Wellcome Open Research (Jan 2022)

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations]

  • Ian M. Dobbie,
  • Mick A. Phillips,
  • Ilan Davis,
  • Nicholas Hall,
  • David Miguel Susano Pinto,
  • Richard M. Parton,
  • Julio Mateos-Langerak,
  • Danail V. Stoychev,
  • Josh Titlow,
  • Tiago Susano Pinto,
  • Thomas Parks,
  • Martin J. Booth,
  • John W. Sedat

Journal volume & issue
Vol. 6

Abstract

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We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based Graphical User Interface (GUI) environment for precision control of both simple and elaborate bespoke microscope systems. The user environment allows next-generation near instantaneous navigation of the entire slide landscape for efficient selection of specimens of interest and automated acquisition without the use of eyepieces. Cockpit uses “Python-Microscope” (Microscope) for high-performance coordinated control of a wide range of hardware devices using open source software. Microscope also controls complex hardware devices such as deformable mirrors for aberration correction and spatial light modulators for structured illumination via abstracted device models. We demonstrate the advantages of the Cockpit platform using several bespoke microscopes, including a simple widefield system and a complex system with adaptive optics and structured illumination. A key strength of Cockpit is its use of Python, which means that any microscope built with Cockpit is ready for future customisation by simply adding new libraries, for example machine learning algorithms to enable automated microscopy decision making while imaging.

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