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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Journal ArticleDOI
NIH Image to ImageJ: 25 years of image analysis
TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Journal ArticleDOI
ImageJ2: ImageJ for the next generation of scientific image data
Curtis Rueden,Johannes Schindelin,Johannes Schindelin,Mark Hiner,Barry E. DeZonia,Alison E. Walter,Alison E. Walter,Ellen T. Arena,Ellen T. Arena,Kevin W. Eliceiri,Kevin W. Eliceiri +10 more
TL;DR: ImageJ2 as mentioned in this paper is the next generation of ImageJ, which provides a host of new functionality and separates concerns, fully decoupling the data model from the user interface.
Journal ArticleDOI
QuPath: Open source software for digital pathology image analysis
Peter Bankhead,Maurice B Loughrey,Maurice B Loughrey,José A Fernández,Yvonne Dombrowski,Darragh G. McArt,Philip D Dunne,Stephen McQuaid,Stephen McQuaid,Ronan T. Gray,Liam J. Murray,Helen G. Coleman,Jacqueline A James,Jacqueline A James,Manuel Salto-Tellez,Manuel Salto-Tellez,Peter W. Hamilton +16 more
TL;DR: QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images, making it suitable for a wide range of additional image analysis applications across biomedical research.
Journal ArticleDOI
TrackMate: An open and extensible platform for single-particle tracking.
Jean-Yves Tinevez,Nick Perry,Johannes Schindelin,Genevieve M. Hoopes,Gregory D. Reynolds,Emmanuel Laplantine,Sebastian Y. Bednarek,Spencer L. Shorte,Kevin W. Eliceiri +8 more
TL;DR: TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment and is validated for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.
Posted Content
ImageJ2: ImageJ for the next generation of scientific image data
Curtis Rueden,Johannes Schindelin,Johannes Schindelin,Mark Hiner,Barry E. DeZonia,Alison E. Walter,Alison E. Walter,Ellen T. Arena,Ellen T. Arena,Kevin W. Eliceiri,Kevin W. Eliceiri +10 more
TL;DR: The entire ImageJ codebase was rewrote, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements.
References
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The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
Ilya G. Goldberg,Chris Allan,Jean-Marie Burel,Doug Creager,Andrea Falconi,Harry Hochheiser,Josiah Johnston,Jeff Mellen,Peter K. Sorger,Jason R. Swedlow +9 more
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