Literature DB >> 25775044

CIDRE: an illumination-correction method for optical microscopy.

Kevin Smith1, Yunpeng Li2, Filippo Piccinini3, Gabor Csucs1, Csaba Balazs1, Alessandro Bevilacqua4, Peter Horvath5.   

Abstract

Uneven illumination affects every image acquired by a microscope. It is often overlooked, but it can introduce considerable bias to image measurements. The most reliable correction methods require special reference images, and retrospective alternatives do not fully model the correction process. Our approach overcomes these issues for most optical microscopy applications without the need for reference images.

Mesh：

Year:  2015        PMID： 25775044     DOI： 10.1038/nmeth.3323

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  10 in total

1.  Correction of uneven illumination (vignetting) in digital microscopy images.

Authors:  F J W-M Leong; M Brady; J O'D McGee
Journal:  J Clin Pathol       Date:  2003-08       Impact factor: 3.411

2.  Scanning fluorescent microscopy is an alternative for quantitative fluorescent cell analysis.

Authors:  Viktor Sebestyén Varga; József Bocsi; Ferenc Sipos; Gábor Csendes; Zsolt Tulassay; Béla Molnár
Journal:  Cytometry A       Date:  2004-07       Impact factor: 4.355

3.  Evaluation of three methods for retrospective correction of vignetting on medical microscopy images utilizing two open source software tools.

Authors:  Georgios Babaloukas; Nicholas Tentolouris; Stavros Liatis; Alexandra Sklavounou; Despoina Perrea
Journal:  J Microsc       Date:  2011-09-27       Impact factor: 1.758

Review 4.  Automated image analysis for high-content screening and analysis.

Authors:  Aabid Shariff; Joshua Kangas; Luis Pedro Coelho; Shannon Quinn; Robert F Murphy
Journal:  J Biomol Screen       Date:  2010-05-20

5.  Vignette and exposure calibration and compensation.

Authors:  Dan B Goldman
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  2010-12       Impact factor: 6.226

6.  Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins.

Authors:  Alex Sigal; Ron Milo; Ariel Cohen; Naama Geva-Zatorsky; Yael Klein; Inbal Alaluf; Naamah Swerdlin; Natalie Perzov; Tamar Danon; Yuvalal Liron; Tal Raveh; Anne E Carpenter; Galit Lahav; Uri Alon
Journal:  Nat Methods       Date:  2006-07       Impact factor: 28.547

7.  Efficient subpixel image registration algorithms.

Authors:  Manuel Guizar-Sicairos; Samuel T Thurman; James R Fienup
Journal:  Opt Lett       Date:  2008-01-15       Impact factor: 3.776

8.  Intensity calibration and flat-field correction for fluorescence microscopes.

Authors:  Michael Model
Journal:  Curr Protoc Cytom       Date:  2014-04-01

9.  Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening.

Authors:  Vebjorn Ljosa; Anne E Carpenter
Journal:  PLoS Comput Biol       Date:  2009-12-24       Impact factor: 4.475

10.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes.

Authors:  Anne E Carpenter; Thouis R Jones; Michael R Lamprecht; Colin Clarke; In Han Kang; Ola Friman; David A Guertin; Joo Han Chang; Robert A Lindquist; Jason Moffat; Polina Golland; David M Sabatini
Journal:  Genome Biol       Date:  2006-10-31       Impact factor: 13.583
  10 in total
  46 in total

1.  Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

Authors:  Ken Y Chan; Nicholas C Flytzanis; Bin Yang; Jennifer B Treweek; Benjamin E Deverman; Alon Greenbaum; Antti Lignell; Cheng Xiao; Long Cai; Mark S Ladinsky; Pamela J Bjorkman; Charless C Fowlkes; Viviana Gradinaru
Journal:  Nat Protoc       Date:  2015-10-22       Impact factor: 13.491

2.  Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition.

Authors:  Neha Daga; Simone Eicher; Abhilash Kannan; Alain Casanova; Shyan H Low; Saskia Kreibich; Daniel Andritschke; Mario Emmenlauer; Jeremy L Jenkins; Wolf-Dietrich Hardt; Urs F Greber; Christoph Dehio; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2018-10-12       Impact factor: 16.971

Review 3.  Machine learning applications in cell image analysis.

Authors:  Andrey Kan
Journal:  Immunol Cell Biol       Date:  2017-03-15       Impact factor: 5.126

4.  Long term morphological characterization of mesenchymal stromal cells 3D spheroids built with a rapid method based on entry-level equipment.

Authors:  Chiara Bellotti; Serena Duchi; Alessandro Bevilacqua; Enrico Lucarelli; Filippo Piccinini
Journal:  Cytotechnology       Date:  2016-03-29       Impact factor: 2.058

5.  Single-Cell Quantification of Protein Degradation Rates by Time-Lapse Fluorescence Microscopy in Adherent Cell Culture.

Authors:  Andrea Brigitta Alber; David Michael Suter
Journal:  J Vis Exp       Date:  2018-02-04       Impact factor: 1.355

6.  Expansion Microscopy of Larval Zebrafish Brains and Zebrafish Embryos.

Authors:  Ory Perelsman; Shoh Asano; Limor Freifeld
Journal:  Methods Mol Biol       Date:  2022

7.  Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins.

Authors:  Eviatar Natan; Tamaki Endoh; Liora Haim-Vilmovsky; Tilman Flock; Guilhem Chalancon; Jonathan T S Hopper; Bálint Kintses; Peter Horvath; Lejla Daruka; Gergely Fekete; Csaba Pál; Balázs Papp; Erika Oszi; Zoltán Magyar; Joseph A Marsh; Adrian H Elcock; M Madan Babu; Carol V Robinson; Naoki Sugimoto; Sarah A Teichmann
Journal:  Nat Struct Mol Biol       Date:  2018-02-12       Impact factor: 15.369

8.  Regression plane concept for analysing continuous cellular processes with machine learning.

Authors:  Abel Szkalisity; Filippo Piccinini; Attila Beleon; Tamas Balassa; Istvan Gergely Varga; Ede Migh; Csaba Molnar; Lassi Paavolainen; Sanna Timonen; Indranil Banerjee; Elina Ikonen; Yohei Yamauchi; Istvan Ando; Jaakko Peltonen; Vilja Pietiäinen; Viktor Honti; Peter Horvath
Journal:  Nat Commun       Date:  2021-05-05       Impact factor: 14.919

9.  Single-probe RNA FISH in Yeast.

Authors:  Gable M Wadsworth; Rasesh Y Parikh; Harold D Kim
Journal:  Bio Protoc       Date:  2018-06-05

10.  Dual-probe RNA FRET-FISH in Yeast.

Authors:  Gable M Wadsworth; Rasesh Y Parikh; Harold D Kim
Journal:  Bio Protoc       Date:  2018-06-05
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