scanning microscopy with a microlens array 18 october, fio 2011 antony orth and kenneth crozier
TRANSCRIPT
Scanning Microscopy with a Microlens Array
18 October, FiO 2011Antony Orth and Kenneth Crozier
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High Throughput Microscopy
http://www.olympus.co.uk/microscopy/22_scan_R.htm#
High throughput fluorescence imaging by scanning sample under widefield microscope.
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What limits high throughput microscopy?
• Specs sheet for typical systems advertise ~1s per image.• Camera sensor typically ~1Mpx, so throughput is ~1Mpx/s,
far below the throughput available with digital cameras.
• Limiting factors: – Motorized stages have small bandwidth.– Scanning procedures (focusing, moving FOV) become temporally
expensive.– Motion blur/lighting.
• Can we alter optics to alleviate these problems?– Break up imaging into small, parallelized fields of view.
http://www.olympus.co.uk/microscopy/22_scan_R_Specifications.htm
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Talk Outline
• Use of microlens arrays for fluorescence imaging– Experimental setup– Array fabrication and characterization– Sample fluorescence images– Large scale imaging example– Image processing
• Summary and outlook
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Experimental Setup
Piezo scan
Movie of microlens apertures as sample is scanned
Scan area: 20μm x 20μmStep size: 175nmFrame rate: 202 Hz
Microlens focal length 40 μm
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Reflow Mold Microlens Array1.3mm
Pitch: 55 μm
100
x 10
0 m
icro
lens
arr
ay
Lens Diameter: 40 μm Lens Height: 15 μm
Lens array molded in optical adhesive (NOA 61, n=1.56)
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Focal Spot Characterization
Microlens Array
532 nm Laser
0.8NA Microscope Objective
FWHM = 790nm
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Scanning Fluorescence Images
2μm, 5μm beads
Rat femur tissue section
3.6 μm
3.6 μm
FWHM = 645 nm500nm beads
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Large-Scale Imaging With Stitching
2μm beads
2μm55 μm x 55 μm
0.8 mm
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Large-Scale Imaging With Stitching
2μm beads40μm
Highest throughput so far:
Frame rate: 202 HzSensor area: 256 x 256 pixels (0.065Mpx)Microlenses: 5000Throughput: 1Mpx/s
With optimal camera (IDT NR5-S2):
Frame rate: 1000 HzSensor area: 2560 x 1920 pixels (4.9Mpx)Microlenses: > 1,000,000Throughput: 1.2Gpx/s
55 μm x 55 μm
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Light Field Parametrization
t
s
(s,t) position on CCD maps to initial ray angle(u,v) is position in object space
Image on CCD
M. Levoy et al., J. Microscopy vol. 235 pt.2 2009 p.144
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Image Reconstruction
Tile red pixels for perspective view
Tile sum of green pixels for full aperture view
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Perspective Fly-Around
Microlens Aperture Microlens Aperture
Extracted Pixel
3.6 μm3.6 μm
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Perspective Fly-Around
3.6 μm
Microlens Aperture
Extracted Pixel
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Summary & Outlook
• Demonstrated parallelized point scanning fluorescence microscopy with a microlens array
• Demonstrated pixel throughput comparable to commercial systems, but with small sensor size*
• Demonstrated viewpoint selection of scene
• *Throughput scales with sensor size: lots of room for speed increase.
• Next: imaging through coverslips – more involved microlens design