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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Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression
Justin Shaffer,Iva Greenwald +1 more
TL;DR: The Floxed exon (Flexon) approach is described, which uses a stop cassette composed of an artificial exon flanked by artificial introns, designed to cause premature termination of translation and nonsense-mediated decay of the mRNA and allowing for flexible placement into a gene.
Journal ArticleDOI
Translatome proteomics identifies autophagy as a resistance mechanism to on-target FLT3 inhibitors in acute myeloid leukemia
Sebastian Koschade,Kevin Klann,Shabnam Shaid,Binje Vick,Jan Stratmann,Marlyn Thölken,Laura M. Meyer,The Duy Nguyen,Julia Campe,Laura M Moser,Susanna Hock,Fatima Baker,Christian T. Meyer,Frank Wempe,Hubert Serve,Evelyn Ullrich,Irmela Jeremias,Christian Münch,Christian Brandts +18 more
TL;DR: In this article , the AKT-mTORC1-ULK1-dependent autophagy was identified as a dominant resistance mechanism to on-target FLT3i therapy.
Posted Content
FastPathology: An open-source platform for deep learning-based research and decision support in digital pathology
André Pedersen,Marit Valla,Anna M. Bofin,Javier Pérez de Frutos,Ingerid Reinertsen,Erik Smistad +5 more
TL;DR: This work has developed a new platform, FastPathology, which minimizes memory usage for reading and processing WSIs, deployment of CNN models, and real-time interactive visualization of results, and includes all steps needed for efficient visualization and processing of WSIs in a single application.
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Preparation of mica supported lipid bilayers for high resolution optical microscopy imaging
Artur Matysik,Rachel Kraut +1 more
TL;DR: This work presents a simple and reproducible method for preparing thin, flat mica surfaces for lipid vesicle deposition and SLB preparation that results in the efficient, simple and inexpensive production of high quality lipid bilayer surfaces that are directly comparable to those used in AFM studies.
Journal ArticleDOI
Functional imaging and quantification of multineuronal olfactory responses in C. elegans
Albert Lin,Shanshan Qin,Helena Casademunt,Min Wu,W. Huang,Greg Cain,Nicolas Z. Tan,Raymond Valenzuela,Leila Lesanpezeshki,Cengiz Pehlevan,Vivek Venkatachalam,Mei Zhen,Aravinthan D. T. Samuel +12 more
TL;DR: The integrated activity of the sensory periphery of C. elegans contains sufficient information to robustly encode the intensity and identity of a broad panel of odorants, and describes the unique contribution of each sensory neuron to an ensemble-level olfactory code.
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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