Literature DB >> 20195255

Visualization of image data from cells to organisms.

Thomas Walter1, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanne Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider, Pavel Tomancak, Jean-Karim Hériché.   

Abstract

Advances in imaging techniques and high-throughput technologies are providing scientists with unprecedented possibilities to visualize internal structures of cells, organs and organisms and to collect systematic image data characterizing genes and proteins on a large scale. To make the best use of these increasingly complex and large image data resources, the scientific community must be provided with methods to query, analyze and crosslink these resources to give an intuitive visual representation of the data. This review gives an overview of existing methods and tools for this purpose and highlights some of their limitations and challenges.

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Year:  2010        PMID: 20195255      PMCID: PMC3650473          DOI: 10.1038/nmeth.1431

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


  75 in total

1.  High angular resolution diffusion imaging reveals intravoxel white matter fiber heterogeneity.

Authors:  David S Tuch; Timothy G Reese; Mette R Wiegell; Nikos Makris; John W Belliveau; Van J Wedeen
Journal:  Magn Reson Med       Date:  2002-10       Impact factor: 4.668

2.  Optical sectioning deep inside live embryos by selective plane illumination microscopy.

Authors:  Jan Huisken; Jim Swoger; Filippo Del Bene; Joachim Wittbrodt; Ernst H K Stelzer
Journal:  Science       Date:  2004-08-13       Impact factor: 47.728

Review 3.  Deep tissue two-photon microscopy.

Authors:  Fritjof Helmchen; Winfried Denk
Journal:  Nat Methods       Date:  2005-12       Impact factor: 28.547

4.  Analysis of functional image analysis contest (FIAC) data with brainvoyager QX: From single-subject to cortically aligned group general linear model analysis and self-organizing group independent component analysis.

Authors:  Rainer Goebel; Fabrizio Esposito; Elia Formisano
Journal:  Hum Brain Mapp       Date:  2006-05       Impact factor: 5.038

5.  Genome-wide atlas of gene expression in the adult mouse brain.

Authors:  Ed S Lein; Michael J Hawrylycz; Nancy Ao; Mikael Ayres; Amy Bensinger; Amy Bernard; Andrew F Boe; Mark S Boguski; Kevin S Brockway; Emi J Byrnes; Lin Chen; Li Chen; Tsuey-Ming Chen; Mei Chi Chin; Jimmy Chong; Brian E Crook; Aneta Czaplinska; Chinh N Dang; Suvro Datta; Nick R Dee; Aimee L Desaki; Tsega Desta; Ellen Diep; Tim A Dolbeare; Matthew J Donelan; Hong-Wei Dong; Jennifer G Dougherty; Ben J Duncan; Amanda J Ebbert; Gregor Eichele; Lili K Estin; Casey Faber; Benjamin A Facer; Rick Fields; Shanna R Fischer; Tim P Fliss; Cliff Frensley; Sabrina N Gates; Katie J Glattfelder; Kevin R Halverson; Matthew R Hart; John G Hohmann; Maureen P Howell; Darren P Jeung; Rebecca A Johnson; Patrick T Karr; Reena Kawal; Jolene M Kidney; Rachel H Knapik; Chihchau L Kuan; James H Lake; Annabel R Laramee; Kirk D Larsen; Christopher Lau; Tracy A Lemon; Agnes J Liang; Ying Liu; Lon T Luong; Jesse Michaels; Judith J Morgan; Rebecca J Morgan; Marty T Mortrud; Nerick F Mosqueda; Lydia L Ng; Randy Ng; Geralyn J Orta; Caroline C Overly; Tu H Pak; Sheana E Parry; Sayan D Pathak; Owen C Pearson; Ralph B Puchalski; Zackery L Riley; Hannah R Rockett; Stephen A Rowland; Joshua J Royall; Marcos J Ruiz; Nadia R Sarno; Katherine Schaffnit; Nadiya V Shapovalova; Taz Sivisay; Clifford R Slaughterbeck; Simon C Smith; Kimberly A Smith; Bryan I Smith; Andy J Sodt; Nick N Stewart; Kenda-Ruth Stumpf; Susan M Sunkin; Madhavi Sutram; Angelene Tam; Carey D Teemer; Christina Thaller; Carol L Thompson; Lee R Varnam; Axel Visel; Ray M Whitlock; Paul E Wohnoutka; Crissa K Wolkey; Victoria Y Wong; Matthew Wood; Murat B Yaylaoglu; Rob C Young; Brian L Youngstrom; Xu Feng Yuan; Bin Zhang; Theresa A Zwingman; Allan R Jones
Journal:  Nature       Date:  2006-12-06       Impact factor: 49.962

6.  Spiny versus stubby: 3D reconstruction of human myenteric (type I) neurons.

Authors:  Tobias M Lindig; Vinod Kumar; Ron Kikinis; Steve Pieper; Falk Schrödl; Winfried L Neuhuber; Axel Brehmer
Journal:  Histochem Cell Biol       Date:  2008-09-20       Impact factor: 4.304

7.  Actin-like protein 1 (ALP1) is a component of dynamic, high molecular weight complexes in Toxoplasma gondii.

Authors:  Jennifer L Gordon; Jeffrey S Buguliskis; Paul J Buske; L David Sibley
Journal:  Cytoskeleton (Hoboken)       Date:  2010-01

8.  A database for mouse development.

Authors:  M Ringwald; R Baldock; J Bard; M Kaufman; J T Eppig; J E Richardson; J H Nadeau; D Davidson
Journal:  Science       Date:  1994-09-30       Impact factor: 47.728

9.  The Neuroterrain 3D Mouse Brain Atlas.

Authors:  Louise Bertrand; Jonathan Nissanov
Journal:  Front Neuroinform       Date:  2008-07-19       Impact factor: 4.081

10.  Global analysis of patterns of gene expression during Drosophila embryogenesis.

Authors:  Pavel Tomancak; Benjamin P Berman; Amy Beaton; Richard Weiszmann; Elaine Kwan; Volker Hartenstein; Susan E Celniker; Gerald M Rubin
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

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  96 in total

1.  In vivo magnetic resonance imaging of ferritin-based reporter visualizes native neuroblast migration.

Authors:  Bistra Iordanova; Eric T Ahrens
Journal:  Neuroimage       Date:  2011-09-13       Impact factor: 6.556

2.  Three-dimensional image quantification as a new morphometry method for tissue engineering.

Authors:  Julie A Rytlewski; Laura R Geuss; Chinedu I Anyaeji; Evan W Lewis; Laura J Suggs
Journal:  Tissue Eng Part C Methods       Date:  2012-02-17       Impact factor: 3.056

3.  BioImageXD: an open, general-purpose and high-throughput image-processing platform.

Authors:  Pasi Kankaanpää; Lassi Paavolainen; Silja Tiitta; Mikko Karjalainen; Joacim Päivärinne; Jonna Nieminen; Varpu Marjomäki; Jyrki Heino; Daniel J White
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

4.  3D Slicer as an image computing platform for the Quantitative Imaging Network.

Authors:  Andriy Fedorov; Reinhard Beichel; Jayashree Kalpathy-Cramer; Julien Finet; Jean-Christophe Fillion-Robin; Sonia Pujol; Christian Bauer; Dominique Jennings; Fiona Fennessy; Milan Sonka; John Buatti; Stephen Aylward; James V Miller; Steve Pieper; Ron Kikinis
Journal:  Magn Reson Imaging       Date:  2012-07-06       Impact factor: 2.546

Review 5.  Multiscale imaging and computational modeling of blood flow in the tumor vasculature.

Authors:  Eugene Kim; Spyros Stamatelos; Jana Cebulla; Zaver M Bhujwalla; Aleksander S Popel; Arvind P Pathak
Journal:  Ann Biomed Eng       Date:  2012-05-08       Impact factor: 3.934

Review 6.  Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

Authors:  David W Knowles; Mark D Biggin
Journal:  Wiley Interdiscip Rev Dev Biol       Date:  2013-02-04       Impact factor: 5.814

7.  Visualizing biological data-now and in the future.

Authors:  Seán I O'Donoghue; Anne-Claude Gavin; Nils Gehlenborg; David S Goodsell; Jean-Karim Hériché; Cydney B Nielsen; Chris North; Arthur J Olson; James B Procter; David W Shattuck; Thomas Walter; Bang Wong
Journal:  Nat Methods       Date:  2010-03       Impact factor: 28.547

Review 8.  Visualization of omics data for systems biology.

Authors:  Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Journal:  Nat Methods       Date:  2010-03       Impact factor: 28.547

Review 9.  Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts.

Authors:  John A Calarco; Mei Zhen; Benjamin J Blencowe
Journal:  RNA       Date:  2011-03-17       Impact factor: 4.942

Review 10.  Understanding paternal genome demethylation through live-cell imaging and siRNA.

Authors:  Kazuo Yamagata; Yuki Okada
Journal:  Cell Mol Life Sci       Date:  2011-01-15       Impact factor: 9.261

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