Metadata matters: access to image data in the real world

被引：644

作者：

Linkert, Melissa ^{[1
,2
,4
]}

Rueden, Curtis T. ^{[1
,2
]}

Allan, Chris ^{[3
,4
]}

Burel, Jean-Marie ^{[3
]}

Moore, Will ^{[3
]}

Patterson, Andrew ^{[3
]}

Loranger, Brian ^{[3
]}

Moore, Josh ^{[4
]}

Neves, Carlos ^{[4
]}

MacDonald, Donald ^{[3
]}

Tarkowska, Aleksandra ^{[3
]}

Sticco, Caitlin ^{[1
,2
]}

Hill, Emma ^{[5
]}

Rossner, Mike ^{[5
]}

Eliceiri, Kevin W. ^{[1
,2
]}

Swedlow, Jason R. ^{[3
,4
]}

机构：

[1] Univ Wisconsin, Grad Sch, Dept Mol Biol, Lab Opt & Computat Instrumentat, Madison, WI 53711 USA

[2] Univ Wisconsin, Grad Sch, Dept Biomed Engn, Madison, WI 53711 USA

[3] Univ Dundee, Coll Life Sci, Wellcome Trust Ctr Gene Regulat & Express, Dundee DD1 5EH, Scotland

[4] Glencoe Software Inc, Seattle, WA 98101 USA

[5] Rockefeller Univ Press, New York, NY 10065 USA

来源：

JOURNAL OF CELL BIOLOGY | 2010年 / 189卷 / 05期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

QUANTITATIVE-ANALYSIS; INFORMATICS; REVEALS; GENOME; TOOLS; MODEL;

D O I：

10.1083/jcb.201004104

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

Data sharing is important in the biological sciences to prevent duplication of effort, to promote scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires centralized repositories, and submission to and utility of these resources require common data formats. This is particularly challenging for multi-dimensional microscopy image data, which are acquired from a variety of platforms with a myriad of proprietary file formats (PFFs). In this paper, we describe an open standard format that we have developed for microscopy image data. We call on the community to use open image data standards and to insist that all imaging platforms support these file formats. This will build the foundation for an open image data repository.

引用

页码：777 / 782

页数：6

共 19 条

[11] Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes [J].

Neumann, Beate ;

Walter, Thomas ;

Heriche, Jean-Karim ;

Bulkescher, Jutta ;

Erfle, Holger ;

Conrad, Christian ;

Rogers, Phill ;

Poser, Ina ;

Held, Michael ;

Liebel, Urban ;

Cetin, Cihan ;

Sieckmann, Frank ;

Pau, Gregoire ;

Kabbe, Rolf ;

Wuensche, Annelie ;

Satagopam, Venkata ;

Schmitz, Michael H. A. ;

Chapuis, Catherine ;

Gerlich, Daniel W. ;

Schneider, Reinhard ;

Eils, Roland ;

Huber, Wolfgang ;

Peters, Jan-Michael ;

Hyman, Anthony A. ;

Durbin, Richard ;

Pepperkok, Rainer ;

Ellenberg, Jan .

NATURE, 2010, 464 (7289) :721-727

[12] In vivo analysis of Cajal body movement, separation, and joining in live human cells [J].

Platani, M ;

Goldberg, I ;

Swedlow, JR ;

Lamond, AI .

JOURNAL OF CELL BIOLOGY, 2000, 151 (07) :1561-1574

[13] Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models [J].

Qian, Yuntao ;

Murphy, Robert F. .

BIOINFORMATICS, 2008, 24 (04) :569-576

[14] The Yeast Resource Center Public Data Repository [J].

Riffle, M ;

Malmström, L ;

Davis, TN .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D378-D382

[15] Post-publication sharing of data and tools [J].

Schofield, Paul N. ;

Bubela, Tania ;

Weaver, Thomas ;

Brown, Stephen D. ;

Hancock, John M. ;

Einhorn, David ;

Tocchini-Valentini, Glauco ;

de Angelis, Martin Hrabe ;

Rosenthal, Nadia .

NATURE, 2009, 461 (7261) :171-173

[16] Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans [J].

Sönnichsen, B ;

Koski, LB ;

Walsh, A ;

Marschall, P ;

Neumann, B ;

Brehm, M ;

Alleaume, AM ;

Artelt, J ;

Bettencourt, P ;

Cassin, E ;

Hewitson, M ;

Holz, C ;

Khan, M ;

Lazik, S ;

Martin, C ;

Nitzsche, B ;

Ruer, M ;

Stamford, J ;

Winzi, M ;

Heinkel, R ;

Röder, M ;

Finell, J ;

Häntsch, H ;

Jones, SJM ;

Jones, M ;

Piano, F ;

Gunsalus, KC ;

Oegema, K ;

Gönczy, P ;

Coulson, A ;

Hyman, AA ;

Echeverri, CJ .

NATURE, 2005, 434 (7032) :462-469

[17] The Zebrafish Information Network: the zebrafish model organism database [J].

Sprague, Judy ;

Bayraktaroglu, Leyla ;

Clements, Dave ;

Conlin, Tom ;

Fashena, David ;

Frazer, Ken ;

Haendel, Melissa ;

Howe, Douglas G. ;

Mani, Prita ;

Ramachandran, Sridhar ;

Schaper, Kevin ;

Segerdell, Erik ;

Song, Peiran ;

Sprunger, Brock ;

Taylor, Sierra ;

Van Slyke, Ceri E. ;

Westerfield, Monte .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D581-D585

[18] Bioimage Informatics for Experimental Biology [J].

Swedlow, Jason R. ;

Goldberg, Ilya G. ;

Eliceiri, Kevin W. .

ANNUAL REVIEW OF BIOPHYSICS, 2009, 38 :327-346

[19] Informatics and quantitative analysis in biological Imaging [J].

Swedlow, JR ;

Goldberg, I ;

Brauner, E ;

Sorger, PK .

SCIENCE, 2003, 300 (5616) :100-102

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