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Vignetting and photo-bleaching correction in automated fluorescence microscopy from an array of overlapping images

Filippo Piccinini, Alessandro Bevilacqua, Kevin Smith, Peter Horvath
2013 2013 IEEE 10th International Symposium on Biomedical Imaging  
We propose a novel acquisition scheme and non-parametric multi-image based method for correcting illumination in fluorescence images.  ...  The acquisition process and learning are performed prior to imaging, and take only a few minutes. Afterwards, images can be corrected for vignetting and photobleaching effects on the fly.  ...  Acknowledgments This work was supported in part by, the Swiss national initiative for Systems Biology, through the SyBIT project.  ... 
doi:10.1109/isbi.2013.6556512 dblp:conf/isbi/PiccininiBSH13 fatcat:egpvgl232jbkpktqqha3ijzane

Extended Field Laser Confocal Microscopy (EFLCM): Combining automated Gigapixel image capture with in silicovirtual microscopy

Emilie Flaberg, Per Sabelström, Christer Strandh, Laszlo Szekely
2008 BMC Medical Imaging  
Methods: Using the combination of microlens enhanced Nipkow spinning disc confocal illumination together with fully automated image capture and large scale in silico image processing we have developed  ...  Conclusion: The observer independent image capture of EFLCM allows quantitative measurements of fluorescence intensities and morphological parameters on a large number of cells.  ...  Acknowledgements This project was supported by grants from the Karolinska Institutet, Swedish Cancer Society (Cancerfonden), Swedish Research Council (Vetenskapsrådet) and from Cancer Research Institute  ... 
doi:10.1186/1471-2342-8-13 pmid:18627634 pmcid:PMC2515298 fatcat:rjj6yjtqjbgrpioxtuasz7wwem

Simultaneous imaging of neural activity in three dimensions

Sean Quirin, Jesse Jackson, Darcy S. Peterka, Rafael Yuste
2014 Frontiers in Neural Circuits  
Using a spatial light modulator and a custom-designed phase mask, we illuminate and collect light simultaneously from different focal planes and perform calcium imaging of neuronal activity in vitro and  ...  We introduce a scanless optical method to image neuronal activity in three dimensions simultaneously.  ...  This material is based upon work supported by, or in part by, the U.S. Army Research Laboratory and the U.S. Army Research Office under contract number W911NF-12-1-0594.  ... 
doi:10.3389/fncir.2014.00029 pmid:24772066 pmcid:PMC3982072 fatcat:n74blmyrlbbxhhh4yvtnc5pg24


Claudio Fiegna, Bevilacqua Alessandro, Mauro Co-Tutor, Ursino
2010 unpublished
In particular we proposed, for both light and fluorescent microscopy, non-parametric multi-image based methods, where the vignetting function is estimated directly from the sample without requiring any  ...  Starting from a set of overlapping images manually acquired, we validated a fast registration approach to accurately stitch together the images previously flatfield corrected.  ...  Horvath, Vignetting and photo-bleaching correction in automated fluorescence microscopy from an array of overlapping images. 10 th IEEE International Symposium on Biomedical Imaging (ISBI), San Francisco  ... 

Digital Imaging Of Biological Type Specimens. A Manual Of Best Practice. Results From A Study Of The European Network For Biodiversity Information

C.L. Häuser, A. Steiner, J. Holstein, M.J. Scoble
2005 Zenodo  
Department of the NHM have generously engaged in discussion concerning the imaging fish specimens -we have benefited greatly from these discussions.  ...  Specimen imaging by HAROLD TAYLOR, Photographic Unit, NHM. Acknowledgements We thank MAARTEN KAPELLE and TINDE VAN ANDEL for their role in NLBIF and funding of this project.  ...  Images taken with transmitted light microscopy sometimes suffer from vignetting or some shading of the background. This problem can be overcome easily with a technique used by S.  ... 
doi:10.5281/zenodo.163941 fatcat:ukeeraeyzngpzm62qjcdsnk2ta

Spaceborne laser instruments for high-resolution mapping

Anthony W. Yu, Michael A. Krainak, David J. Harding, James B. Abshire, Xiaoli Sun, Susan Valett, John Cavanaugh, Luis Ramos-Izquierdo, W. Andrew Clarkson, Norman Hodgson, Ramesh K. Shori
2010 Solid State Lasers XIX: Technology and Devices  
This We report on the results of an experimental and theoretical investigation of the relevant performance attributes of Yb:YAG thin disk gain elements for use in high brightness resonators.  ...  Use of the model for determining optimum configuration the edge pumping array is discussed. Simulations of thermal performance of the disk and the heat sink are also included.  ...  It can be used for nonlinear optical imaging using CARS, multi photon absorption and STED for high resolution microscopy.  ... 
doi:10.1117/12.843191 fatcat:6ouzsdkdknh63ordfsktdz3lqq

Optical Methods For Deep-Tissue Imaging, Precise Mapping Of Cellular Topography And Single-Molecule Stoichiometry Analysis

Avtar Singh
We begin with an investigation into the depth limit of two-photon microscopy and its dependence on tissue scattering.  ...  Fluorescence microscopy and spectroscopy have proven crucial to biological investigations because of their superior contrast, molecular specificity, gentle nature and diverse information content.  ...  Localization Microscopy (PALM) [148] and Fluorescence Photo-Activated Localization Microscopy (FPALM) [149] (Figure 1.4a,d).  ... 
doi:10.7298/x4sx6b5c fatcat:ho5inxkjhfef7jjqvisrfp2kky

Development of multidimensional fluorescence imaging technology with a view towards the imaging of signalling at the immunological synapse

Sunil Kumar, Paul French, Mark Neil
A comparison of the sectioning abilities of single point confocal and multiphoton microscopy with multipoint spinning disk based systems is made and a means of achieving an increased rate of imaging for  ...  The primary techniques used in this work are intensity imaging, ratiometric spectral fluorescence imaging and fluorescence lifetime imaging, which have been applied to live and fixed cells.  ...  One such example uses an array of microlenses to generate an array of points which is then imaged through some pinholes, then scanned onto the sample [149] .  ... 
doi:10.25560/5572 fatcat:7f3piae65vchzda5uvrug7d5la

Cellular Dynamics and Three-Dimensional Refractive Index Distribution Studied with Quantitative Phase Imaging

Nicolas Pavillon
imaging or electrophysiology.  ...  In this context, phase signal measurement can bring further insights in cellular dynamics studies, by bringing information which is classically not covered by standard investigation tools such as fluorescence  ...  These features distinguish DHM technology from for example fluorescence methods, as frame rate, photo-damage and bleaching are common issues in this case.  ... 
doi:10.5075/epfl-thesis-5100 fatcat:4pvdg4uwjrfgvgku6bs6xzbmpq

Hybrid organic/inorganic micro-pixellated light-emitting devices based on the optical pumping of organic polymer gain media

Diego Andersen, Donal Bradley, Paul Stavrinou, Engineering And Physical Sciences Research Council
State-of-the-art generations of inorganic light-emitting diodes are presented, along with an overview of the evolution of such devices over the years.  ...  A deviation of under 10 % from absorbance values calculated for the samples using a commercial spectrometer is shown.  ...  lower output powers that these devices have, which prevents biological samples from being photo-bleached as rapidly.  ... 
doi:10.25560/30919 fatcat:t7fdymlnqjhv7jimndampweide