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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Differential roles of the ubiquitin proteasome system and autophagy in the clearance of soluble and aggregated TDP-43 species
Emma L. Scotter,Caroline Vance,Agnes L. Nishimura,Youn-Bok Lee,Han-Jou Chen,Hazel Urwin,Valentina Sardone,Valentina Sardone,Jacqueline C. Mitchell,Boris Rogelj,Boris Rogelj,David C. Rubinsztein,Christopher Shaw +12 more
TL;DR: It is found that soluble TDP-43 is degraded primarily by the UPS, whereas the clearance of aggregated T DP-43 requires autophagy, andTherapies for clearing excess TTP-43 should target a combination of these pathways.
Journal ArticleDOI
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues.
Jocelyn Y. Kishi,Sylvain W. Lapan,Brian J. Beliveau,Brian J. Beliveau,Brian J. Beliveau,Emma R. West,Allen Zhu,Allen Zhu,Hiroshi Sasaki,Hiroshi Sasaki,Sinem K. Saka,Sinem K. Saka,Yu Wang,Yu Wang,Constance L. Cepko,Constance L. Cepko,Peng Yin,Peng Yin +17 more
TL;DR: This work introduces signal amplification by exchange reaction (SABER), which endows oligonucleotide-based FISH probes with long, single-stranded DNA concatemers that aggregate a multitude of short complementary fluorescent imager strands, resulting in up to 450-fold signal amplification.
Journal ArticleDOI
Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.
Aurélien Rizk,Gregory Paul,Pietro Incardona,Milica Bugarski,Maysam Mansouri,Axel Niemann,Urs Ziegler,Philipp Berger,Ivo F. Sbalzarini +8 more
TL;DR: A versatile protocol for a method named 'Squassh' (segmentation and quantification of subcellular shapes), which is used for detecting, delineating and quantifyingSubcellular structures in fluorescence microscopy images, implemented in freely available, user-friendly software.
Journal ArticleDOI
High-Content Screening for Quantitative Cell Biology.
Mojca Mattiazzi Usaj,Erin B. Styles,Adrian J. Verster,Helena Friesen,Charles Boone,Brenda J. Andrews +5 more
TL;DR: Some recent applications of HCS are described, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions, and major challenges associated with each are described.
Journal ArticleDOI
Image Data Resource: a bioimage data integration and publication platform
Eleanor Williams,Josh Moore,Simon Li,Gabriella Rustici,Aleksandra Tarkowska,Anatole Chessel,Simone Leo,Balint Antal,Richard K. Ferguson,Ugis Sarkans,Alvis Brazma,Rafael E. Carazo Salas,Jason R. Swedlow +12 more
TL;DR: IDR provides an online resource and a software infrastructure that promotes and extends publication and reanalysis of scientific image data and is also an open-source platform for publishing imaging data.
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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