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High-speed device synchronization in optical microscopy with an open-source hardware control platform

View ORCID ProfileMarshall J. Colville, View ORCID ProfileSangwoo Park, View ORCID ProfileWarren R. Zipfel, View ORCID ProfileMatthew J. Paszek
doi: https://doi.org/10.1101/533349
Marshall J. Colville
aField of Biophysics, Cornell University, Ithaca, NY, 14853, USA
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  • For correspondence: mjc449@cornell.edu mjp31@cornell.edu
Sangwoo Park
aField of Biophysics, Cornell University, Ithaca, NY, 14853, USA
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Warren R. Zipfel
aField of Biophysics, Cornell University, Ithaca, NY, 14853, USA
bNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
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Matthew J. Paszek
aField of Biophysics, Cornell University, Ithaca, NY, 14853, USA
bNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
cRobert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
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  • For correspondence: mjc449@cornell.edu mjp31@cornell.edu
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Abstract

Recent advances in fluorescence microscopy have enabled the visualization of subcellular structures at unprecedented resolution. However, the complexity of state-of-the-art microscopes has increased considerably, often requiring the precise control and synchronization of multiple peripheral devices at high speeds. Drawing inspiration from open-source prototyping systems, like the Arduino, we describe the development of a new control platform that adopts the best features of these systems – affordability, facile programmability, and flexible connectivity – but with the scientific-grade inputs and outputs (I/O) and built-in routines that are necessary to control peripherals in advanced microscopy applications. Notably, our platform includes waveform generators and I/O for point-and azimuthal-scanning of excitation in laser-based applications. As a proof of concept, we show how the integration of waveform generation, multiplexed analog outputs, and native hardware triggers into a single central hub provides a versatile platform for performing fast circle-scanning acquisitions, including ring scanning-angle interference microscopy (SAIM), total internal reflection fluorescence (TIRF and ring TIRF) microscopy, and multiangle TIRF (MA-TIRF). We also demonstrate how the low communication latency of our hardware platform can reduce image intensity and reconstruction artifacts arising from synchronization errors produced by software control. Our complete platform, including hardware design files, firmware, API, software, and all associated source code, will be hosted for community-based development and collaboration.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 29, 2019.
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High-speed device synchronization in optical microscopy with an open-source hardware control platform
Marshall J. Colville, Sangwoo Park, Warren R. Zipfel, Matthew J. Paszek
bioRxiv 533349; doi: https://doi.org/10.1101/533349
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High-speed device synchronization in optical microscopy with an open-source hardware control platform
Marshall J. Colville, Sangwoo Park, Warren R. Zipfel, Matthew J. Paszek
bioRxiv 533349; doi: https://doi.org/10.1101/533349

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