Fluorescence Microscope on a Hacker’s Budget

Some of biology’s most visually striking images come from fluorescence microscopes. Their brilliant colors on black look like a neon sign from an empty highway. A brand new fluorescence microscope is beyond a hacker’s budget and even beyond some labs’, but there are ways to upgrade an entry-level scope for the cost of a few cups of coffee. [Justin Atkin] of The Thought Emporium published a scope hacking video which can also be seen below. He is becoming a reputed scope modder.

This video assumes a couple of things for the $10 price tag. The first premise is that you already have a scope, a camera adapter, and a camera capable of shooting long exposures. The second premise is that you are willing to break the seals and open the scope to make some reversible mods. Since you are reading Hackaday, maybe that is a given.

The premise is simple compared to the build, which is not rocket surgery, the light source from below illuminates the subject like a raver, and the filter removes any light that isn’t spectacular before it gets to the camera.

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Open Source Biological Gear For the Masses

At the risk of putting too fine a point on it, Hackaday exists because people are out there building and documenting open source gadgets. If the person who built a particular gizmo is willing to show the world how they did it, consider us interested. Since you’re reading this, we’ll assume you are as well. Over the years, this mentality has been spreading out from the relatively niche hacker community into the greater engineering world, and we couldn’t be happier.

Case in point, the Poseidon project created at the California Institute of Technology. Developed by students [Sina Booeshaghi], [Eduardo Beltrame], and [Dylan Bannon], along with researcher [Jase Gehring] and professor [Lior Pachter], Poseidon consists of an open source digital microscope and syringe pump which can be used for microfluidics experiments. The system is not only much cheaper than commercial offerings, but is free from the draconian modification and usage restrictions that such hardware often comes with.

Of course, one could argue that major labs have sufficient funding to purchase this kind of gear without having to take the DIY route. That’s true enough, but what benefit is there to limiting such equipment to only the established institutions? As in any other field, making the tools available to a wider array of individuals (from professionals to hobbyists alike) can only serve to accelerate progress and move the state of the art forward.

The Poseidon microscope consists of a Raspberry Pi, touch screen module, and commercially available digital microscope housed in a 3D printed stage. This device offers a large and clear view of the object under the microscope, and by itself makes an excellent educational tool. But when running the provided Python software, it doubles as a controller for the syringe pumps which make up the other half of the Poseidon system.

Almost entirely 3D printed, the pumps use commonly available components such as NEMA 17 stepper motors, linear bearings, and threaded rods to move the plunger on a syringe held in the integrated clamp. Controlled by an Arduino and CNC shield, these pumps are able to deliver extremely precise amounts of liquid which is critical for operations such as Single-cell RNA sequencing. All told a three pump system can be built for less than $400 USD, compared to the tens of thousands one might pay for commercially available alternatives.

The Poseidon project joins a relatively small, but very exciting, list of DIY biology projects that we’ve seen over the years. From the impressive open source CO2 incubator we saw a few years ago to the quick and dirty device for performing polymerase chain reaction experiments, there’s little doubt about it: biohacking is slowly becoming a reality.

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3D Printed Microscope Stage Offers Precise Movement

3D printing isn’t something you would usually associate with a high precision device, but this one shows that it can be used to create rather intricate things when needed. The Openflexure is a microscope stage that offers a mechanical stage that can be maneuvered precisely. The optics can be swapped out so it uses anything from a webcam to a very high-powered 100x magnification lens, but still move the stage smoothly and precisely. It can be driven by turning a knob or by three small motors. The plan is that the motors will eventually be driven by the software that is being written for the device.

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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.

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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.

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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.