130
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      ImageJ2: ImageJ for the next generation of scientific image data

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background

          ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software’s ability to handle the requirements of modern science.

          Results

          We rewrote the entire ImageJ codebase, 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. This next-generation ImageJ, called “ImageJ2” in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace.

          Conclusions

          Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ’s development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12859-017-1934-z) contains supplementary material, which is available to authorized users.

          Related collections

          Most cited references42

          • Record: found
          • Abstract: found
          • Article: not found

          NIH Image to ImageJ: 25 years of image analysis.

          For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Computer control of microscopes using µManager.

            With the advent of digital cameras and motorization of mechanical components, computer control of microscopes has become increasingly important. Software for microscope image acquisition should not only be easy to use, but also enable and encourage novel approaches. The open-source software package µManager aims to fulfill those goals. This unit provides step-by-step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software. © 2010 by John Wiley & Sons, Inc.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Metadata matters: access to image data in the real world

              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.
                Bookmark

                Author and article information

                Contributors
                eliceiri@wisc.edu
                Journal
                BMC Bioinformatics
                BMC Bioinformatics
                BMC Bioinformatics
                BioMed Central (London )
                1471-2105
                29 November 2017
                29 November 2017
                2017
                : 18
                : 529
                Affiliations
                [1 ]ISNI 0000 0001 2167 3675, GRID grid.14003.36, Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, ; Madison, Wisconsin USA
                [2 ]ISNI 0000 0001 2167 3675, GRID grid.14003.36, Morgridge Institute for Research, ; Madison, Wisconsin USA
                Author information
                http://orcid.org/0000-0001-8678-670X
                Article
                1934
                10.1186/s12859-017-1934-z
                5708080
                29187165
                a6488aeb-2db4-44a3-b3ee-6434a07bf4d1
                © The Author(s) 2017

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 19 January 2017
                : 14 November 2017
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;
                Award ID: RC2 GM092519-01
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: 1148362
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome Trust;
                Award ID: 095931
                Award Recipient :
                Categories
                Software
                Custom metadata
                © The Author(s) 2017

                Bioinformatics & Computational biology
                imagej,imagej2,image processing,n-dimensional,interoperability,extensibility,reproducibility,open source,open development

                Comments

                Comment on this article