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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The BEACH Domain Is Critical for Blue Cheese Function in a Spatial and Epistatic Autophagy Hierarchy.
Joan Sim,Kathleen Amy Osborne,Irene Argudo Garcia,Irene Argudo Garcia,Artur Matysik,Rachel Kraut,Rachel Kraut +6 more
TL;DR: The autophagic adaptor blue cheese is placed in an epistatic hierarchy, using pharmacological and genetic modulation of bchs- motor neuron degeneration, and an intact BEACH isoform can promote autophile proliferation, and in primary larval brain neurons Bchs shuttles to different components of the autophagy machinery, dependent on the stimulus.
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Hindbrain and Spinal Cord Contributions to the Cutaneous Sensory Innervation of the Larval Zebrafish Pectoral Fin.
TL;DR: Reconstructions indicate that this sensory system breaks from the canonical somatotopic organization of sensory systems by lacking a clear organization with reference to fin region, and suggests that these fin sensory neurons report on general conditions of the fin area rather than providing fine location specificity, as has been demonstrated in other vertebrate limbs.
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Artificial intelligence in breast cancer histopathology
Ronald C. K. Chan,Chun Kit Curtis To,Ka Chuen Tom Cheng,Tada Yoshikazu,Lai Ling Amy Yan,Gary Tse +5 more
TL;DR: A systematic search on PubMed was conducted, identifying 17,324 research papers related to breast cancer pathology as mentioned in this paper, following a semimanual screening, 664 papers were retrieved and pursued.
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Transcriptional regulation of alcohol induced liver fibrosis in a translational porcine hepatocellular carcinoma model.
Alvi Yasmin,Daniel P. Regan,Lawrence B. Schook,Ron C. Gaba,Kyle M. Schachtschneider,Kyle M. Schachtschneider +5 more
TL;DR: The Oncopig Cancer Model as discussed by the authors is a transgenic pig model that recapitulates human hepatocellular carcinoma (HCC) through induced expression of KRASG12D and TP53R167H driver mutations.
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An in silico Model of T Cell Infiltration Dynamics Based on an Advanced in vitro System to Enhance Preclinical Decision Making in Cancer Immunotherapy
Thomas D. Lewin,Blandine Avignon,Alessio Tovaglieri,Lauriane Cabon,Nikolce Gjorevski,Lucy Hutchinson +5 more
TL;DR: A mechanistic, mathematical model is developed of a novel microphysiological in vitro platform that recapitulates T cell infiltration into epithelial tissue, which may be normal or transformed, and describes the spatiotemporal dynamics of infiltrating T cells in response to chemotactic cytokine signalling.
References
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Journal ArticleDOI
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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