near real-time deconvolution for 3d fluorescence microscopy...near real-time deconvolution for 3d...
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Near Real-Time Deconvolution for 3D Fluorescence Microscopy
Marc Bruce, PhD
CEO, Microvolution
GPU Accelerated Deconvolution Software
Microvolution offers faster and more accurate deconvolution
Thin Filaments Are Missing Preserves Thin Filaments: 16 sec
Image Courtesy of Molecular Devices
Other Deconvolution10.7 Min
After 3-D Deconvolution 16 Seconds
Basics of Fluorescence Microscopy
Sample
Objective
Basics of Fluorescence Microscopy
IlluminationDichroic mirror
Basics of Fluorescence Microscopy
Emission
Basics of Fluorescence Microscopy
• Damage to sample from high intensity light
• Haze from out-of-plane fluorescence
• Blurriness due to diffraction reduces resolution of small objects
Derived from Wikipedia, “Light sheet fluorescence microscopy”
Diffraction Limits 3D Resolution
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Point Spread Function
The Solution: Deconvolution Software
http://www.leica-microsystems.com/science-lab/deconvolution
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Richardson Lucy Algorithm
Iterative algorithm operating under the assumptions of Poisson-distributed noise
Real-time Deconvolution is Now Possible
• GPU yields speeds up to 200X faster than old methods
• Allows for real-time deconvolution • Optimize image capture
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190 MB1080x1080x50
890 MB2160x2160x50
1246 MB2160x2160x70
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Old methods
GPU accelerated
Higher Signal-to-Noise Ratio Yields Better Data
• Analysis of raw FRET images showed low contrast
• 4x effective increase in contrast post-deconvolution
• Expected cell features can now be seen
Miskolci, V., Hodgson, L. & Cox, D. Using Fluorescence Resonance Energy Transfer-Based Biosensors to Probe Rho GTPase Activation During Phagocytosis. Methods in Molecular Biology 1519, 125-43 (2017)
Diffraction-Limited Resolution Limit
Increased Resolution to 180 nm
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Tong Zhang and Puifai Santisakultarm,Salk Institute
Microscopy in Dim Light
Before
2048 x 2048 x 51
After 3D Deconvolution
8.5 seconds
Image Courtesy of Technical Instruments
Widefield Microscopy
Dennis Hughes, MD, PhD, Assoc Prof of Pediatrics, Jared Mortus, Lead Researcher, Laurence Cooper, MD, PhD, Professor of Pediatrics, George McNamara, PhD, Senior Research Scientist, The Children’s Cancer Hospital, MD Anderson Cancer Center, Houston, TX
Widefield Image Before
1024 x 1024 x 34
After 3D Deconvolution
1.6 seconds
Light Sheet Microscopy
Derived from Wikipedia, “Light sheet fluorescence microscopy”
Light Sheet Microscopy
Light Sheet Image Before
946 x 768 x 321
After 3D Deconvolution
22.5 seconds
Dong-Yuan Chen in the Bilder lab, UC Berkeley
Lattice Light Sheet Microscopy
Dr. Boyd Butler using 3i Lattice LightSheet
LLSM Before
1167 x 512 x 401
After 3D Deconvolution
10.2 seconds
Instant SIM
VisiTech
Instant SIM Image Before
1446 x 1131 x 14
After 3D Deconvolution
4.9 seconds
FINCH (Fresnel incoherent correlation holography)
Siegel, N., Lupashin, V., Storrie, B. & Brooker, G. High-magnification super-resolution FINCH microscopy using birefringent crystal lens interferometers. Nature Photonics 10, 802-808 (2016)
After Propagation and 3D Deconvolution
10 seconds
Widefield Image
2048 x 2048 x 21
Usable on All Tiers of GPUs
• HPC clusters• Split large multi-channel, multi-timepoint images onto independent nodes
• Let peer GPUs collaborate
• Desktops• Run alongside acquisition
• Embedded systems• Currently developing for TX1
Usable on All Tiers of GPUs
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970M
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