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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Lithographically patterned micro-nozzles for controlling fluid flow profiles for drug delivery and in vitro imaging applications
TL;DR: In this article, photolithographic integration of micro-nozzles onto a microfluidic platform was performed to tune the fluid flow profile and depth of penetration into biological tissue mimics.
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Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo
TL;DR: A versatile and robust semi-automated image acquisition, processing and analysis workflow to investigate bacterial cell morphology in a quantitative manner is demonstrated and aims at supporting life-scientists to establish their own imaging-pipeline in order to exploit their data as versatile as possible and in a reproducible manner.
Journal ArticleDOI
Quantitative analysis of myofiber type composition in human and mouse skeletal muscles
Tooba Abbassi-Daloii,Salma el Abdellaoui,Hermien E. Kan,Erik B. van den Akker,Peter A C 't Hoen,Vered Raz,Lenard M. Voortman +6 more
TL;DR: Abbassi-Daloii et al. as discussed by the authors presented a high-throughput semi-automated approach for performing myofiber type quantification of entire human or mouse muscle tissue sections, including immunofluorescence staining, image acquisition, processing and quantification.
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Aptamer Detection of Mycobaterium tuberculosis Mannose-Capped Lipoarabinomannan in Lesion Tissues for Tuberculosis Diagnosis.
Yuanyuan Zhou,Huan Xiong,Rong Chen,Lixia Wan,Ying Kong,Jianwei Rao,Yan Xie,Chaolin Huang,Xiao-Lian Zhang +8 more
TL;DR: In this paper, a ManLAM aptamer-based immunohistochemistry (IHC) method was proposed for TB diagnosis. But the accuracy of the IHC was not evaluated.
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High Throughput Traction Force Microscopy for Multicellular Islands on Combinatorial Microarrays.
Ian C. Berg,Gregory H. Underhill +1 more
TL;DR: A TFM system using polyacrylamide substrates and a microarray spotter to fabricate arrays of multicellular islands on various combinations of extra cellular matrix (ECM) proteins or other biomolecules is described.
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.
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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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