Python-Microscope: high performance control of arbitrarily complex and scalable bespoke microscopes

Susano Pinto, D. M. M. S.; Phillips, M. A.; Hall, N.; Mateos-Langerak, J.; Stoychev, D.; Pinto, T. S.; Booth, M. J.; Davis, I.; Dobbie, I. M.

doi:10.1101/2021.01.18.427171

bioRxiv · 10.1101/2021.01.18.427171

Python-Microscope: high performance control of arbitrarily complex and scalable bespoke microscopes

Susano Pinto, D. M. M. S.·Phillips, M. A.·Hall, N.·Mateos-Langerak, J.·Stoychev, D.·Pinto, T. S.·Booth, M. J.·Davis, I.·Dobbie, I. M.

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Abstract

Custom built microscopes often require control of multiple hardware devices and precise hardware coordination. It is also desirable to have a solution that is scalable to complex systems and translatable between components from different manufacturers. Here we report Python-Microscope, a free and open source Python library for high performance control of arbitrarily complex and scalable custom microscope systems. Python-Microscope offers simple to use Python-based tools, abstracting differences between physical devices by providing a defined interface for different device types. Concrete implementations are provided for a range of specific hardware and a framework exists for further expansion. Python-Microscope supports the distribution of devices over multiple computers while maintaining synchronisation via highly precise hardware triggers. We discuss the architecture choices of Python-Microscope that overcome the performance problems often raised against Python and demonstrate the different use cases that drove its design: its integration in user facing projects, namely in the Microscope-Cockpit project; in controlling complex microscopes at high speed while using the Python programming language; and as a microscope simulation tool for software development.

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Susano Pinto, D. M. M. S., Phillips, M. A., Hall, N., Mateos-Langerak, J., Stoychev, D., Pinto, T. S., Booth, M. J., Davis, I., Dobbie, I. M.. 2021-01-19. Python-Microscope: high performance control of arbitrarily complex and scalable bespoke microscopes. https://doi.org/10.1101/2021.01.18.427171

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