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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Plant Biology is a Gateway

Too many college students have been subject to teachers’ aids who think they are too clever to be stuck teaching mere underclassmen. For that reason, [The Thought Emporium] is important because he approaches learning with gusto and is always ready to learn something new himself and teach anyone who wants to learn. When he released a video about staining and observing plant samples, he avoided the biggest pitfalls often seen in college or high school labs. Instead of calling out the steps by rote, he walks us through them with useful camera angles and close-ups. Rather than just pointing at a bottle and saying, “the blue one,” he tells us what is inside and why it is essential. Instead of telling us precisely what we need to see to get a passing grade, he lets our minds wonder about what we might see and shows us examples that make the experiment seem exciting. The video can also be seen below the break.

The process of staining can be found in a biology textbook, and some people learn best by reading, but we haven’t read a manual that makes a rudimentary lab seem like the wardrobe to Narnia, so he gets credit for that. Admittedly, you have to handle a wicked sharp razor, and the chance of failure is never zero. In fact, he will tell you, the opportunities to fail are everywhere. The road to science isn’t freshly paved, it needs pavers.

If a biology lab isn’t in your personal budget, a hackerspace may have one or need one. If you are wondering where you’ve heard [The Thought Emporium]’s voice before, it is because he is fighting lactose intolerance like a hacker.

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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.

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Impossibly Huge Depth of Focus in Microscope Photographs

Sometimes, less is more. Sometimes, more is more. There is a type of person who believes that if enough photos of the same subject are taken, one of them will shine above the rest as a gleaming example of what is possible with a phone camera and a steady hand. Other people know how to frame a picture before hitting the shutter button. In some cases, the best method may be snapping a handful of photos to get one good one, not by chance, but by design.

[The Thought Emporium]’s video, also below the break, is about getting crisp pictures from a DSLR camera and a microscope using focus stacking, sometimes called image stacking. The premise is to take a series of photos that each have a different part of the subject in focus. In a microscope, this range will be microscopic but in a park, that could be several meters. When the images are combined, he uses Adobe products, the areas in focus are saved while the out-of-focus areas are discarded and the result is a single photo with an impossible depth of focus. We can’t help but remember those light-field cameras which didn’t rely on moving lenses to focus but took many photos, each at a different focal range.

[The Thought Emporium] has shown us his photography passion before, as well as his affinity for taking the cells out of plants and unusual cuts from the butcher and even taking a noble stab at beating lactose intolerance.

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Laser Sequencer uses Arduino to Enable Super-Microscope!

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[Philip]’s Laser control Arduino shield.

[Philip Nicovich] has been building laser sequencers over at the University of New South Wales. His platform is used to sequence laser excitation on his fluorescence microscopy systems. In [Philip]’s case, these systems are used for super-resolution microscopy, that is breaking the diffraction limit allowing the imaging of structures of only a few nanometers (1 millionth of a millimeter) in size.

Using an Arduino shield he designed in Eagle, [Philip] was able to build the system for less than half the cost of a commercial platform.

The control system is build around the simple Arduino shield shown to the right, which uses simple 74 series logic to send TTL control signals to the laser diodes used in his rig. The Arduino runs code which allows laser firing sequences to be programmed and executed.

[Philip] also provides scripts which show how the Arduino can be interfaced with the open source micro manager control software.

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As well as the schematics [Philip] has provided STEP files and drawings for the enclosure and mounts used in the system and a detailed BOM.

More useful than all this perhaps is the comprehensive write-up he provides. This describes the motivation for decisions such as the use of aluminum over steel due to its ability to transfer heat more effectively, and not to use thermal paste due to out-gassing.

While I can almost hear the cries of “not a hack”, the growing use of open source platforms and tool in academia fills us with joy. Thanks for the write-up [Philip] we look forward to hearing more about your laser systems in the future!

Hackaday Prize Entry: A Cheap Robotic Microscope

The microscope is one of the most useful instruments for the biological sciences, but they are expensive. Lucky for us, a factory in China can turn out webcams and plastic lenses and sell them for pennies. That’s the idea behind Flypi – a cheap microscope for scientific experiments and diagnostics that’s based on the ever-popular Raspberry Pi.

Flypi is designed to be a simple scientific tool and educational device. With that comes the challenges of being very cheap and very capable. It’s based around a Raspberry Pi and the Pi camera, with the relevant software for taking snapshots, recording movies, and controlling a few different modules that extend the capabilities of this machine. These modules include a Peltier element to heat or cool the sample, a temperature sensor, RGB LED, LED ring, LED matrix, and a special blue LED for activating fluorescent molecules in a sample.

The brains behind the Flypi, [Andre Chagas], designed the Flypi to be cheap. He’s certainly managed that with a frame that is mostly 3D printed, and some surprisingly inexpensive electronics. Already the Flypi is doing real science, including tracking bugs wandering around a petri dish and fluorescence microscopy of a zebrafish’s heart. Not bad for a relatively simple tool, and a great entry for the Hackaday Prize.

3D Printed Microscope Chamber Saves Big Bucks

Optical microscopy is over 400 years old, and in that time, it has come a long way. There are many variations of microscopes both in the selection of lenses, lighting, and other tricks to allow an instrument to coax out more information about a sample.

One proven way to increase the resolving power of a microscope is oil immersion. The sample and the lens are placed in oil that is transparent and has a high refractive index. This prevents light from refracting at the air-coverslip interface, improving the microscope’s overall performance.

The University of New South Wales has a lab that uses such a microscope. They use a special (and expensive) chamber to hold down the glass coverslip and contain the oil. The problem? At nearly $400 a pop, the chambers are a constant expense to replace, and they are not flexible enough to handle custom size requirements.

[Ben Goodnow], a first year student at the university, applied his 3D printing and laser cutting know-how to design and build a suitable chamber that costs much less and can be adapted to different projects. In addition to all the design files on GitHub, there’s also a document (PDF) that describes the design iterations and the total cost savings.

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