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
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Posted ContentDOI
Efficient data management infrastructure for the integration of imaging and omics data in life science research
Luis Kuhn Cuellar,Andreas Friedrich,Gisela Gabernet,Luis de la Garza,Sven Fillinger,Adrian Seyboldt,Sven zur Oven-Krockhaus,Friederike Wanke,Sandra Richter,Wolfgang M. Thaiss,Marius Horger,Nisar P. Malek,Klaus Harter,Michael Bitzer,Sven Nahnsen +14 more
TL;DR: It is anticipated that FAIR data management systems for multi-modal data repositories will play a pivotal role in data-driven research, as the joint analysis of omics and imaging data becomes not only desirable but necessary to derive novel insights into biological processes.
Journal ArticleDOI
Hard and soft plastic resin embedding for single-cell element uptake investigations of marine-snow-associated microorganisms using nano-scale secondary ion mass spectrometry
Andreas Rogge,Clara M. Flintrop,Clara M. Flintrop,Morten Hvitfeldt Iversen,Ian Salter,Allison A. Fong,Angela Vogts,Anya M. Waite +7 more
TL;DR: In this paper, a nanoSIMS-optimized method for fixation, embedding, and sectioning of marine snow aggregates is presented, which enables combined investigations of 3D aggregate structure, spatial microbial distribution, and singlecell activity within individual aggregates and provides new possibilities for future studies on microbial interactions and elemental uptake within marine snow.
Journal ArticleDOI
Metadata Extraction for Calculating Object Perimeter in Images
Marcio Hosoya Name,Sergio Silva Ribeiro,Teruo Matos Maruyama,Henrique de Padua Valle,Rosane Falate,Maria Salete Marcon Gomes Vaz +5 more
TL;DR: A class developed with routines in Java language, and contribution of OpenCV library, for analysis and extraction of metadata from images presents satisfactory results and is recommended to extract and calculate measures of an object present in the image.
Journal ArticleDOI
Software tool for 3D extraction of germinal centers
TL;DR: The pyBioImage software framework seeks to be a general purpose image application for immunological research based on 4D imaging and uses a novel clustering algorithm for automatically extracting quantitative spatial information of a large number of GCs from a collection of confocal microscopy images.
Book ChapterDOI
Introduction to ImageJ Macro Language in a Particle Counting Analysis: Automation Matters.
TL;DR: This chapter focuses on the main concepts of ImageJ macro programming with special emphasis on the image analysis pipeline automation.
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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