Metadata matters: access to image data in the real world
Melissa Linkert,Curtis Rueden,Chris Allan,Jean-Marie Burel,William J. Moore,Andrew J. Patterson,Brian Loranger,Josh Moore,Carlos H. Neves,Donald MacDonald,Aleksandra Tarkowska,J Caitlin Sticco,Emma Hill,Mike Rossner,Kevin W. Eliceiri,Jason R. Swedlow +15 more
TLDR
An open standard format for multidimensional microscopy image data is described and it is called on the community to use open image data standards and to insist that all imaging platforms support these file formats.Abstract:
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 multidimensional 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.read more
Citations
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Diversity in Starvation Survival Strategies and Outcomes among Heterotrophic Proteobacteria.
TL;DR: In this paper, the authors focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity.
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Serotonin Signals Overcome Loser Mentality in Drosophila.
TL;DR: It is reported that elevated serotonin (5-HT) signaling helps a loser to overcome suppressive neurological states and demonstrate an ancient neural mechanism of regulating depressive behavioral states after distressing events.
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Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages.
Andreas Dander,Matthias Baldauf,Michael Sperk,Stephan Pabinger,Stephan Pabinger,Benjamin Hiltpolt,Zlatko Trajanoski +6 more
TL;DR: A bioinformatics platform – Personalized Oncology Suite (POS) – that integrates clinical data, NGS data and whole-slide bioimages from tissue sections and provides different visualization techniques and offers sophisticated upload and download possibilities.
Journal ArticleDOI
Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned
Gerald Li,Peter Bankhead,Philip D Dunne,Paul G. O’Reilly,Jacqueline James,Manuel Salto-Tellez,Peter W. Hamilton,Darragh G. McArt +7 more
TL;DR: The essential elements of assembling an integromics framework from a more detailed perspective are explored and it is stressed thatIntegromics is not just a set of tools, but rather a cohesive paradigm for how modern bioinformatics can be enhanced.
Journal ArticleDOI
GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
Anne Trinh,Inga H. Rye,Vanessa Almendro,Åslaug Helland,Åslaug Helland,Hege G. Russnes,Hege G. Russnes,Florian Markowetz +7 more
TL;DR: GoIFISH is a widely applicable, user-friendly system tailored for the objective and semi-automated visualization, detection and quantification of genomic alterations and protein expression obtained from fluorescence in situ analysis.
References
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Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function
Eric Lécuyer,Hideki Yoshida,Neela Parthasarathy,Christina Alm,Tomas Babak,Tanja Cerovina,Timothy P. Hughes,Pavel Tomancak,Henry M. Krause +8 more
TL;DR: A high-resolution fluorescent in situ hybridization procedure was developed and employed to comprehensively evaluate mRNA localization dynamics during early Drosophila embryogenesis, indicating major roles for mRNA localization in nucleating localized cellular machineries.
Journal ArticleDOI
Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans
Birte Sönnichsen,Liisa Koski,Andrew Walsh,P. Marschall,Beate Neumann,M. Brehm,Anne-Marie Alleaume,J. Artelt,Paulo Bettencourt,Etienne Cassin,M. Hewitson,C. Holz,Moddasar N. Khan,S. Lazik,Charles E. Martin,Björn Nitzsche,Martine Ruer,Joanne Stamford,Maria Winzi,R. Heinkel,Marion S. Röder,J. Finell,H. Häntsch,Steven J.M. Jones,Martin R. Jones,Martin R. Jones,Fabio Piano,Kristin C. Gunsalus,Karen Oegema,Pierre Gönczy,Pierre Gönczy,Alan Coulson,Alan Coulson,Anthony A. Hyman,Christophe Echeverri +34 more
TL;DR: This work used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy and developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling to predict new functions for previously uncharacterized genes.
Journal ArticleDOI
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
Beate Neumann,Thomas Walter,Jean-Karim Hériché,Jutta Bulkescher,Holger Erfle,Christian Conrad,Phill Rogers,Ina Poser,Michael Held,Urban Liebel,Cihan Cetin,Frank Sieckmann,Gregoire Pau,Rolf Kabbe,Annelie Wünsche,Venkata P. Satagopam,Michael H.A. Schmitz,Catherine Chapuis,Daniel W. Gerlich,Reinhard Schneider,Roland Eils,Wolfgang Huber,Jan-Michael Peters,Anthony A. Hyman,Richard Durbin,Rainer Pepperkok,Jan Ellenberg +26 more
TL;DR: This study carried out a genome-wide phenotypic profiling of each of the ∼21,000 human protein-coding genes by two-day live imaging of fluorescently labelled chromosomes, which allowed us to identify hundreds of human genes involved in diverse biological functions including cell division, migration and survival.
Journal ArticleDOI
The Zebrafish Information Network: the zebrafish model organism database
Judy Sprague,Leyla Bayraktaroglu,Dave Clements,Tom Conlin,David Fashena,Ken Frazer,Melissa A. Haendel,Douglas G. Howe,Prita Mani,Sridhar Ramachandran,Kevin Schaper,Erik Segerdell,Peiran Song,Brock Sprunger,Sierra Taylor,Ceri E. Van Slyke,Monte Westerfield +16 more
TL;DR: The Zebrafish Information Network (ZFIN) provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community resources such as meeting announcements and contact information.
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