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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Book ChapterDOI
Automated Analysis of Intracellular Dynamic Processes.
TL;DR: Two key tasks in extracting biologically meaningful information about intracellular dynamics from image data are particle tracking and particle trajectory analysis are presented and state-of-the-art software tools are presented.
Multiscale activity imaging in mammary gland reveals how oxytocin enables lactation
Alexander J. Stevenson,Gilles Vanwalleghem,Teneale A. Stewart,Nicholas D. Condon,Bethan Lloyd-Lewis,Natascia Marino,James W. Putney,Ethan K. Scott,Adam D. Ewing,Felicity M. Davis +9 more
TL;DR: The spatiotemporal properties of physiological signals that orchestrate milk ejection are unveiled and it is demonstrated that individual oscillators can be electrically coupled to achieve global synchrony, a phenomenon that has not yet been observed in the mammary gland.
Journal ArticleDOI
A Synthetic Lethal Screen Identifies a Role for Lin-44/Wnt in C. elegans Embryogenesis.
TL;DR: The SynLet phenotype provides a robust platform to identify ptp-3 and sdn-1 interacting genes, as well as other genes that function in development, yet might be missed in traditional forward genetic screens.
Proceedings ArticleDOI
Cyberinfrastructure of a Multi-Petabyte Microscopy Resource for Neuroscience Research
Kathy Benninger,Greg Hood,Derek Simmel,Luke Tuite,Arthur W. Wetzel,Alexander J. Ropelewski,Simon C. Watkins,Alan M. Watson,Marcel P. Bruchez +8 more
TL;DR: The Brain Image Library (BIL) serves the neuroscience community by providing a persistent repository for the massive amounts of data being generated and by offering brain researchers supercomputing-class processing and visualization capabilities for working with high-resolution brain image datasets.
Posted ContentDOI
Transport of Alzheimer’s Associated Amyloid-β Catalyzed by P-glycoprotein
TL;DR: This work uses molecular dynamics simulations, transport substrate accumulation studies in cell culture, and biochemical activity assays to show that P-gp actively transports Aβ, and expands the substrate profile of P-GP, and suggests that it may contribute to the onset and progression of AD.
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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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