High-throughput cellular imaging with high-speed asymmetric-detection time-stretch optical microscopy under FPGA platform

H. C. Ng, M. Wang, B. M. F. Chung, B. S. C. Varma, M. K. Jaiswal, S. M. H. Ho, K. K. Tsia, H. C. Shum, H. K. H. So

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

Asymmetric-Detection Time-Stretch Optical Microscopy (ATOM) is a recently emerged technology that provides ultra-fast cell imaging with a frame rate up to MHz - orders-of-magnitude higher than any classical imaging systems. However, existing measuring instruments are unable to fully exploit the capability of ATOM. For example, the volume of imaging data-set of ATOM quickly increases beyond the capacity of available onboard buffer of a modern high-speed oscilloscope. This paper presents an open source, FPGA-based solution which serves as a dual role of collecting low-level signals from ATOM frontend as well as processing and transferring data to backing store. Optical signals are sampled by a high-speed analog-to-digital converter and the resulting values are collected by an FPGA. The quantized values received are then further processed and divided into four segments for subsequent data transfer with 10 Gbit Ethernet. Four computing units are attached to these channels with direct connection in order to reliably receive the data for post-processing. Experiments show that, with decent quality images for single-cell analysis, the proposed system can store 10x more dataset than existing high-end oscilloscope. With 8x decrease in equipment cost, the proposed FPGA-based system will definitely be beneficial for many bio imaging applications with ATOM technology such as rare cancer cell imaging and identification.
LanguageEnglish
Title of host publication2016 International Conference on ReConFigurable Computing and FPGAs (ReConFig)
Pages1-6
Number of pages6
DOIs
Publication statusPublished - 16 Feb 2017

Fingerprint

Optical microscopy
Field programmable gate arrays (FPGA)
Throughput
Imaging techniques
Digital to analog conversion
Data transfer
Processing
Ethernet
Imaging systems
Image quality
Cells
Costs
Experiments

Keywords

  • analogue-digital conversion
  • biomedical optical imaging
  • cellular biophysics
  • field programmable gate arrays
  • medical image processing
  • optical microscopy
  • ATOM
  • Ethernet
  • FPGA
  • data transfer
  • high-speed analog-to-digital converter
  • high-speed asymmetric-detection time-stretch optical microscopy
  • high-throughput cellular imaging
  • low-level signals
  • optical signals
  • quality images
  • single-cell analysis
  • ultra-fast cell imaging
  • Atom optics
  • Biomedical optical imaging
  • Clocks
  • Field programmable gate arrays
  • Optical imaging
  • Optical pulses

Cite this

Ng, H. C., Wang, M., Chung, B. M. F., Varma, B. S. C., Jaiswal, M. K., Ho, S. M. H., ... So, H. K. H. (2017). High-throughput cellular imaging with high-speed asymmetric-detection time-stretch optical microscopy under FPGA platform. In 2016 International Conference on ReConFigurable Computing and FPGAs (ReConFig) (pp. 1-6) https://doi.org/10.1109/ReConFig.2016.7857175
Ng, H. C. ; Wang, M. ; Chung, B. M. F. ; Varma, B. S. C. ; Jaiswal, M. K. ; Ho, S. M. H. ; Tsia, K. K. ; Shum, H. C. ; So, H. K. H. / High-throughput cellular imaging with high-speed asymmetric-detection time-stretch optical microscopy under FPGA platform. 2016 International Conference on ReConFigurable Computing and FPGAs (ReConFig). 2017. pp. 1-6
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abstract = "Asymmetric-Detection Time-Stretch Optical Microscopy (ATOM) is a recently emerged technology that provides ultra-fast cell imaging with a frame rate up to MHz - orders-of-magnitude higher than any classical imaging systems. However, existing measuring instruments are unable to fully exploit the capability of ATOM. For example, the volume of imaging data-set of ATOM quickly increases beyond the capacity of available onboard buffer of a modern high-speed oscilloscope. This paper presents an open source, FPGA-based solution which serves as a dual role of collecting low-level signals from ATOM frontend as well as processing and transferring data to backing store. Optical signals are sampled by a high-speed analog-to-digital converter and the resulting values are collected by an FPGA. The quantized values received are then further processed and divided into four segments for subsequent data transfer with 10 Gbit Ethernet. Four computing units are attached to these channels with direct connection in order to reliably receive the data for post-processing. Experiments show that, with decent quality images for single-cell analysis, the proposed system can store 10x more dataset than existing high-end oscilloscope. With 8x decrease in equipment cost, the proposed FPGA-based system will definitely be beneficial for many bio imaging applications with ATOM technology such as rare cancer cell imaging and identification.",
keywords = "analogue-digital conversion, biomedical optical imaging, cellular biophysics, field programmable gate arrays, medical image processing, optical microscopy, ATOM, Ethernet, FPGA, data transfer, high-speed analog-to-digital converter, high-speed asymmetric-detection time-stretch optical microscopy, high-throughput cellular imaging, low-level signals, optical signals, quality images, single-cell analysis, ultra-fast cell imaging, Atom optics, Biomedical optical imaging, Clocks, Field programmable gate arrays, Optical imaging, Optical pulses",
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Ng, HC, Wang, M, Chung, BMF, Varma, BSC, Jaiswal, MK, Ho, SMH, Tsia, KK, Shum, HC & So, HKH 2017, High-throughput cellular imaging with high-speed asymmetric-detection time-stretch optical microscopy under FPGA platform. in 2016 International Conference on ReConFigurable Computing and FPGAs (ReConFig). pp. 1-6. https://doi.org/10.1109/ReConFig.2016.7857175

High-throughput cellular imaging with high-speed asymmetric-detection time-stretch optical microscopy under FPGA platform. / Ng, H. C.; Wang, M.; Chung, B. M. F.; Varma, B. S. C.; Jaiswal, M. K.; Ho, S. M. H.; Tsia, K. K.; Shum, H. C.; So, H. K. H.

2016 International Conference on ReConFigurable Computing and FPGAs (ReConFig). 2017. p. 1-6.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AU - Ng, H. C.

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AU - Chung, B. M. F.

AU - Varma, B. S. C.

AU - Jaiswal, M. K.

AU - Ho, S. M. H.

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N2 - Asymmetric-Detection Time-Stretch Optical Microscopy (ATOM) is a recently emerged technology that provides ultra-fast cell imaging with a frame rate up to MHz - orders-of-magnitude higher than any classical imaging systems. However, existing measuring instruments are unable to fully exploit the capability of ATOM. For example, the volume of imaging data-set of ATOM quickly increases beyond the capacity of available onboard buffer of a modern high-speed oscilloscope. This paper presents an open source, FPGA-based solution which serves as a dual role of collecting low-level signals from ATOM frontend as well as processing and transferring data to backing store. Optical signals are sampled by a high-speed analog-to-digital converter and the resulting values are collected by an FPGA. The quantized values received are then further processed and divided into four segments for subsequent data transfer with 10 Gbit Ethernet. Four computing units are attached to these channels with direct connection in order to reliably receive the data for post-processing. Experiments show that, with decent quality images for single-cell analysis, the proposed system can store 10x more dataset than existing high-end oscilloscope. With 8x decrease in equipment cost, the proposed FPGA-based system will definitely be beneficial for many bio imaging applications with ATOM technology such as rare cancer cell imaging and identification.

AB - Asymmetric-Detection Time-Stretch Optical Microscopy (ATOM) is a recently emerged technology that provides ultra-fast cell imaging with a frame rate up to MHz - orders-of-magnitude higher than any classical imaging systems. However, existing measuring instruments are unable to fully exploit the capability of ATOM. For example, the volume of imaging data-set of ATOM quickly increases beyond the capacity of available onboard buffer of a modern high-speed oscilloscope. This paper presents an open source, FPGA-based solution which serves as a dual role of collecting low-level signals from ATOM frontend as well as processing and transferring data to backing store. Optical signals are sampled by a high-speed analog-to-digital converter and the resulting values are collected by an FPGA. The quantized values received are then further processed and divided into four segments for subsequent data transfer with 10 Gbit Ethernet. Four computing units are attached to these channels with direct connection in order to reliably receive the data for post-processing. Experiments show that, with decent quality images for single-cell analysis, the proposed system can store 10x more dataset than existing high-end oscilloscope. With 8x decrease in equipment cost, the proposed FPGA-based system will definitely be beneficial for many bio imaging applications with ATOM technology such as rare cancer cell imaging and identification.

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KW - data transfer

KW - high-speed analog-to-digital converter

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KW - optical signals

KW - quality images

KW - single-cell analysis

KW - ultra-fast cell imaging

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KW - Clocks

KW - Field programmable gate arrays

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KW - Optical pulses

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Ng HC, Wang M, Chung BMF, Varma BSC, Jaiswal MK, Ho SMH et al. High-throughput cellular imaging with high-speed asymmetric-detection time-stretch optical microscopy under FPGA platform. In 2016 International Conference on ReConFigurable Computing and FPGAs (ReConFig). 2017. p. 1-6 https://doi.org/10.1109/ReConFig.2016.7857175