine, we suspect that anything capable of accurately and smoothly transitioning a camera vertically could be used. The idea is simple: the height of the camera over the object to be measured is increased in fine increments, with an image acquired in OpenCV at each stop. A Laplace transformation is performed to assess the sharpness of each image, which when plotted against the frame number shows peaks where the image is most in focus. If you know the distance the lens traveled between peaks, you can estimate the height of the object. [Salius] measured a coin using this technique and it was spot on compared to a caliper. We could see this method being useful for getting an accurate vertical profile of a more complex object.

From home-brew lidar to detecting lightning in video, [Saulius] has an interesting skill set at the intersection of optics and electronics. We’re looking forward to what he comes up with next.

Wireless Ring Light For SMD Microscope

When [Felix Rusu], maker of the popular Moteino boards which started life as wireless Arduino compatibles, says he’s made a wireless ring light for his SMD microscope, we redirect our keystrokes to have a look. Of course, it’s a bit of wordplay on his part. What he’s done is made a new ring light which uses a battery instead of having annoying wires go to a wall wart. That’s important for someone who spends so much time hunched over the microscope. Oh, and he’s built the ring light on a rather nice looking SMD board.

The board offers a few power configurations. Normally he powers it from a 1650 mAh LiPo battery attached to the rear of his microscope. The battery can be charged using USB or through a DC jack for which there’s a place on the board, though he hasn’t soldered one on yet. In a pinch, he can instead power the light from the USB or the DC jack, but so far he’s getting over 6 hours on a single charge, good enough for an SMD session.

The video below shows his SMD board manufacturing process, from drawing up the board in Eagle, laser cutting holes for a stencil, pasting, populating the board, and doing the reflow, along with all sorts of tips along the way. Check it out, it makes for enjoyable viewing.

Here’s another microscope ring light with selectable lighting patterns for getting rid of those pesky shadows. What features would make your SMD sessions go a little easier?

Continue reading “Wireless Ring Light For SMD Microscope”

Motorized Stage Finesses the Microscopic World

No matter how fine your fine motor skills may be, it’s really hard to manipulate anything on the stage of a microscope with any kind of accuracy. One jitter or caffeine-induced tremor means the feature of interest on the sample you’re looking at shoots off out of the field of view, and getting back to where you were is a tedious matter of trial and error.

Mechanical help on the microscope stage is nice, and electromechanical help is even better, but a DIY fully motorized microscope stage with complete motion control is the way to go for the serious microscopist on a budget. Granted, not too many people are in [fabiorinaldus]’ position of having a swell microscope like the Olympus IX50, and those that do probably work for an outfit that can afford all the bells and whistles. But this home-brew stage ticks off all the boxes on design and execution. The slide is moved across the stage in two dimensions with small NEMA-8 steppers and microstepping controllers connected to two linear drives that are almost completely 3D-printed. The final resolution on the drives is an insane 0.000027344 mm. An Arduino lives in the custom-built control box and a control pad with joystick, buttons, and an OLED display allow the stage to return to set positions of interest. It’s really quite a build.

We’ve featured a lot of microscope hacks before, most of them concerning the reflective inspection scopes we all seem to covet for SMD work. But that doesn’t mean we haven’t shown love for optical scopes before, and electron microscopes have popped up a time or two as well.

Continue reading “Motorized Stage Finesses the Microscopic World”

Dark Field Microscopy on the Cheap with a PCB

It might seem like a paradox that you want a dark field to see things with an expensive microscope. As [IMSAI Guy] explains, a dark field microscope doesn’t make the subject dark. It makes the area surrounding the subject dark. After selling his expensive microscope, he found he missed having the capability, so he decided to make one cheaply. You can see how he did it in the video, below.

Dark field microscopy gives better contrast and resolution by discarding light that shines directly through or reflects directly from a sample. The only light you see is any that scatters. If you think about a normal microscope, you can imagine a cone of light coming from the top or the bottom. The tip of the cone hits the sample and then spreads back out into another cone of light. What hits your eye –well, actually, the eyepiece — is all the light from that cone. In a dark field instrument, the illumination cone is hollow — the light is just a ring. That means any light the sample doesn’t scatter gets blocked by a stop in the objective. When there is no sample, there’s no unblocked light, so you see a “dark field.”

Light that either refracts through the sample (from below) or bounces off a feature (from the top) will wind up in the hollow area that passes through the objective and you’ll see the image. It may surprise you that you may already have a piece of dark field technology on your desk. Optical computer mice that can work on glass surfaces use this same technique. If you want to see some examples and a diagram of how it all works, we did a post on a similar lower tech mod. There’s also Wikipedia.

The secret to doing this cheaply was to get a used dark field objective with a little rust on the barrel and then modify them with a custom PC board to create an LED ring light. This is different from the usual illuminator which shines a light through a patch stop to block the inner light. In this case, the light is made into a ring shape by virtue of the arrangement of the LEDs.

Continue reading “Dark Field Microscopy on the Cheap with a PCB”