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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Proceedings ArticleDOI
OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale
Josh Moore,Melissa Linkert,Colin Blackburn,Mark Carroll,Richard K. Ferguson,Helen Flynn,Kenneth Gillen,Roger Leigh,Simon Li,Dominik Lindner,William J. Moore,Andrew J. Patterson,Blazej Pindelski,B. Ramalingam,E. Rozbicki,Aleksandra Tarkowska,Petr Walczysko,Chris Allan,Jean-Marie Burel,Jason R. Swedlow +19 more
TL;DR: New versions of Bio-Formats and OMERO are described that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research.
Book ChapterDOI
Correlative two-photon and serial block face scanning electron microscopy in neuronal tissue using 3D near-infrared branding maps.
TL;DR: Here, near-infrared branding (NIRB) overcomes this by using the laser from a multiphoton microscope to create fiducial markers for accurate correlation of 2P and electron microscopy (EM) imaging volumes.
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Vps13-like proteins provide phosphatidylethanolamine for GPI anchor synthesis in the ER
Alexandre Toulmay,Fawn B. Whittle,Jerry Yang,Xiaofei Bai,Jessica Diarra,Subhrajit Banerjee,Tim P. Levine,Andy Golden,William A. Prinz +8 more
TL;DR: Glycosylphosphatidylinositol anchors attach many proteins to the extracellular surface of the plasma membrane and tubelike lipid transport proteins bring PE to the ER to support GPI anchor production.
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Imaging the future: the emerging era of single-cell spatial proteomics
TL;DR: In this article, the authors introduce diverse platform technologies developed for subcellular proteomics and high-throughput systems biology, with the aim of providing mechanistic insights into fundamental cell biological processes underlying healthy and diseased states, and valuable public data resources.
Journal ArticleDOI
Deep learning for automatic segmentation of the nuclear envelope in electron microscopy data, trained with volunteer segmentations.
Helen Spiers,Helen Spiers,Harry Songhurst,Harry Songhurst,Luke Nightingale,Joost de Folter,Zooniverse Volunteer Community,Roger Hutchings,Christopher J. Peddie,Anne Weston,Amy Strange,Steve Hindmarsh,Chris Lintott,Chris Lintott,Lucy M. Collinson,Martin L. Jones +15 more
TL;DR: Etch a Cell as mentioned in this paper is a citizen science project to enable volunteers to manually segment the nuclear envelope (NE) of HeLa cells imaged with serial blockface scanning electron microscopy.
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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
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Journal ArticleDOI
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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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