Python-Microscope - a new open-source Python library for the control of microscopes
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 fre...
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| Vydáno v: | Journal of cell science Ročník 134; číslo 19 |
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| Hlavní autoři: | , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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England
01.10.2021
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| ISSN: | 1477-9137, 1477-9137 |
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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 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. |
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| AbstractList | 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.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. 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. |
| Author | Hall, Nicholas Stoychev, Danail Davis, Ilan Susano Pinto, David Miguel Susano Pinto, Tiago Booth, Martin J Mateos-Langerak, Julio Dobbie, Ian M Phillips, Mick A |
| Author_xml | – sequence: 1 givenname: David Miguel orcidid: 0000-0003-2710-0186 surname: Susano Pinto fullname: Susano Pinto, David Miguel organization: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK – sequence: 2 givenname: Mick A orcidid: 0000-0003-3578-7301 surname: Phillips fullname: Phillips, Mick A organization: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK – sequence: 3 givenname: Nicholas orcidid: 0000-0003-2259-8755 surname: Hall fullname: Hall, Nicholas organization: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK – sequence: 4 givenname: Julio orcidid: 0000-0003-1579-0773 surname: Mateos-Langerak fullname: Mateos-Langerak, Julio organization: Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094 Montpellier, France – sequence: 5 givenname: Danail orcidid: 0000-0001-5539-2206 surname: Stoychev fullname: Stoychev, Danail organization: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK – sequence: 6 givenname: Tiago surname: Susano Pinto fullname: Susano Pinto, Tiago organization: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK – sequence: 7 givenname: Martin J orcidid: 0000-0002-9525-8981 surname: Booth fullname: Booth, Martin J organization: Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK – sequence: 8 givenname: Ilan orcidid: 0000-0002-5385-3053 surname: Davis fullname: Davis, Ilan organization: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK – sequence: 9 givenname: Ian M orcidid: 0000-0002-5531-5865 surname: Dobbie fullname: Dobbie, Ian M organization: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK |
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| Copyright | 2021. Published by The Company of Biologists Ltd. |
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| Issue | 19 |
| Keywords | Microscope Adaptive optics Open source Super resolution Python |
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| Title | Python-Microscope - a new open-source Python library for the control of microscopes |
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