Wavefront‐sensorless adaptive optics with a laser‐free spinning disk confocal microscope

Hussain, Syed Asad; Kubo, Takanori; Hall, Nicholas; Gala, Dalia S; Hampson, Karen M.; Parton, Richard M.; Phillips, Michael A.; Wincott, Matthew; Fujita, Katsumasa; Davis, Ilan; Dobbie, Ian M.; Booth, Martin J.

doi:10.1111/jmi.12976

Cited by 14 publications

(12 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This happens even if all devices are connected on the same computer since the client can connect to the server either locally or remotely. CryoSIM (Phillips et al, 2020) and Aurox AO (Hussain et al, 2020) are two example setups that use the Python-Microscope device-server for hardware control in different ways. CryoSIM incorporates four lasers and two filter wheels on one computer, a spatial light modulator on a second computer, two cameras on a third computer, and a fourth computer for overall system control, utilising the device-server to distribute many devices over several computers.…”

Section: Arbitrarily Complex Mixture and Number Of Microscope Devicesmentioning

confidence: 99%

Python-Microscope – a new open-source Python library for the control of microscopes

Pinto

Phillips

Hall

et al. 2021

Journal of Cell Science

Self Cite

View full text Add to dashboard Cite

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 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 architecture choices of Python-Microscope that overcome the performance problems often raised against Python and demonstrate the different use cases that drove its design: its integration in user facing projects, namely in the Microscope-Cockpit project; in controlling complex microscopes at high speed while using the Python programming language; and as a microscope simulation tool for software development.

show abstract

Section: Arbitrarily Complex Mixture and Number Of Microscope Devicesmentioning

confidence: 99%

Python-Microscope – a new open-source Python library for the control of microscopes

Pinto

Phillips

Hall

et al. 2021

Journal of Cell Science

Self Cite

View full text Add to dashboard Cite

show abstract

“…The first is a cryo-super resolution microscope for correlative imaging, CryoSIM [28,29] (Figure 5(a)). The second demonstration was a laser-free spinning disk confocal microscope using adaptive optics (AO) for aberration correction [30] (Figure 5(b)). Additionally, Cockpit was the basis of the control software in the implementation of a novel technique, IsoSense, for improved aberration correction in widefield microscopes and structured illumination [31].…”

Section: Previously Published Systems and Microscopes In Development mentioning

confidence: 99%

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

Phillips

Pinto

Hall

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

We have developed “Microscope-Cockpit” (Cockpit), a highly adaptable open source user-friendly Python-based 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.HighlightsUser-friendly setup and use for simple to complex bespoke microscopes.Facilitates collaborations between biomedical scientists and microscope technologists.Touchscreen for near-instantaneous navigation of specimen landscape.Uses Python-Microscope, for abstracted open source hardware device control.Well-suited for user training of AI-algorithms for automated microscopy.

show abstract

“…The first is a cryo-super resolution microscope for correlative imaging, CryoSIM 28,29 (Figure 5(a)). The second demonstration was a laser-free spinning disk confocal microscope using adaptive optics (AO) for aberration correction 30 (Figure 5(b)). Additionally, Cockpit was the basis of the control software in the implementation of a novel technique, IsoSense, for improved aberration correction in widefield microscopes and structured illumination 31 .…”

Section: Previously Published Systems and Microscopes In Development Using Cockpitmentioning

confidence: 99%

“…The Aurox Clarity AO system is as previously published, the system utilised an Olympus IX70 microscope with a 60× 1.42NA objective. Illumination was provided by a CoolLED p-300 30 . This system was used to image Drosophila melanogaster neuro-muscular junctions (NMJ).…”

Section: Aurox Ao Imagingmentioning

confidence: 99%

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

Phillips¹,

Pinto²,

Hall³

et al. 2021

Wellcome Open Res

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Wavefront‐sensorless adaptive optics with a laser‐free spinning disk confocal microscope

Cited by 14 publications

References 30 publications

Python-Microscope – a new open-source Python library for the control of microscopes

Python-Microscope – a new open-source Python library for the control of microscopes

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

Contact Info

Product

Resources

About