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Variational attenuation correction in two-view confocal microscopy

Thorsten Schmidt, Jasmin Dürr, Margret Keuper, Thomas Blein, Klaus Palme, Olaf Ronneberger
2013 BMC Bioinformatics  
Results: We present a variational approach to estimate both, the real intensities and the spatially variant attenuation from two views of the same sample from opposite sides.  ...  Absorption and refraction induced signal attenuation can seriously hinder the extraction of quantitative information from confocal microscopic data.  ...  We thank Meta Rath, Alida Fillipi and Wolfgang Driever for providing the zebrafish recordings.  ... 
doi:10.1186/1471-2105-14-366 pmid:24350574 pmcid:PMC3878336 fatcat:rxkuwe2ik5c6ph5u5jpa2o5fha

Attenuation correction in confocal laser microscopes: a novel two-view approach

A. Can, O. Al-Kofahi, S. Lasek, D. H. Szarowski, J. N. Turner, B. Roysam
2003 Journal of Microscopy  
We present a practical two-view method that increases the overall imaging depth, corrects signal attenuation and improves the SNR.  ...  The SNR of the reconstructed image is maximized by the method, and it is significantly higher than in the single views after applying our attenuation model.  ...  Acknowledgements This work was supported in part by CenSSIS, the Center for Subsurface Sensing and Imaging Systems, under the Engineering Research Centers Program of the National Science Foundation (Award  ... 
doi:10.1046/j.1365-2818.2003.01195.x pmid:12839553 fatcat:sn7zac46nrexvm4yswly7d7zge

Aberration control in quantitative imaging of botanical specimens by multidimensional fluorescence microscopy

N. S. WHITE, R. J. ERRINGTON, M. D. FRICKER, J. L. WOOD
1996 Journal of Microscopy  
Three dimensional (3-D) fluorescence microscopes, including conventional instruments with digital deblurring, confocal systems and two-photon excitation, all exhibit monochromatic and chromatic aberrations  ...  Improved images of the 3-D morphology of stomatal guard cells are then obtained by digital correction of attenuation and spatial distortion.  ...  Acknowledgments N.S.W. thanks the Department of Plant Sciences, Oxford, for support and is now a Royal Society Industry Fellow. R.J.E. is supported by the Wellcome Trust.  ... 
doi:10.1046/j.1365-2818.1996.113392.x fatcat:ibzwm2q5abfkljpwbo4a4hr5fq

Description and Performance of a Fiber-Optic Confocal Fluorescence Spectrometer

Rebecca Richards-Kortum, Anthony Durkin, Jing Zeng
1994 Applied Spectroscopy  
We describe a fiber-optic-based confocal fluorescence spectrometer for obtaining depth-resolved, attenuated fluorescence emission spectra with lateral resolution of several microns and depth resolution  ...  The confocal optics of the spectrometer are small, inexpensive, and easy to construct and to interface to existing spectrometers.  ...  Although spectrometers based on confocal microscopes provide measurements of depth-resolved attenuated fluorescence, confocal microscopes are large and relatively expensive, making potential in vivo use  ... 
doi:10.1366/0003702944028227 fatcat:3m23bkz6jbdubiscocl6g66yxi

Optical properties of mutant versus wild-type mouse skin measured by reflectance-mode confocal scanning laser microscopy (rCSLM)

Ravikant Samatham, Steven L. Jacques, Paul Campagnola
2008 Journal of Biomedical Optics  
Separation of the two optical scattering properties, the scattering coefficient ͑ s ͒ and the anisotropy of scattering ͑g͒, has been experimentally difficult in tissues.  ...  The measured data is the exponential decay of the confocal reflectance signal as a function of the depth of the focal volume, R͑z͒ = exp͑−z͒, summarized as a local reflectivity ͑͒ and an exponential decay  ...  In summary, the and for the reticular dermis were determined after correcting for the average attenuation of the overlying epidermis and papillary dermis. 3 ͑a͒ As the focus of the microscope is scanned  ... 
doi:10.1117/1.2953195 pmid:19021317 fatcat:u2krqxizjbb75aulta2wp47upe

Computational confocal tomography for simultaneous reconstruction of objects, occlusions, and aberrations

Keith Dillon, Yeshaiahu Fainman
2010 Applied Optics  
We also show how these image parameters may be combined with the conventional confocal image reconstruction of the object reflectivity.  ...  We show how this method may be used to tomographically reconstruct attenuation, aberration, and even occlusion.  ...  We are thankful to Fabio Bonomelli and Lin Pang for helping in the assembly and operation of the experiments performed in this research.  ... 
doi:10.1364/ao.49.002529 fatcat:zq65fjim3neetar3l2peelyvvy

Correction of artefacts in optical projection tomography

Johnathon R Walls, John G Sled, James Sharpe, R Mark Henkelman
2005 Physics in Medicine and Biology  
This solution also provides OPT with the ability to obtain a high-resolution reconstruction from a region of interest of a specimen that is larger than the field of view.  ...  Implementation of these corrections and modifications increases the accuracy of the OPT imaging technique and extends its capabilities to obtain higher resolution data from within a whole specimen.  ...  The magnification of the microscope was then reduced to 1.25×, and an eOPT scan of the complete specimen was recorded.  ... 
doi:10.1088/0031-9155/50/19/015 pmid:16177495 fatcat:7efq2i54ojcptcng4sfu7sipsm

Image Enhancement by Deconvolution [chapter]

Mark B. Cannell, Angus McMorland, Christian Soeller
2006 Handbook Of Biological Confocal Microscopy  
rays must originate in the finite field of view of the microscope.  ...  (It is the reduction of this effect by confocal microscopes that makes them so useful.)  ... 
doi:10.1007/978-0-387-45524-2_25 fatcat:v2e6wbhkufaufgz3wbpceu7vpi

Wavelength considerations in confocal microscopy of botanical specimens

M. D. Fricker, N. S. White
1992 Journal of Microscopy  
Chromatic corrections are more important in confocal microscope optics than in conventional microscopy.  ...  S U M M A R Y We have used a multiple-laser confocal microscope with lines at 325,442, 488, 514 and 633 nm to investigate optical sectioning of botanical specimens over a wide range of wavelengths.  ...  Chromatic corrections are more important in confocal microscope optics than in conventional microscopy.  ... 
doi:10.1111/j.1365-2818.1992.tb01505.x fatcat:f6efpiiujzdjxkhen55pobd4yy

Anti-confocal assessment of middle ear inflammation

David S. Jung, John A. Crowe, John P. Birchall, Michael G. Somekh, Chung W. See
2016 Biomedical Optics Express  
Confocal detection of eardrum properties was shown to be a promising approach to correct measurements.  ...  To improve the diagnostic prediction of recurrence of otitis media with effusion after surgery, an anti-confocal system combined with spectroscopic measurements is proposed to reject unwanted signals from  ...  The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research or the Department of Health. We thank Prof.  ... 
doi:10.1364/boe.8.000230 pmid:28101414 pmcid:PMC5231295 fatcat:zelw2s7ufbak7j66t5lyhsrwk4

Methods for Imaging Thick Specimens: Confocal Microscopy, Deconvolution, and Structured Illumination

John M. Murray
2011 Cold Spring Harbor Protocols  
When a thick specimen is viewed through a conventional microscope, one sees the sum of a sharp image of an in-focus region plus blurred images of all of the out-of-focus regions.  ...  ., confocal microscopy, multiphoton microscopy), primarily computational (e.g., deconvolution techniques), and mixed (e.g., structured illumination) approaches.  ...  ., completely "unstructured") across the entire field of view, so that variations in intensity across the image arise solely from variations in the structure of the object.  ... 
doi:10.1101/pdb.top066936 pmid:22135661 fatcat:q4bmpe76v5f3xmax2ahh5e3z7y

Waveform-Based Analysis of Acoustic Emission from Fiber Fracture in Model Composite Plates [chapter]

T. Bidlingmaier, A. Wanner, S. Ritter
1998 Review of Progress in Quantitative Nondestructive Evaluation  
EXPERIMENTAL 400 ~m thick tensile specimens with the two different geometries shown in Figs. 5 and 7 were fabricated using polycarbonate (Bayer AG, PC32OO) as the matrix material and E-glass fibers of  ...  Details of specimen  ...  ACKNOWLEDGEMENTS We gratefully acknowledge funding of our work by the Deutsche Forschungsgemeinschaft (DFG), projects SFB 3811Al and SFB 3811B1.  ... 
doi:10.1007/978-1-4615-5339-7_67 fatcat:mcarhbe45neapgqqqmbjjive3m

Computational adaptive optics for live three-dimensional biological imaging

Z. Kam, B. Hanser, M. G. L. Gustafsson, D. A. Agard, J. W. Sedat
2001 Proceedings of the National Academy of Sciences of the United States of America  
Light microscopy of thick biological samples, such as tissues, is often limited by aberrations caused by refractive index variations within the sample itself.  ...  This problem is particularly severe for live imaging, a field of great current excitement due to the development of inherently fluorescent proteins.  ...  For viewing purposes, the in-focus image is 30 times attenuated with respect to the out-of-focus images shown (unaberrated cases would have 300 times the corresponding attenuation).  ... 
doi:10.1073/pnas.071275698 pmid:11274396 pmcid:PMC31131 fatcat:ozoccbpmgva63da7j5ng5udpve

Nontranslational three-dimensional profilometry by chromatic confocal microscopy with dynamically configurable micromirror scanning

Sungdo Cha, Paul C. Lin, Lijun Zhu, Pang-Chen Sun, Yeshaiahu Fainman
2000 Applied Optics  
The total longitudinal field of view is 26.4 m for a wavelength tuning range of 48.3 nm. The FWHM value of the longitudinal point-spread function is measured to be 0.99 m.  ...  A confocal microscope profilometer, which incorporates chromatic depth scanning with a diffractive optical element and a digital micromirror device for configurable transverse scanning, provides threedimensional  ...  A confocal microscope works by geometrically matching two conjugate focal points in image space. 6 When the two points, a point source and a point detector, are well matched, satisfying the confocal  ... 
doi:10.1364/ao.39.002605 pmid:18345178 fatcat:l2h5ycevnrhqfniqpprraupw3m

Image heterogeneity correction in large-area, three-dimensional multiphoton microscopy

Vladimir A. Hovhannisyan, Ping-Jung Su, Yang-Fang Chen, Chen Y. Dong
2008 Optics Express  
The method consists of multiplying the measured nonlinear signal by a three-dimensional correction factor, determined by the use of twophoton images of the appropriate specimens and specimen absorption  ...  The proposed methodology is demonstrated in correcting multiphoton images of objects imbedded in uniform fluorescent background, lung tissue, and Drosophila larva.  ...  Core Facility (A5) of NRPGM.  ... 
doi:10.1364/oe.16.005107 pmid:18542610 fatcat:kyonlw54ajebvdu5po4izozquu
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