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Open source, 3D printed microscope runs on Raspberry Pi

Jan 12, 2017 — by Eric Brown — 3,129 views
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WaterScope has launched an open source, 3D printable “OpenFlexure” microscope for testing water quality, powered by a Raspberry Pi 3.

A Cambridge University spinoff called WaterScope has launched a low-cost, 3D printable microscope called OpenFlexure. The open source microscope, which is controlled by a Raspberry Pi 3 SBC, is designed for low-cost water testing in the developing world. Non-profit charity organization Oxfam has begun testing the beta-stage kit.

The OpenFlexure microscope is available for 50 Pounds ($61) in a Microscope Kit V1 that also includes a water sampling kit, a Raspberry Pi camera module V2, and Raspbian Linux based image processing software. Users need to bring their own RPi board and 16GB microSD card.

OpenFlexure microscope (left) and full, unassembled Microscope Kit V1
(click images to enlarge)

Schematics and STL files have been posted on GitHub under a CERN license so anyone with a Raspberry Pi and a 3D printer can build their own microscope. There’s also a version that connects via USB to any computer.

As reported in this post, the OpenFlexure microscope is designed to help reduce the 2.2 million deaths per year from waterborne diseases linked to bacterial pathogens such as such as cholera, dysentery, and typhoid fever. Globally, one in ten people lack access to safe drinking water, in part due to the challenges involved in testing water quality in the developing world, says WaterScope.

“Water testing kits are typically time-consuming, require power, and cannot be used by scientifically unskilled workers,” says the organization. “As a consequence, water quality databases lack up-to-date, accurate test results.”

The kit is “smaller, lighter, and cheaper than today’s testing kits,” and “once fully developed, it will be the fastest bacterial test kit available,” claims WaterScope. The kit supports testing of pathogens including E. coli, Listeria, Legionella, and pathogenic E. coli 0157.

Rather than requiring samples to be sent back to a lab, the WaterScope test kit is designed to be used on location, thereby taking 1-2 hours instead of 24. The process is sufficiently simple so that no scientists are required on site.

RPi camera v2

The aseptic microbiology testing kit filters water samples for greater concentration, then transfers bacteria to a specific selection medium. The RPi camera connects to the microscope to capture time-lapse images of bacterial growth, which are sent to the Raspberry Pi for image processing. The Raspbian Linux-based image processing software enhances contrast, removes defects, and transforms images to standard formats.

The RPi software then transmits the results wirelessly to a smartphone, tablet, or PC. With an hour or two of initial testing, the results can be uploaded to a server along with GPS coordinates.

The OpenFlexure microscope features a flexure-based design, with motion free from friction and vibration, thereby achieving sub-micron precision and a range of 8mm, says WaterScope. The design integrates stepper motors controlled by Arduino microcontrollers.

According to, WaterScope is also looking at other applications for the OpenFlexure microscope beyond water testing.

Timelapse video of 3D printing of OpenFlexure microscope

Further information

WaterScope’s Microscope Kit V1, featuring the OpenFlexure microscope, is available for 50 Pounds ($61), including the Raspberry Pi V2 camera, but not counting the Raspberry Pi 3 and 16GB microSD card. The kit is currently listed as out of stock, but should soon be available soon at WaterScope’s shopping page. More information may be found in this DocuBricks instructions page and this AIP Review of Scientific Instruments scientific paper.

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