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.
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.
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.
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.
Very interesting setup! I’m not sure why there is a long-travel vertical axis, as well as the X-Y travel, but maybe it is intended to have other functions beyond that shown here. I hope it enables some useful research!
This is a fantastic project and we are honored to see you are using the OpenBuilds V-Slot system.
We would like to invite you to share this project with the OpenBuilds community of thinkers and makers. We have category where we have some other samplers under Other Builds/Projects.
This would be a great addition to all the many amazing machines being made using the V-Slot modular building system.