In culturing microbial samples, researchers often need to select a specific colony and duplicate it. Scientists use colony picking in many applications, from biofuels research and clinical microbiology to monoclonal antibody production and synthetic biology, plus many things in between. To make the most of this technology, especially where throughput and accuracy really matter, scientists turn to automated colony picking.
Colony picking can be done manually, by hand, or automatically, by a robotic platform. When asked when his lab uses automated colony picking, Oliver Griesbeck—research group leader at the Max-Planck-Institute of Neurobiology—says, “It is an optional feature. Typically, we use automated colony picking when single plates are screened.” Nonetheless, Griesbeck and his team don’t always take the automated approach, “as often data from several hundred plates may be processed before a pick decision is made.”
Even with so many potential applications of colony picking, some commonalities can be found. “The core workflow for the different applications is very similar,” explains Jana Langhoff, application specialist at Tecan. “Usually, the colonies are picked from agar in either a Petri dish or ANSI/SLAS format plate—up to 24-well—and then transferred to an inoculation plate, usually filled with growth media, usually a 96-well plate.” What is done before—upstream, or after, downstream—depends on the applications.
One typical upstream workflow is: genome editing, cloning, colony plating, and sampling. Downstream processes can include PCR, nucleic-acid purification, protein purification, mass spectrometry, fermentation, and enzymatic assays. As this indicates, colony picking can make up a component in complex workflows.
Processes that use picking
Exploring colony picking at a finer level reveals the many ways that this technology has been used for years, as well as new applications. In microbial screening, for example, colony picking is used in identifying new strains with undiscovered behavior, biological activities, or chemical structures. Colony picking is also used with microbial screening, says Langhoff, to “discover new natural products or molecules like, for example, enzymes for drug development or commercial products, such as washing powder or food-improvement agents.”
This technology can also be used in developing immunotherapies for cancer. Here, monoclonal hybridoma colonies can be picked from semi-solid media to produce therapeutic monoclonal antibodies.
In molecular cloning, Langhoff notes, “colonies with the right genetic profile have to be found.” The colonies can then be used in the production of recombinant proteins and transgenic organisms. Colony picking is also used in genetic engineering, such as editing a genome with CRISPR systems. Molecular cloning is also part of the process of developing gene therapies.
Beyond the classical microbial picking, other applications can also be found. As examples, Langhoff points out sorting zebrafish eggs, transferring plant embryos, and separating plant seeds.
Even with the wide range of examples mentioned here, it’s just a fraction of what can be done with colony picking. In many cases, going from manual colony picking to automated provides various benefits. As examples, Griesbeck notes that it’s “less error prone and time saving.”
Challenges of automation
Despite the value in automating colony picking, it’s not simple to accomplish. One challenge is actually recognizing the colony. “By hand, one can simply pick the colonies that look best according to experience or preference,” Langhoff explains. “Automated, the software needs to learn what colonies are the ‘best’ depending on an extensive set of parameters.” Not surprising, it’s a challenge to teach software to recognize a ‘good’ colony.
Getting that recognition right, demands the right hardware and software. As Griesbeck points out, “Superior, flexible image analysis is crucial and a key feature of our screening station.”
Once a colony has been identified, an automated system must accurately pick it. That requires the hardware and software working together, and accurately locating and picking the desired colony.
As noted above, scientists integrate colony picking into a variety of workflows. With automation, it takes some thinking and engineering to put it all together. Consequently, the automated colony picker must be integrated with upstream and downstream processes, such as setting up dilutions, running PCR, and so on.
Adding automation
Various options can be used to automate colony picking. For example, the Pickolo colony picker from SciRobotics can be added to Tecan’s robots, such as the Freedom EVO platform. “Because the Pickolo is just a camera that is fixed to the robotic pipetting arm and a light table, Pickolo can literally pick anything that can be seen by eye and be picked up by a regular pipette tip,” Langhoff explains.
When asked about Tecan’s latest advance in automated colony picking, Langhoff says that “novel software features are constantly being developed to ensure that colonies can be precisely recognized, distinguished, or categorized as ‘good’.” In addition, the Pickolo can now be used on Tecan’s Fluent laboratory automation workstation, and the Pickolo itself has a higher resolution camera, increasing from 2.5 to 10 megapixels. Langhoff adds that Tecan completed “the workflow by adding a module for spiral bacteria plating with the PetriPlater, another add-on from SciRobotics.”
Technological advances in automated colony picking expand the reach of the technology. When asked about some of the advanced uses, Langhoff mentions several. For one thing, she says, “On Freedom EVO, we could pick up to 800 colonies per hour, on Fluent we could increase the throughput to up to 1000 colonies per hour.” She adds, “Fluent brings higher position accuracy compared with the Freedom EVO.”
Today’s platforms can also make life easier in the lab by covering more in one device. “On one robotic platform, one can now automate the entire workflow—preparation of bacteria samples, plating of bacteria—in a flexible and reproducible way and continue with the downstream applications,” Langhoff says. “This gives an advantage over stand-alone colony pickers because the downtime of the instrument can be minimized.”
Lots of things, though, can be minimized by moving to automate colony picking. It can minimize errors and the time required to complete some workflows. As Griesbeck points out, scientists don’t always need to automate colony picking, but it’s really helpful when needed.