1
|
Susano Pinto DM, Phillips MA, Hall N, Mateos-Langerak J, Stoychev D, Susano Pinto T, Booth MJ, Davis I, Dobbie IM. Python-Microscope - a new open-source Python library for the control of microscopes. J Cell Sci 2021; 134:jcs258955. [PMID: 34448002 PMCID: PMC8520730 DOI: 10.1242/jcs.258955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/23/2021] [Indexed: 01/25/2023] Open
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 that is 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 architectural features of Python-Microscope that overcome the performance problems often raised against Python and demonstrate the different use cases that drove its design: integration with user-facing projects, namely the Microscope-Cockpit project; control of complex microscopes at high speed while using the Python programming language; and use as a microscope simulation tool for software development.
Collapse
Affiliation(s)
- David Miguel Susano Pinto
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mick A. Phillips
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Nicholas Hall
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Julio Mateos-Langerak
- IGH, University of Montpellier, CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
- Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094 Montpellier, France
| | - Danail Stoychev
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tiago Susano Pinto
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Ilan Davis
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ian M. Dobbie
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| |
Collapse
|
2
|
Hall N, Titlow J, Booth MJ, Dobbie IM. Microscope-AOtools: a generalised adaptive optics implementation. OPTICS EXPRESS 2020; 28:28987-29003. [PMID: 33114806 PMCID: PMC8219375 DOI: 10.1364/oe.401117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Aberrations arising from sources such as sample heterogeneity and refractive index mismatches are constant problems in biological imaging. These aberrations reduce image quality and the achievable depth of imaging, particularly in super-resolution microscopy techniques. Adaptive optics (AO) technology has been proven to be effective in correcting for these aberrations, thereby improving the image quality. However, it has not been widely adopted by the biological imaging community due, in part, to difficulty in set-up and operation of AO. The methods for doing so are not novel or unknown, but new users often waste time and effort reimplementing existing methods for their specific set-ups, hardware, sample types, etc. Microscope-AOtools offers a robust, easy-to-use implementation of the essential methods for set-up and use of AO elements and techniques. These methods are constructed in a generalised manner that can utilise a range of adaptive optics elements, wavefront sensing techniques and sensorless AO correction methods. Furthermore, the methods are designed to be easily extensible as new techniques arise, leading to a streamlined pipeline for new AO technology and techniques to be adopted by the wider microscopy community.
Collapse
Affiliation(s)
- Nicholas Hall
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Josh Titlow
- Davis Lab, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin J. Booth
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Ian M. Dobbie
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| |
Collapse
|
3
|
Abstract
BeamDelta is a tool to help align optical systems. It greatly assists in assembling bespoke optical systems by providing a live view of the current laser beam position and a reference position. Even a simple optical setup has multiple degrees of freedom that affect the alignment of beam paths. These degrees of freedom rise exponentially with the complexity of the system. The process of aligning all the optical components for a specific system is often esoteric and poorly documented, if it is documented at all. Alignment methods used often rely on visual inspection of beams impinging on pinholes in the beam path, typically requiring an experienced operator staring at diffuse reflections for extended periods of time. This can lead to a decline in accuracy due to eye strain, flash blindness as well as symptoms such as headaches and, possibly, more serious retinal damage. Here we present BeamDelta a simple alignment tool and accompanying software interface which allows users to obtain accurate alignment as well as removing the necessity of staring at diffuse laser reflections. BeamDelta is a robust alignment tool as it doesn't require any precise alignment itself.
Collapse
|