An Open-Source Modular Framework for Automated Pipetting and Imaging Applications

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Published: 2021-09-24

Formatted citation

Ouyang W, Bowman R, Wang H, Bumke KE, Collins JT, Spjuth O, Carreras-Puigvert J and Diederich B. An Open-Source Modular Framework for Automated Pipetting and Imaging Applications.
Advanced Biology. 2101063 (2021). DOI: 10.1002/adbi.202101063


The number of samples in biological experiments are continuously increasing, but complex protocols and human experimentation in many cases lead to suboptimal data quality and hence difficulties in reproducing scientific findings. Laboratory automation can alleviate many of these problems by precisely reproducing machine-readable protocols. These instruments generally require high up-front investments and due to lack of open APIs they are notoriously difficult for scientists to customize and control outside of the vendor-supplied software. Here, we demonstrate automated, high-throughput experiments for interdisciplinary research in life science that can be replicated on a modest budget, using open tools to ensure reproducibility by combining the tools Openflexure, Opentrons, ImJoy and UC2. Our automated sample preparation and imaging pipeline can easily be replicated and established in many laboratories as well as in educational contexts through easy-to-understand algorithms and easy-to-build microscopes. Additionally, the creation of feedback loops, with later pipetting or imaging steps depending on analysis of previously acquired images, enables the realization of smart microscopy experiments, featuring completely autonomously performed experiments. All documents and source-files are publicly available ( to prove the concept of smart lab automation using inexpensive, open tools. We believe this democratizes access to the power and repeatability of automated experiments.