An Open-Source Framework for Automated High-Throughput Cell Biology Experiments

Katunin, Pavel; Zhou, Jianbo; Shehata, Ola M.; Peden, Andrew A.; Cadby, Ashley J.; Nikolaev, Anton

doi:10.3389/fcell.2021.697584

Cited by 5 publications

(1 citation statement)

References 43 publications

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“…Recent work such as the Incubot [ 34 ] or the open‐source Lab Platform [ 35 ] had already shown how parts from a 3D printer or computer numerical control (CNC) machine could be used to create low‐cost, high‐throughput microscopes. The ideas presented there were taken up and two new compact 3D printed devices with a similar range of functions were demonstrated.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2021

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The number of samples in biological experiments is continuously increasing, but complex protocols and human error 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 the lack of open application programming interfaces (APIs), they are notoriously difficult for scientists to customize and control outside of the vendor‐supplied software. Here, automated, high‐throughput experiments are demonstrated 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. This 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 the analysis of previously acquired images, enables the realization of fully autonomous “smart” microscopy experiments. All documents and source files are publicly available to prove the concept of smart lab automation using inexpensive, open tools. It is believed this democratizes access to the power and repeatability of automated experiments.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2021

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A review on low‐cost microscopes for Open Science

Tercero

Bueno

Ruíz-Santaquiteria

et al. 2022

Microscopy Res & Technique

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This article presents a review after an exhaustive search that yielded 23 works carried out in the last decade for the availability of optical microscopes with open hardware as a low‐cost alternative to commercial systems. These works were developed with the aim of covering needs within several areas such as: Bio Sciences research in institutions with limited resources, diagnosis of diseases and health screenings in large populations in developing countries, and training in educational contexts with a need for high availability of equipment and low replacement cost. The analysis of the selected works allows us to classify the analyzed solutions into two main categories, for which their essential characteristics are enumerated: portable field microscopes and multipurpose automated microscopes. Moreover, this work includes a discussion on the degree of maturity of the solutions in terms of the adoption of practices aligned with the development of Open Science. Research Highlights Concise review on low‐cost microscopes for developing Open Science, exposing the role of smartphone‐based microscopy. The work classifies microscopes in two main categories: (1) portable field microscopes, and (2) multipurpose automated microscopes.

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