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1. Fast, high precision autofocus on a motorised microscope: automating blood sample imaging on the OpenFlexure Microscope

Author

Knapper, Joe, Collins, Joel T., Stirling, Julian, McDermott, Samuel, Wadsworth, William, and Bowman, Richard

Subjects
Physics - Instrumentation and Detectors
Abstract

The OpenFlexure Microscope is a 3D printed, low-cost microscope capable of automated image acquisition through the use of a motorised translation stage and a Raspberry Pi imaging system. This automation has applications in research and healthcare, including in supporting the diagnosis of malaria in low resource settings. The plasmodium parasites which cause malaria require high magnification imaging, which has a shallow depth of field, necessitating the development of an accurate and precise autofocus procedure. We present methods of identifying the focal plane of the microscope, and procedures for reliably acquiring a stack of focused images on a system affected by backlash and drift. We also present and assess a method to verify the success of autofocus during the scan. The speed, reliability and precision of each method is evaluated, and the limitations discussed in terms of the end users' requirements.

Published
2021

2. Modern Microscopy with the Web of Things: The OpenFlexure Microscope Software Stack

Author

Collins, Joel T., Knapper, Joe, Stirling, Julian, McDermott, Samuel, and Bowman, Richard

Subjects
Physics - Instrumentation and Detectors
Abstract

Automated and computerised control of scientific instrumentation is almost ubiquitous in the modern laboratory. Most instrumentation is controlled over decades old communication busses or is accessed via proprietary system libraries. This limits which languages and operating systems can be used to control instruments, and poses a significant problem when interfacing multiple instruments into the same experiment. Here we present the OpenFlexure Microscope software stack as an example of how a scientific instrument can be controlled using existing, cross-platform, language-independent, industry-supported standards. We split the control code into client and server applications interfaced via a web API that conforms to the W3C Web of Things standard. This enables simple control of the microscope from multiple languages, provides a modern graphical control interface, and minimises duplicated code. Network control also makes the software stack more robust, allows multiple microscopes to be controlled by one computer, and facilitates sharing of equipment between local or remote users. Using a Web of Things approach in research laboratories has the potential to solve many of the key challenges of experiment integration, using technology that is already well established.

Published
2021
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10. Fast, high‐precision autofocus on a motorised microscope: Automating blood sample imaging on the OpenFlexure Microscope.

Author

Knapper, Joe, Collins, Joel T., Stirling, Julian, McDermott, Samuel, Wadsworth, William, and Bowman, Richard W.

Subjects
*FOCAL planes, *IMAGING systems, *BLOOD sampling, *RASPBERRY Pi, *MICROSCOPY
Abstract

The OpenFlexure Microscope is a 3D‐printed, low‐cost microscope capable of automated image acquisition through the use of a motorised translation stage and a Raspberry Pi imaging system. This automation has applications in research and healthcare, including in supporting the diagnosis of malaria in low‐resource settings. The plasmodium parasites that cause malaria require high magnification imaging, which has a shallow depth of field, necessitating the development of an accurate and precise autofocus procedure. We present methods of identifying the focal plane of the microscope, and procedures for reliably acquiring a stack of focused images on a system affected by backlash and drift. We also present and assess a method to verify the success of autofocus during the scan. The speed, reliability and precision of each method are evaluated, and the limitations discussed in terms of the end users' requirements. [ABSTRACT FROM AUTHOR]

Published
2022
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11. Robotic microscopy for everyone: the OpenFlexure microscope

Author

Collins, Joel T., primary, Knapper, Joe, additional, Stirling, Julian, additional, Mduda, Joram, additional, Mkindi, Catherine, additional, Mayagaya, Valeriana, additional, Mwakajinga, Grace A., additional, Nyakyi, Paul T., additional, Sanga, Valerian L., additional, Carbery, Dave, additional, White, Leah, additional, Dale, Sara, additional, Jieh Lim, Zhen, additional, Baumberg, Jeremy J., additional, Cicuta, Pietro, additional, McDermott, Samuel, additional, Vodenicharski, Boyko, additional, and Bowman, Richard, additional

Published
2020
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13. Robotic microscopy for everyone: the OpenFlexure Microscope

Author

Collins, Joel T., primary, Knapper, Joe, additional, Stirling, Julian, additional, Mduda, Joram, additional, Mkindi, Catherine, additional, Mayagaya, Valeriana, additional, Mwakajinga, Grace A., additional, Nyakyi, Paul T., additional, Sanga, Valerian L., additional, Carbery, Dave, additional, White, Leah, additional, Dale, Sara, additional, Lim, Zhen Jieh, additional, Baumberg, Jeremy J., additional, Cicuta, Pietro, additional, McDermott, Samuel, additional, Vodenicharski, Boyko, additional, and Bowman, Richard, additional

Published
2019
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15. Nonlinear circular dichroism in GaAs nanowires partially covered by gold (Conference Presentation)

Author

Belardini, Alessandro, primary, Collins, Joel T., additional, Hooper, David C., additional, Leahu, Grigore, additional, Petronijevic, Emilija, additional, Centini, Marco, additional, Hakkarainen, Teemu, additional, Koivusalo, Eero, additional, Rizzo Piton, Marcelo, additional, Suomalainen, Soile, additional, Guina, Mircea, additional, Valev, Ventsislav K., additional, and Sibilia, Concita, additional

Published
2019
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17. Pembrolizumab-induced thrombotic thrombocytopenic purpura.

Author

Dickey, Marcus SR, Raina, Anant J, Gilbar, Peter J, Wisniowski, Brendan L, Collins, Joel T, Karki, Bhaskar, and Nguyen, Andrew DK

Subjects
THROMBOTIC thrombocytopenic purpura treatment, ANTINEOPLASTIC agents, COMBINED modality therapy, DRUG side effects, HEMOLYTIC anemia, IMMUNOTHERAPY, INTRAVENOUS therapy, LUNG cancer, MONOCLONAL antibodies, ORAL drug administration, PLASMA exchange (Therapeutics), THROMBOTIC thrombocytopenic purpura, TERMINATION of treatment, COMMUNITY-acquired pneumonia, DISEASE remission, METHYLPREDNISOLONE, PREDNISOLONE, PLATELET count, ROUTINE diagnostic tests
Abstract

Introduction: Pembrolizumab is a humanised monoclonal antibody targeting the receptor programmed cell death protein-1 (PD-1), with anti-tumour activity demonstrated for many malignancies. Such immune checkpoint inhibitors are associated with many immune-related adverse events including rash, colitis, hepatitis, pneumonitis, endocrinopathy and, rarely, haematological adverse events, including immune-related thrombocytopenia. Case report: We report a 60-year-old female with metastatic non-small cell lung cancer treated with pembrolizumab every three weeks. Following her fifth cycle, she presented to our hospital with community-acquired pneumonia. Thrombocytopenia developed the next day and, after detailed investigations, thrombotic thrombocytopenic purpura was diagnosed. Management and outcome: Pembrolizumab was immediately ceased and plasma exchange commenced along with IV methylprednisolone 250 mg daily for three days followed by oral prednisolone. After five days of plasma exchange, platelet counts normalised and haemolytic anaemia resolved. Discussion: Acquired thrombotic thrombocytopenic purpura is an autoimmune disorder caused by an inhibitory autoantibody against ADAMTS-13. While most cases of acquired thrombotic thrombocytopenic purpura are idiopathic, certain conditions (e.g. bacterial infection, autoimmune disorders, malignancies) and medications are associated with thrombotic thrombocytopenic purpura. Other potential causes were eliminated in our patient. As acquired thrombotic thrombocytopenic purpura is an autoimmune disorder, pembrolizumab, given its unique mechanism of action and association with immune-related adverse events, is believed to be implicated in the development of thrombotic thrombocytopenic purpura. This case is one of only two linking anti-PD-1 therapy to thrombotic thrombocytopenic purpura development (the other occurring in a patient on nivolumab plus ipilimumab). Thrombotic thrombocytopenic purpura is life-threatening and clinicians are advised to be aware of its possible occurrence in immune checkpoint inhibitor-treated patients. [ABSTRACT FROM AUTHOR]

Published
2020
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18. Chiral Nanomaterials: Enantiomorphing Chiral Plasmonic Nanostructures: A Counterintuitive Sign Reversal of the Nonlinear Circular Dichroism (Advanced Optical Materials 14/2018)

Author

Collins, Joel T., primary, Zheng, Xuezhi, additional, Braz, Nuno V. S., additional, Slenders, Eli, additional, Zu, Shuai, additional, Vandenbosch, Guy A. E., additional, Moshchalkov, Victor V., additional, Fang, Zheyu, additional, Ameloot, Marcel, additional, Warburton, Paul A., additional, and Valev, Ventsislav K., additional

Published
2018
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21. Enantiomorphing Chiral Plasmonic Nanostructures: A Counterintuitive Sign Reversal of the Nonlinear Circular Dichroism

Author

Collins, Joel T., primary, Zheng, Xuezhi, additional, Braz, Nuno V. S., additional, Slenders, Eli, additional, Zu, Shuai, additional, Vandenbosch, Guy A. E., additional, Moshchalkov, Victor V., additional, Fang, Zheyu, additional, Ameloot, Marcel, additional, Warburton, Paul A., additional, and Valev, Ventsislav K., additional

Published
2018
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28. Robotic microscopy for everyone: the OpenFlexure microscope

Author

Collins, Joel T, Knapper, Joe, Stirling, Julian, Mduda, Joram, Mkindi, Catherine, Mayagaya, Valeriana, Mwakajinga, Grace A, Nyakyi, Paul T, Sanga, Valerian L, Carbery, Dave, White, Leah, Dale, Sara, Jieh Lim, Zhen, Baumberg, Jeremy J, Cicuta, Pietro, McDermott, Samuel, Vodenicharski, Boyko, and Bowman, Richard

Subjects
Bioengineering, Generic health relevance, 4014 Manufacturing Engineering, 3. Good health, 40 Engineering
Abstract

Optical microscopes are an essential tool for both the detection of disease in clinics, and for scientific analysis. However, in much of the world access to high-performance microscopy is limited by both the upfront cost and maintenance cost of the equipment. Here we present an open-source, 3D-printed, and fully-automated laboratory microscope, with motorised sample positioning and focus control. The microscope is highly customisable, with a number of options readily available including trans- and epi- illumination, polarisation contrast imaging, and epi-florescence imaging. The OpenFlexure microscope has been designed to enable low-volume manufacturing and maintenance by local personnel, vastly increasing accessibility. We have produced over 100 microscopes in Tanzania and Kenya for educational, scientific, and clinical applications, demonstrating that local manufacturing can be a viable alternative to international supply chains that can often be costly, slow, and unreliable.

29. Simplifying the OpenFlexure microscope software with the web of things

Author

Kaspar E Bumke, Samuel McDermott, Julian Stirling, Joe Knapper, Richard Bowman, Filip Ayazi, Joel T. Collins, Collins, Joel T [0000-0002-9382-7511], Knapper, Joe [0000-0002-5519-1700], McDermott, Samuel [0000-0003-2736-5467], Ayazi, Filip [0000-0003-4521-9826], Bumke, Kaspar E [0000-0001-7603-0861], Stirling, Julian [0000-0002-8270-9237], Bowman, Richard W [0000-0002-1531-8199], Apollo - University of Cambridge Repository, and McDermott, Samuel J [0000-0003-2736-5467]

Subjects
Computer science, Science, computer.software_genre, 01 natural sciences, Web API, 010305 fluids & plasmas, 03 medical and health sciences, Web of Things, Software, Engineering, Stack (abstract data type), system architectures, Research articles, 0103 physical sciences, MATLAB, 030304 developmental biology, computer.programming_language, Graphical user interface, 0303 health sciences, Multidisciplinary, business.industry, web technologies, Python (programming language), Automation, Operating system, hardware/software interfaces, business, computer, integration and modelling
Abstract

We present the OpenFlexure Microscope software stack which provides computer control of our open source motorised microscope. Our diverse community of users needs both graphical and script-based interfaces. We split the control code into client and server applications interfaced via a web API conforming to the W3C Web of Things standard. A graphical interface is viewed either in a web browser or in our cross-platform Electron application, and gives basic interactive control including common operations such as Z stack acquisition and tiled scanning. Automated control is possible from Python and M atlab , or any language that supports HTTP requests. Network control makes the software stack more robust, allows multiple microscopes to be controlled by one computer, and facilitates sharing of equipment. Graphical and script-based clients can run simultaneously, making it easier to monitor ongoing experiments. We have included an extension mechanism to add functionality, for example controlling additional hardware components or adding automation routines. Using a Web of Things approach has resulted in a user-friendly and extremely versatile software control solution for the OpenFlexure Microscope, and we believe this approach could be generalized in the future to make automated experiments involving several instruments much easier to implement.

Published
2021
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30. Robotic microscopy for everyone: the OpenFlexure microscope

Author

Joel T. Collins, Pietro Cicuta, Dave Carbery, Sara E. C. Dale, Julian Stirling, Grace A. Mwakajinga, Valerian L. Sanga, Jeremy J. Baumberg, Catherine Mkindi, Richard Bowman, Zhen Jieh Lim, Paul T. Nyakyi, Joram Mduda, Joe Knapper, Boyko Vodenicharski, Valeriana S. Mayagaya, Samuel McDermott, Leah White, Collins, Joel T [0000-0002-9382-7511], Knapper, Joe [0000-0002-5519-1700], Stirling, Julian [0000-0002-8270-9237], Bowman, Richard [0000-0002-1531-8199], and Apollo - University of Cambridge Repository

Subjects
Microscope, Computer science, Supply chain, Bioengineering, Laboratory microscope, Contrast imaging, 01 natural sciences, Article, law.invention, 010309 optics, 03 medical and health sciences, Scientific analysis, Optical microscope, law, 0103 physical sciences, Microscopy, 030304 developmental biology, 40 Engineering, 0303 health sciences, business.industry, 4014 Manufacturing Engineering, Atomic and Molecular Physics, and Optics, 3. Good health, Generic health relevance, business, Computer hardware, Biotechnology
Abstract

Optical microscopes are an essential tool for both the detection of disease in clinics, and for scientific analysis. However, in much of the world access to high-performance microscopy is limited by both the upfront cost and maintenance cost of the equipment. Here we present an open-source, 3D-printed, and fully-automated laboratory microscope, with motorised sample positioning and focus control. The microscope is highly customisable, with a number of options readily available including trans- and epi-illumination, polarisation contrast imaging, and epi-florescence imaging. The OpenFlexure Microscope has been designed to enable low-volume manufacturing and maintenance by local personnel, vastly increasing accessibility. We have produced over 100 microscopes in Tanzania and Kenya for educational, scientific, and clinical applications, demonstrating that local manufacturing can be a viable alternative to international supply chains that can often be costly, slow, and unreliable.

Published
2020

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