Literature DB >> 19416072

Bioimage informatics for experimental biology.

Jason R Swedlow1, Ilya G Goldberg, Kevin W Eliceiri.   

Abstract

Over the past twenty years there have been great advances in light microscopy with the result that multidimensional imaging has driven a revolution in modern biology. The development of new approaches of data acquisition is reported frequently, and yet the significant data management and analysis challenges presented by these new complex datasets remain largely unsolved. As in the well-developed field of genome bioinformatics, central repositories are and will be key resources, but there is a critical need for informatics tools in individual laboratories to help manage, share, visualize, and analyze image data. In this article we present the recent efforts by the bioimage informatics community to tackle these challenges, and discuss our own vision for future development of bioimage informatics solutions.

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Mesh:

Year:  2009        PMID: 19416072      PMCID: PMC3522875          DOI: 10.1146/annurev.biophys.050708.133641

Source DB:  PubMed          Journal:  Annu Rev Biophys        ISSN: 1936-122X            Impact factor:   12.981


  23 in total

Review 1.  To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era.

Authors:  Paul D Andrews; Ian S Harper; Jason R Swedlow
Journal:  Traffic       Date:  2002-01       Impact factor: 6.215

2.  Informatics and quantitative analysis in biological imaging.

Authors:  Jason R Swedlow; Ilya Goldberg; Erik Brauner; Peter K Sorger
Journal:  Science       Date:  2003-04-04       Impact factor: 47.728

3.  High-throughput RNAi screening by time-lapse imaging of live human cells.

Authors:  Beate Neumann; Michael Held; Urban Liebel; Holger Erfle; Phill Rogers; Rainer Pepperkok; Jan Ellenberg
Journal:  Nat Methods       Date:  2006-05       Impact factor: 28.547

4.  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

5.  Automated learning of generative models for subcellular location: building blocks for systems biology.

Authors:  Ting Zhao; Robert F Murphy
Journal:  Cytometry A       Date:  2007-12       Impact factor: 4.355

6.  The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

Authors:  Ilya G Goldberg; Chris Allan; Jean-Marie Burel; Doug Creager; Andrea Falconi; Harry Hochheiser; Josiah Johnston; Jeff Mellen; Peter K Sorger; Jason R Swedlow
Journal:  Genome Biol       Date:  2005-05-03       Impact factor: 13.583

7.  The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data.

Authors:  Jules J Berman; Mary E Edgerton; Bruce A Friedman
Journal:  BMC Med Inform Decis Mak       Date:  2003-05-23       Impact factor: 2.796

8.  Open tools for storage and management of quantitative image data.

Authors:  Joshua Moore; Chris Allan; Jean-Marie Burel; Brian Loranger; Donald MacDonald; Jonathan Monk; Jason R Swedlow
Journal:  Methods Cell Biol       Date:  2008       Impact factor: 1.441

9.  WormBase 2007.

Authors:  Anthony Rogers; Igor Antoshechkin; Tamberlyn Bieri; Darin Blasiar; Carol Bastiani; Payan Canaran; Juancarlos Chan; Wen J Chen; Paul Davis; Jolene Fernandes; Tristan J Fiedler; Michael Han; Todd W Harris; Ranjana Kishore; Raymond Lee; Sheldon McKay; Hans-Michael Müller; Cecilia Nakamura; Philip Ozersky; Andrei Petcherski; Gary Schindelman; Erich M Schwarz; Will Spooner; Mary Ann Tuli; Kimberly Van Auken; Daniel Wang; Xiaodong Wang; Gary Williams; Karen Yook; Richard Durbin; Lincoln D Stein; John Spieth; Paul W Sternberg
Journal:  Nucleic Acids Res       Date:  2007-11-08       Impact factor: 16.971

10.  The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.

Authors:  Richard G Côté; Philip Jones; Lennart Martens; Rolf Apweiler; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2008-05-08       Impact factor: 16.971

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  42 in total

1.  Extensible visualization and analysis for multidimensional images using Vaa3D.

Authors:  Hanchuan Peng; Alessandro Bria; Zhi Zhou; Giulio Iannello; Fuhui Long
Journal:  Nat Protoc       Date:  2014-01-02       Impact factor: 13.491

Review 2.  Neuronal tracing for connectomic studies.

Authors:  Ju Lu
Journal:  Neuroinformatics       Date:  2011-09

3.  Histology image analysis for carcinoma detection and grading.

Authors:  Lei He; L Rodney Long; Sameer Antani; George R Thoma
Journal:  Comput Methods Programs Biomed       Date:  2012-03-20       Impact factor: 5.428

4.  Parsing Stem Cell Lineage Development Using High Content Image Analysis of Epigenetic Spatial Markers.

Authors:  Joseph J Kim; Prabhas V Moghe
Journal:  Curr Protoc Stem Cell Biol       Date:  2018-06-14

5.  Metadata matters: access to image data in the real world.

Authors:  Melissa Linkert; Curtis T Rueden; Chris Allan; Jean-Marie Burel; Will Moore; Andrew Patterson; Brian Loranger; Josh Moore; Carlos Neves; Donald Macdonald; Aleksandra Tarkowska; Caitlin Sticco; Emma Hill; Mike Rossner; Kevin W Eliceiri; Jason R Swedlow
Journal:  J Cell Biol       Date:  2010-05-31       Impact factor: 10.539

6.  Sds22 regulates aurora B activity and microtubule-kinetochore interactions at mitosis.

Authors:  Markus Posch; Guennadi A Khoudoli; Sam Swift; Emma M King; Jennifer G Deluca; Jason R Swedlow
Journal:  J Cell Biol       Date:  2010-10-04       Impact factor: 10.539

7.  Trait variability of cancer cells quantified by high-content automated microscopy of single cells.

Authors:  Vito Quaranta; Darren R Tyson; Shawn P Garbett; Brandy Weidow; Mark P Harris; Walter Georgescu
Journal:  Methods Enzymol       Date:  2009       Impact factor: 1.600

8.  PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO.

Authors:  Johnny Hay; Eilidh Troup; Ivan Clark; Julian Pietsch; Tomasz Zieliński; Andrew Millar
Journal:  Wellcome Open Res       Date:  2020-08-26

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.  PDBe: Protein Data Bank in Europe.

Authors:  S Velankar; C Best; B Beuth; C H Boutselakis; N Cobley; A W Sousa Da Silva; D Dimitropoulos; A Golovin; M Hirshberg; M John; E B Krissinel; R Newman; T Oldfield; A Pajon; C J Penkett; J Pineda-Castillo; G Sahni; S Sen; R Slowley; A Suarez-Uruena; J Swaminathan; G van Ginkel; W F Vranken; K Henrick; G J Kleywegt
Journal:  Nucleic Acids Res       Date:  2009-10-25       Impact factor: 16.971

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