Microscope-Cockpit: Python-based Bespoke Microscopy for Bio-medical Science

Overview

Journal Wellcome Open Res

Specialty Biomedical Engineering

Date 2023 Jun 7

PMID 37283605

Authors

Mick A Phillips

David Miguel Susano Pinto

Nicholas Hall

Julio Mateos-Langerak

Richard M Parton

Josh Titlow

Danail V Stoychev

Thomas Parks

Tiago Susano Pinto

John W Sedat

Martin J Booth

Ilan Davis

Ian M Dobbie

Affiliations

Soon will be listed here.

Abstract

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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