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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Periductal stromal collagen topology of pancreatic ductal adenocarcinoma differs from that of normal and chronic pancreatitis.
Cole R. Drifka,Joanne Tod,Agnes G. Loeffler,Yuming Liu,Gareth J. Thomas,Kevin W. Eliceiri,W. John Kao +6 more
TL;DR: Findings indicate that second harmonic generation imaging can provide quantitative information about fibrosis that complements traditional histopathologic insights and can serve as a rich field for investigation into pathogenic and clinical implications of reorganized collagen as a pancreatic ductal adenocarcinoma disease marker.
Journal ArticleDOI
Cholestasis-induced adaptive remodeling of interlobular bile ducts.
Nachiket Vartak,Amruta Damle-Vartak,Beate Richter,Olaf Dirsch,Uta Dahmen,Seddik Hammad,Jan G. Hengstler +6 more
TL;DR: BDL causes adaptive remodeling that aims at optimizing the intraluminal surface area by way of corrugation and branching that is analogous to the function of villi in the intestine or sulci in the brain.
Journal ArticleDOI
Emergent functional properties of neuronal networks with controlled topology.
Emanuele Marconi,Thierry Nieus,Alessandro Maccione,Pierluigi Valente,Alessandro Simi,Mirko Messa,Silvia Dante,Pietro Baldelli,Pietro Baldelli,Luca Berdondini,Fabio Benfenati,Fabio Benfenati +11 more
TL;DR: This work validated the use of a new bio-printing approach, which effectively maintains the topology of hippocampal cultures in vitro and investigated the emerging functional properties of these grid-confined networks, and showed that reliable functional studies can nowadays be performed on large neuronal networks in the presence of sustained changes in the physical network connectivity.
Posted ContentDOI
BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples
David Hörl,David Hörl,Fabio Rojas Rusak,Friedrich Preusser,Paul W. Tillberg,Nadine Randel,Nadine Randel,Raghav K. Chhetri,Albert Cardona,Albert Cardona,Philipp J. Keller,Hartmann Harz,Heinrich Leonhardt,Mathias Treier,Mathias Treier,Stephan Preibisch +15 more
TL;DR: The BigStitcher software is developed that efficiently handles and reconstructs large multi-tile, multi-view acquisitions compensating all major optical effects, thereby making single-cell resolved whole-organ datasets amenable to biological studies.
Journal ArticleDOI
BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes.
TL;DR: This work introduces BEMOVI, a package using the R and ImageJ software, to extract abundance, morphology, and movement data for tens to thousands of individuals in a video and demonstrates how the trait data can be used with machine learning to automatically classify individuals into species and that information on movement behavior improves the predictive ability.
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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