Technical upgrade of an open-source liquid handler to support bacterial colony screening
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Abstract
The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, entails extra workload for researchers during the screening stage of candidate variants. Despite the existence of commercial colony pickers, their high price excludes small research laboratories and budget-adjusted institutions from accessing such extensive screening capability. In this work we present COPICK, a technical solution to automatize colony picking in an open-source liquid handler Opentrons OT-2. COPICK relies on a mounted camera to capture images of regular Petri dishes and detect microbial colonies for automated screening. COPICK’s software can then automatically select the best colonies according to different criteria (size, color and fluorescence) and execute a protocol to pick them for further analysis. Benchmark tests performed for E. coli and P. putida colonies delivers a raw picking performance over pickable colonies of 82% with an accuracy of 73.4% at an estimated rate of 240 colonies/h. These results validate the utility of COPICK, and highlight the importance of ongoing technical improvements in open-source laboratory equipment to support smaller research teams.
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laboratories.
I really enjoyed reading about this project and am curious about implementing something like this for our lab! It would be great to see a video of it in action. It would also be great to know how quickly COPICK can pick colonies from a plate vs a person in the lab?
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At present time (early 2023), there is still a lack of open-source tools on the web to label and create datasets of images using a panoptic segmentation format in a straightforward fashion.
Has this changed in the last year? Would love to know where advancements are being made
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using a reflex camera with a macro objective (Nikon D60 with AF-S Micro NIKKOR 60 mm f/2.8G ED lens)
I'm curious if there are any drawbacks to training the model using a different camera than the one that is implemented on the OT-2?
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