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.

Hackaday Prize Entry: An Internet Of Things Microscope

For their entry into the Citizen Scientist portion of the Hackaday Prize, the folks at Arch Reactor, the St. Louis hackerspace, are building a microscope. Not just any microscope – this one is low-cost, digital, and has a surprisingly high magnification and pretty good optics. It’s the Internet of Things Microscope, and like all good apparatus for Citizen Scientist, it’s a remarkable tool for classrooms and developing countries.

When you think of ‘classroom microscope’, you’re probably thinking about a pile of old optics sitting in the back of a storage closet. These microscopes are purely optical, without the ability to take digital pictures. The glass is good, but you’re not going to get a scanning stage when you’re dealing with 30-year-old gear made for a classroom full of sticky-handed eighth graders.

The Internet of Things Microscope includes a scanning stage that moves across the specimen on the X and Y axes, stitching digital images together to create a very large image. That’s a killer feature for a cheap digital microscope, and the folks at Arch Reactor are doing this with a few cheap stepper motors and stepper motor drivers.

The rest of the electronics are built around a Raspberry Pi, Raspberry Pi camera (which recently got a nice resolution upgrade), and a some microscope eyepieces and objectives. Everything else is 3D printed, making this a very cheap and very accessible microscope that has some killer features.

Automating A Microscope For CNC Micrographs

[Maurice] is a photographer specializing in micrographs. These very large images of very small things are beautiful, but late last year he’s been limited by his equipment. He needed a new microscope, one designed for photography, that had a scanning stage, and ideally one that was cheap. He ended up choosing a microscope from the 80s. Did it meet all his qualifications? No, but it was good enough, and like all good tools, capable of being modified to make a better tool.

This was a Nikon microscope, and [Maurice] shoots a Canon. This, of course, meant the camera mount was incompatible with a Canon 5D MK III, but with a little bit of milling and drilling, this problem could be overcome.

That left [Maurice] with a rather large project on his hands. He had a microscope that met all his qualifications save for one: he wanted a scanning stage, or a bunch of motors and a camera controller that could scan over a specimen and shoot gigapixel images. This was easily accomplished with a few 3D printed parts, stepper motors, and a Makeblock Orion, an Arduino-based board designed for robotics that also has two stepper motor drivers.

With a microscope that could automatically scan over a specimen and snap a picture, the only thing left to build was a piece of software that automated the entire process. This software was built with Processing. While this sketch is very minimal, it does allow [Maurice] to set the step size and how many pictures to take in the X and Y axis. The result is easy automated micrographs. You can see a video of the process below.

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Hackaday Prize Entry: Microscopy With Blu-ray

Confocal microscopy is an imaging technique that provides higher resolution micrographs than that of traditional optical microscopy. Confocal microscopes attain this higher resolution from an image sensor behind a pinhole. By eliminating out of focus light, and by scanning the specimen back and forth under the microscope, a very high resolution image may be produced. This technique has applications ranging from life sciences to semiconductor work. For this year’s Hackaday Prize, [andreas.betz] is building a confocal microscope using little more than a Blu-ray drive read head.

[andreas]’ build uses a standard Playstation 3 Blu-ray drive mechanism. The read head for this mechanism is well documented, but [andreas] still has to drive the laser and the voice coils for this machine to do anything. With the Blu-ray drive working, only the optics remained.

Just this last week, [andreas] imaged the die of a transistor with a resolution of about 680nm. An inductor was also imaged, showing a track separation of about 10um. This is approaching the limits of optical microscopy, and the apparatus is simple enough for anyone to replicate.

As a feat of technical ingenuity, this is a great project. It’s one of the best we’ve seen for the Citizen Science portion of the Hackaday Prize, and can’t wait to see what other images [andreas] can make with this machine.

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Hacklet 111 – Advanced Microscopy Projects

Last week on the Hacklet we covered optical microscopy projects. Those are the familiar scopes that many of us have at work or even at home on our benches. These are scopes that you typically can use with your eye, or an unmodified camera. This week we’re taking a look at more extreme ways of making small things look big. Electron streams and the forces of a single atom can be used to create incredibly magnified images. So let’s jump right in and check out the best advanced microscopy projects on Hackaday.io!

blubeamWe start with [andreas.betz] and BluBEAM – a scanning laser microscope. [Andreas] aims to create a scanning confocal microscope. The diffraction limit is the law of the land for standard optical microscopes. While you can’t break the law, you can find ways around it. Confocal microscopy is one technique used quite a bit in medicine and industry. Confocal scopes are generally very expensive, well outside the budget of the average hacker. [Andreas] hopes to break that barrier by creating a scanning confocal microscope using parts from a Playstation 3 BluRay optical drive. Optical drives use voice coils to maintain focus. [Andreas] had to create a custom PCB with a voice coil driver to operate the PS3 optics assembly. He also needed to drive the laser. BluBeam is still very much a work in progress, so keep an eye on it!

stmNext up is [MatthiasR.] with DIY Scanning tunneling microscope. Open atmosphere scanning tunneling microscopes are popular on Hackaday.io. I covered [Dan Berard’s] creation in Hacklet 103. Inspired by Dan, [Matthias] is building his own STM.

Environmental vibration is a huge problem with high magnification microscopes. [Matthias] is combating this by building a vibration isolation platform using extruded aluminum. He’s currently working on the STM preamplifier, which amplifies and converts the nano amp STM values to voltages which can be read by a digital to analog converter. [Matthias] is using the venerable Analog ADA4530 for this task. With an input bias of 20 femtoamps (!) it should be up to the task.

desemNext we have [Jerry Biehler] with Hitachi S-450 Scanning Electron Microscope. Scanning electron microscopes have to be the top of the microscopy food chain. Jerry got his hands on a 1980’s vintage Hitachi SEM which was no longer working. The problem turned out to be a dodgy repair made years earlier with electrical tape. Fast forward a couple of years of use, and [Jerry] has done quite a lot to his old machine. He’s learned how to make his own filaments from tungsten wire. The slow oil diffusion vacuum pump has been replaced with a turbomolecular pump. The SEM now resides in [Jerry’s] living room, which keeps it at a relatively constant temperature.

Bild1Finally, we have [beniroquai] with Holoscope – Superresolution Holographic Microscope. Holoscope is a device which increases the resolution of a standard camera by using the physical properties of light to its advantage. Precise tiny shifts of the object being magnified cause minute changes in a reflected image, which is captured by a Raspberry Pi camera. The Pi can then reconstruct a higher resolution image using the phase data. [Beniroquai] has put a lot of time into this project, even sacrificing an expensive Sony connected camera to the ESD gods. I’m following along with this one. I can’t wait to see [beniroquai’s] first few images.

If you want to see more advanced microscopy projects, check out our new advanced microscope projects list! If I missed your project, don’t be shy, just drop me a message on Hackaday.io. That’s it for this week’s Hacklet. As always, see you next week. Same hack time, same hack channel, bringing you the best of Hackaday.io!

Hackaday Prize Entry: Automatic Digital Microscope

Ziehl-Neelsen Sputum Smear Microscopy (ZN) is one of most common methods for diagnosing Tuberculosis. On the equipment side, it requires not much more than an optical microscope, although it still needs a trained professional to look through the glass, identify and count the number of bacteria in a sample. To provide reliable and effective Tuberculosis diagnostic to regions, where both equipment and trained personnel is in short supply, [Rodrigo Loza] and [khalilnallar] are developing an automated digital microscope based on computer vision and machine learning, their entry for the Hackaday Prize.

automated_microscope_detection_1They started out gathering images of Tuberculosis bacteria from the internet and experimented with color threshold algorithms to detect dyed bacteria, as well as algorithms for counting individual and clusters of bacteria. This process alone can, according to the team, take a trained professional 30 minutes or more. A graphical interface highlights identified bacteria and reads the bacteria count.

[Rodrigo Loza] and [khalilnallar] are testing their device at the Dr. Roberto Galindo Teran hospital in Cobija, Bolivia. However, getting access to a lab environment is one thing, and being given access to a steady supply of fresh M. Tuberculosis samples is another. Unable to obtain samples, which they need to test their algorithms on live subjects, they turned to another front of their project: The hardware. In several iterations, they developed a low-cost, 3D-printable kit, which transforms a laboratory-grade optical microscope into an embedded CNC-controlled microscopy platform. Their kit comprises three stepper-motor-based axis for the X, Y and Z direction, as well as a webcam mount. An Intel Edison and a custom, Arduino compatible shield control the system to achieve features such as homing procedures, autofocus and bacteria detection.

The team is currently in the process of refining their bacteria detection pipeline, exploring the feasibility of semi-automated detection methods, machine learning and neural networks for classification of bacteria within the hardware constraints. The video below shows their latest update on the Z-axis of their microscope.

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Hacklet 110 – Optical Microscopy Projects

Humans have always wanted to make small things bigger. To see that which is unseen with the naked eye. The inventor of the original microscope happened sometime in the 1600’s, though the inventor is still contested. Some say it was Cornelis Drebbel, while others say Hans Lippershey. Galileo Galilei’s compound microscope is probably the most well-known ancient magnifier. Regardless of who created the device, hackers, makers, engineers, and scientists have used microscopes to study mysteries of biology, geology, electronics, and just about anything else you can imagine.

This is a fitting topic for this week’s Hacklet at is aligns well with the Citizen Scientist challenge round of the Hackaday Prize which began on Monday. Making quality microscopes more widely available is one of many great starting ideas for an entry. Let’s take a look at some of the best microscopy projects on Hackaday.io!

scope1We start with [J. Kha] and Armed Microscope. [J. Kha] was one of the backers of the original uArm over at Kickstarter. He also does quite a bit of work with electronics. After fighting with a cheap USB microscope, he realized he had the perfect platform to control it. Microscopes usually are stationary, with the object being viewed moved on a stage. [J. Kha] turned things upside down by mounting the microscope on his uArm. An Arduino Yun controls the system. The Yun also allows him to stream the microscope’s video over the internet using the mjpg-streamer library. [J. Kha] did have some power issues at first, but he’s got his regulators all sorted out now.

scope2Next we have [andyhull] with Adding a light touch to a “classic” microscope. A lucky dumpster find netted [Andy] a pile of old broken microscopes. From this he was able to build a working classic stereo scope. This was a Gillet & Sibert stereo compound scope. Like most microscopes of its time, the old GS used standard incandescent or halogen lights for illumination. The old bulbs were long gone, and would have been a pain to replace. [Andy] switched his scope over to LED illumination. He ended up using a commercially available LED “bulb” designed to replace type 1157 automotive tail light bulbs. This type of LED is designed to run on 12 volt power which simplifies the wiring. The small LED flashlight in a custom mount also provides a bit of help for opaque subjects.

scope3Next up is [Andre Maia Chagas] with Flypi – cheap microscope/experimental setup. Flypi is [Andre’s] entry in the 2106 Hackaday Prize. Flypi is more than just a microscope, it’s a 3D printed data collection and image analysis device for hackers and scientists alike. A Raspberry Pi 2 or 3 controls the show. Images come in through Pi Camera with an M12 lens. The Pi runs some open source Python code allowing it to acquire and analyze images. It also has an Arduino as a co-processor to handle anything a particular experiment may need – like RGB LEDs, heaters, manipulators, you name it. Andre sees Flypi as having uses in everything from fluorescence imaging to optogenetics and thermogenetics.

scope5Finally we have [Jarred Heinrich] with Stagmo: Microscope Stage Automator. Positioning samples under high magnification requires a steady hand. Trying to image them makes things even harder. To help with this, microscopes have stages. Fine lead screws manually controlled by knobs allow the user to precisely position any subject. Automated stages are available as well, but they can get quite expensive. [Jarred] recognized that the microscope stage is an X-Y platform like any CNC, laser, or 3D printer. He used an Arduino and a motor shield to control a couple of stepper motors. The motors are coupled to the stage knobs with rubber belts. While the mounting system looks a little wobbly, but it got the job done, and didn’t require any modifications to the microscope itself.

Optical microscopes are just one type of scope you’ll find on Hackaday.io. There are also atomic force microscopes, scanning electron microscopes, and more! I’ll cover those on a future Hacklet. If you want to see more awesome optical microscopy projects, check out our new optical microscope projects list! If I missed your project, don’t be shy, just drop me a message on Hackaday.io. That’s it for this week’s Hacklet. As always, see you next week. Same hack time, same hack channel, bringing you the best of Hackaday.io!