Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations]
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 navigat...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wellcome
2022-01-01
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| Series: | Wellcome Open Research |
| Subjects: | |
| Online Access: | https://wellcomeopenresearch.org/articles/6-76/v2 |
| _version_ | 1797813775607267328 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Ian M. Dobbie |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-13T07:57:46Z |
| format | Article |
| id | doaj.art-1587fdc0d1a6481ba0dd87bd1e181e34 |
| institution | Directory Open Access Journal |
| issn | 2398-502X |
| language | English |
| last_indexed | 2024-03-13T07:57:46Z |
| publishDate | 2022-01-01 |
| publisher | Wellcome |
| record_format | Article |
| series | Wellcome Open Research |
| spelling | doaj.art-1587fdc0d1a6481ba0dd87bd1e181e342023-06-02T01:00:00ZengWellcomeWellcome Open Research2398-502X2022-01-01619384Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations]Ian M. Dobbie0https://orcid.org/0000-0002-5531-5865Mick A. Phillips1https://orcid.org/0000-0003-3578-7301Ilan Davis2Nicholas Hall3https://orcid.org/0000-0003-2259-8755David Miguel Susano Pinto4https://orcid.org/0000-0003-2710-0186Richard M. Parton5https://orcid.org/0000-0002-2152-4271Julio Mateos-Langerak6https://orcid.org/0000-0003-1579-0773Danail V. Stoychev7https://orcid.org/0000-0001-5539-2206Josh Titlow8Tiago Susano Pinto9Thomas Parks10Martin J. Booth11https://orcid.org/0000-0002-9525-8981John W. Sedat12Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKIGH, Univ Montpellier, Montpellier, 34396, FranceMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UKDiamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UKDepartment of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UKDepartment of Biochemistry & Biophysics, UCSF, San Francisco, CA, 94158, USAWe 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.https://wellcomeopenresearch.org/articles/6-76/v2Microscope-Python Bespoke microscope Microscope hardware device control Free and open source software Imaging Machine Learning (ML)eng |
| spellingShingle | 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 Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations] Wellcome Open Research Microscope-Python Bespoke microscope Microscope hardware device control Free and open source software Imaging Machine Learning (ML) eng |
| title | Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations] |
| title_full | Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations] |
| title_fullStr | Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations] |
| title_full_unstemmed | Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations] |
| title_short | Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science [version 2; peer review: 2 approved, 2 approved with reservations] |
| title_sort | microscope cockpit python based bespoke microscopy for bio medical science version 2 peer review 2 approved 2 approved with reservations |
| topic | Microscope-Python Bespoke microscope Microscope hardware device control Free and open source software Imaging Machine Learning (ML) eng |
| url | https://wellcomeopenresearch.org/articles/6-76/v2 |
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