Tag Archives: open labware

Raspberry Pi vs antibiotic resistance: microbiology imaging with open source hardware

Post Syndicated from Helen Lynn original https://www.raspberrypi.org/blog/raspberry-pi-vs-antibiotic-resistance-microbiology-imaging-with-open-source-hardware/

The Edwards Lab at the University of Reading has developed a flexible, low-cost, open source lab robot for capturing images of microbiology samples with a Raspberry Pi camera module. It’s called POLIR, for Raspberry Pi camera Open-source Laboratory Imaging Robot. Here’s a timelapse video of them assembling it.

Measuring antibiotic resistance with colour-changing dye

The robot is useful for all kinds of microbiology imaging, but at the moment the lab is using it to measure antimicrobial resistance in bacteria. They’re doing this by detecting the colour change in a dye called resazurin, which changes from blue to pink in the presence of metabolically active cells: if bacteria incubated with antibiotics grow, their metabolic activity causes the dye to turn pink. However, if the antibiotics stop or impede the growth of the bacteria, their lower levels of metabolic activity will cause less colour change, or none at all. In the photo below, the colourful microtitre plate holds bacterial samples with and without resistance to the antibiotics against which they’re being tested.

POLIR, an open source 3D printer-based Raspberry Pi lab imaging robot

An imaging system based on 3D-printer designs

The researchers adapted existing open source 3D printer designs and used v-slot aluminium extrusion (this stuff) with custom 3D-printed joints to make a frame. Instead of a printer extrusion head, a Raspberry Pi and camera module are mounted on the frame. An Arduino running open-source Repetier software controls x-y-z stepper motors to adjust the position of the computer and camera.

Front and top views of POLIR

Open-source OctoPrint software controls the camera position by supplying scripts from the Raspberry Pi to the Arduino. OctoPrint also allows remote access and control, which gives researchers flexibility in when they run experiments and check progress. Images are acquired using a Python script configured with the appropriate settings (eg image exposure), and are stored on the Raspberry Pi’s SD card. From there, they can be accessed via FTP.

More flexibility, lower cost

Off-the-shelf lab automation systems are extremely expensive and remain out of the reach of most research groups. POLIR cost just £600.

The system has a number of advantages over higher-cost off-the-shelf imaging systems. One is its flexibility: the robot can image a range of sample formats, including agar plates like those in the video above, microtitre plates like the one in the first photograph, and microfluidic “lab-on-a-comb” devices. A comb looks much like a small, narrow rectangle of clear plastic with striations running down its length; each striation is a microcapillary with capacity for a 1μl sample, and each comb has ten microcapillaries. These microfluidic devices let scientists run experiments on a large number of samples at once, while using a minimum of space on a lab bench, in an incubator, or in an imaging robot like POLIR.

POLIR accommodates 2160 individual capillaries and a 96 well plate, with room to spare

High spatial and temporal resolution

For lab-on-a-comb images, POLIR gives the Reading team four times the spatial resolution they get with a static camera. The moveable Raspberry Pi camera with a short focus yields images with 6 pixels per capillary, compared to 1.5 pixels per capillary using a $700 static Canon camera with a macro lens.

Because POLIR is automated, it brings higher temporal resolution within reach, too. A non-automated system, by contrast, can only be used for timelapse imaging if a researcher repeatedly intervenes at fixed time intervals. Capturing kinetic data with timelapse imaging is valuable because it can be significant if different samples reach the same endpoint but at different rates, and because some dyes can give a transient signal that would be missed by an endpoint measurement alone.

Dr Alexander Edwards of the University of Reading comments:

We built the robot with a simple purpose, to make antimicrobial resistance testing more robust without resorting to expensive and highly specialised lab equipment […] The beauty of the POLIR kit is that it’s based on open source designs and we have likewise published our own designs and modifications, allowing everyone and anyone to benefit from the original design and the modifications in other contexts. We believe that open source hardware is a game changer that will revolutionise microbiological and other life science lab work by increasing data production whilst reducing hands-on labour time in the lab.

You can find POLIR on GitLab here. You can also read more, and browse more figures, in the team’s open-access paper, Exploiting open source 3D printer architecture for laboratory robotics to automate high-throughput time-lapse imaging for analytical microbiology.

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Growth Monitor pi: an open monitoring system for plant science

Post Syndicated from Helen Lynn original https://www.raspberrypi.org/blog/growth-monitor-pi-an-open-monitoring-system-for-plant-science/

Plant scientists and agronomists use growth chambers to provide consistent growing conditions for the plants they study. This reduces confounding variables – inconsistent temperature or light levels, for example – that could render the results of their experiments less meaningful. To make sure that conditions really are consistent both within and between growth chambers, which minimises experimental bias and ensures that experiments are reproducible, it’s helpful to monitor and record environmental variables in the chambers.

A neat grid of small leafy plants on a black plastic tray. Metal housing and tubing is visible to the sides.

Arabidopsis thaliana in a growth chamber on the International Space Station. Many experimental plants are less well monitored than these ones.
(“Arabidopsis thaliana plants […]” by Rawpixel Ltd (original by NASA) / CC BY 2.0)

In a recent paper in Applications in Plant Sciences, Brandin Grindstaff and colleagues at the universities of Missouri and Arizona describe how they developed Growth Monitor pi, or GMpi: an affordable growth chamber monitor that provides wider functionality than other devices. As well as sensing growth conditions, it sends the gathered data to cloud storage, captures images, and generates alerts to inform scientists when conditions drift outside of an acceptable range.

The authors emphasise – and we heartily agree – that you don’t need expertise with software and computing to build, use, and adapt a system like this. They’ve written a detailed protocol and made available all the necessary software for any researcher to build GMpi, and they note that commercial solutions with similar functionality range in price from $10,000 to $1,000,000 – something of an incentive to give the DIY approach a go.

GMpi uses a Raspberry Pi Model 3B+, to which are connected temperature-humidity and light sensors from our friends at Adafruit, as well as a Raspberry Pi Camera Module.

The team used open-source app Rclone to upload sensor data to a cloud service, choosing Google Drive since it’s available for free. To alert users when growing conditions fall outside of a set range, they use the incoming webhooks app to generate notifications in a Slack channel. Sensor operation, data gathering, and remote monitoring are supported by a combination of software that’s available for free from the open-source community and software the authors developed themselves. Their package GMPi_Pack is available on GitHub.

With a bill of materials amounting to something in the region of $200, GMpi is another excellent example of affordable, accessible, customisable open labware that’s available to researchers and students. If you want to find out how to build GMpi for your lab, or just for your greenhouse, Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers by Brandin et al. is available on PubMed Central, and it includes appendices with clear and detailed set-up instructions for the whole system.

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A low-cost, open-source, computer-assisted microscope

Post Syndicated from Helen Lynn original https://www.raspberrypi.org/blog/a-low-cost-open-source-computer-assisted-microscope/

Low-cost open labware is a good thing in the world, and I was particularly pleased when micropalaeontologist Martin Tetard got in touch about the Raspberry Pi-based microscope he is developing. The project is called microscoPI (what else?), and it can capture, process, and store images and image analysis results. Martin is engaged in climate research: he uses microscopy to study tiny fossil remains, from which he gleans information about the environmental conditions that prevailed in the far-distant past.

microscoPI: a microcomputer-assisted microscope

microscoPI a project that aims to design a multipurpose, open-source and inexpensive micro-computer-assisted microscope (Raspberry PI 3). This microscope can automatically take images, process them, and save them altogether with the results of image analyses on a flash drive. It it multipurpose as it can be used on various kinds of images (e.g.

Martin repurposed an old microscope with a Z-axis adjustable stage for accurate focusing, and sourced an inexpensive X/Y movable stage to allow more accurate horizontal positioning of samples under the camera. He emptied the head of the scope to install a Raspberry Pi Camera Module, and he uses an M12 lens adapter to attach lenses suitable for single-specimen close-ups or for imaging several specimens at once. A Raspberry Pi 3B sits above the head of the microscope, and a 3.5-inch TFT touchscreen mounted on top of the Raspberry Pi allows the user to check images as they are captured and processed.

The Raspberry Pi runs our free operating system, Raspbian, and free image-processing software ImageJ. Martin and his colleagues use a number of plugins, some developed themselves and some by others, to support the specific requirements of their research. With this software, microscoPI can capture and analyse microfossil images automatically: it can count particles, including tiny specimens that are touching, analyse their shape and size, and save images and results before prompting the user for the name of the next sample.

microscoPI is compact – less than 30cm in height – and it’s powered by a battery bank secured under the base of the microscope, so it’s easily portable. The entire build comes in at under 160 Euros. You can find out more, and get in touch with Martin, on the microscoPI website.

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