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Announcing the JCB DataViewer, a browser-based application for viewing original image files

Announcing the JCB DataViewer, a browser-based application for viewing original image files JCB: EDITORIAL Announcing the JCB DataViewer , a browser-based application for viewing original image fi les Emma Hill Executive Editor, The Journal of Cell Biology Over the lifetime of the JCB , the technol- ogy available to cell biologists has ad- vanced immensely, producing more complex data with higher information content. Despite the advent of the Internet, the presentation of data in publications has not kept pace. Authors still present single, static, “representative” images and compressed movie fi les. I am therefore excited and proud to an- nounce the launch of the JCB DataViewer ( http://jcb-dataviewer.rupress.org ). The JCB DataViewer pro vides our authors with the option to present the original image data associated with their articles, and enables our readers to view and interact with these data. It is the fi rst browser-based system for viewing and analyzing multi- dimensional microscope image data. The JCB DataViewer was developed by The A screenshot of the full viewer within the JCB DataViewer. This link http://jcb-dataviewer.rupress.org/jcb/ Rockefeller University Press in collabora- img_detail/127/134/ will open the full viewer displaying these data; take a look and see what it can do. tion with Glencoe Software, Inc. using technology developed by the Open Mi- For multi-dimensional microscopy im- more than can be gleaned from a single, croscopy Environment ( Swedlow et al., ages, users can scroll through a stack of two-dimensional optical slice. 2003 ). Access to original data provides full image sections or a stack of images The data in the JCB DataViewer transparency in data presentation and her- from a time course. Users can view spe- are uploaded by authors at the time of alds a completely new scope of analysis cifi c image channels and use a built-in submission. Although the system was and discussion within scientifi c articles. tool to calculate plots of signal intensi- designed for microscopy image data, ties along any horizontal or vertical line it can also display the output from gel How it works within an image to compare signal and documentation systems. The JCB Data- The JCB DataViewer makes any pub- background. Three-dimensional data Viewer is compatible with an extensive lished image as accessible to readers as can be viewed either as individual sec- list of proprietary fi le types (see Table I), if they had acquired it. The user can in- tions or as a two-dimensional projection which are rendered into JPEG images teract with the data in a variety of ways; of the maximum intensities from the for all images, users can rescale the im- complete stack. In addition, image © 2008 Hill. This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No ages and adjust the intensity range of metadata, such as rendering details, di- Mirror Sites license for the fi rst six months after the the display, just like they normally do mensions, and acquisition conditions publication date (see http://www.jcb.org/misc/terms. with their own image display software. shtml). After six months it is available under a Creative are readily available. The reader can Commons License (Attribution–Noncommercial–Share thus access a maximum amount of in- Alike 3.0 Unported license, as described at http:// Correspondence to Emma Hill: [email protected] formation from published images, far creativecommons.org/licenses/by-nc-sa/3.0/). The Rockefeller University Press $30.00 J. Cell Biol. Vol. 183 No. 6 969–970 www.jcb.org/cgi/doi/10.1083/jcb.200811132 JCB 969 THE JOURNAL OF CELL BIOLOGY Table I. File types supported by the JCB DataViewer at the time of publication verify the fi gures presented in a JCB article with the original data from the acquisition Supported format File extensions apparatus represents the next step in our on- Bio-Rad .pic going commitment to image data integrity Bitmap .pic ( Rossner and Yamada, 2004 ). Although we DeltaVision .dv, .r3d, .r3d_d3d don ’ t require our authors to submit their Digital Imaging and Communications in Medicine .dicom, .dic, .dcm original data to the JCB DataViewer , we en- Amersham Biosciences GEL .gel courage it, as providing them ensures com- Graphics Interchange Format .gif Image Cytometry Standard .ics, .ids plete transparency. We are not just asking to Bitplane Imaris .ims see a larger section of a microscope fi eld or Improvision Tiff .tif a larger piece of a blot, but the actual data Joint Photographic Experts Group .jpeg, .jpg fi les acquired by authors (that have not had Leica “ lei ” Format .lei a whiff of Photoshop!). As we have done for Leica Image Format .lif the past six years, we will continue to screen Li-Cor L2D .l2d MetaMorph .stk all assembled fi gures in JCB articles for evi- Nikon NIS-Elements .nd2 dence of manipulation. Olympus FluoView FV1000 .oib, .oif Openlab Raw .raw Who can upload their data Openlab LIFF .liff to the JCB DataViewer ? PerkinElmer UltraView .tif, 0.2, 0.3, etc. As of December 1, 2008, all submitting au- PICT (Macintosh Picture) .pict thors have the option to upload their data to Portable Gray Map .pgm the JCB DataViewer . Authors submitting Portable Network Graphic .png Prairie Technologies TIFF .png new manuscripts to the JCB will indicate Tagged Image File Format .tif, .tiff during the submission process whether Visitech XYS .xys they have original data they wish to upload. Zeiss LSM .lsm The Editorial Offi ce will then send instruc- Zeiss AxioVision .zvi tions on how to do so. These data will be peer reviewed alongside the article. that can be viewed in a web browser. tion information, to enhance the search In addition, over the past few weeks, We will add support for other formats potential. we have invited authors who recently pub- as they become prevalent. An up-to- lished in the JCB to upload the original date list of all supported formats can be Data sharing data corresponding to their articles. All found here: http://jcb-dataviewer.rupress For several years, major funding agen- such retrospectively uploaded data have .org/jcb/page/imageformats/ . cies have stipulated that the original data not been peer reviewed. A disclaimer to generated using their research funds this effect will be posted prominently on What ’ s in it for our authors? must be made available to the public. For the JCB DataViewer website. We encour- The JCB DataViewer not only benefi ts many types of data, such as protein struc- age authors to continue the retrospective readers, but also the authors of our papers. tures, sequence data, or microarray and upload of data for papers already published All uploaded original data can be accessed gene expression data, there are estab- in the Journal. If you published a paper in directly from the published article at lished databases for complying with this the JCB that was submitted before Decem- http://www.jcb.org . This truly harnesses stipulation. The same has not been true ber 1, 2008 and would like to upload your the power of the Internet; it enables au- for image data — until now. original data, please contact us. thors to better showcase their data and to While a manuscript is under review, The JCB DataViewer is the next better substantiate the conclusions drawn uploaded data will only be visible to a pa- logical step in publishing image data and in their JCB article. Such transparency en- per ’ s authors and reviewers. Once a paper sets a new standard for making primary hances the value of the science presented, is published, the associated original data data accessible. We are convinced that it as readers have all of the information nec- will be made available to all readers, will be a useful tool for cell biologists essary to evaluate authors ’ interpretations. whether or not they have a subscription to and will facilitate and improve the com- A further benefi t to the author is the cre- the JCB . As with all material submitted to munication of scientifi c data. Try it out as ation of an archive of all of the primary the JCB , the copyright to the submitted a user and benefi t from it as an author! data that accompany an article. data remains with the author. At this time, Data submitted to the JCB Data- uploaded data fi les will not be available References Viewer will become part of a searchable for others to download; viewers will only Rossner , M. , and K.M. Yamada . 2004 . What ’ s in a database, which we provide as a resource have access to the rendered JPEG images. picture? The temptation of image manipula- for the community. Authors are encour- tion. J. Cell Biol. 166 : 11 – 15 . aged to input legends with details be- Data integrity Swedlow , J.R. , I. Goldberg , E. Brauner, and P.K. Sorger . 2003 . Informatics and quantitative yond those provided in the article itself, The JCB DataV iewer is also an important analysis in biological imaging. Science . such as precise methodology or acquisi- tool to ensure data integrity. The ability to 300 : 100 – 102 . 970 JCB • VOLUME 183 • NUMBER 6 • 2008 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png The Journal of Cell Biology Pubmed Central

Announcing the JCB DataViewer, a browser-based application for viewing original image files

The Journal of Cell Biology , Volume 183 (6) – Dec 15, 2008

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Publisher
Pubmed Central
Copyright
© 2008 Hill.
ISSN
0021-9525
eISSN
1540-8140
DOI
10.1083/jcb.200811132
Publisher site
See Article on Publisher Site

Abstract

JCB: EDITORIAL Announcing the JCB DataViewer , a browser-based application for viewing original image fi les Emma Hill Executive Editor, The Journal of Cell Biology Over the lifetime of the JCB , the technol- ogy available to cell biologists has ad- vanced immensely, producing more complex data with higher information content. Despite the advent of the Internet, the presentation of data in publications has not kept pace. Authors still present single, static, “representative” images and compressed movie fi les. I am therefore excited and proud to an- nounce the launch of the JCB DataViewer ( http://jcb-dataviewer.rupress.org ). The JCB DataViewer pro vides our authors with the option to present the original image data associated with their articles, and enables our readers to view and interact with these data. It is the fi rst browser-based system for viewing and analyzing multi- dimensional microscope image data. The JCB DataViewer was developed by The A screenshot of the full viewer within the JCB DataViewer. This link http://jcb-dataviewer.rupress.org/jcb/ Rockefeller University Press in collabora- img_detail/127/134/ will open the full viewer displaying these data; take a look and see what it can do. tion with Glencoe Software, Inc. using technology developed by the Open Mi- For multi-dimensional microscopy im- more than can be gleaned from a single, croscopy Environment ( Swedlow et al., ages, users can scroll through a stack of two-dimensional optical slice. 2003 ). Access to original data provides full image sections or a stack of images The data in the JCB DataViewer transparency in data presentation and her- from a time course. Users can view spe- are uploaded by authors at the time of alds a completely new scope of analysis cifi c image channels and use a built-in submission. Although the system was and discussion within scientifi c articles. tool to calculate plots of signal intensi- designed for microscopy image data, ties along any horizontal or vertical line it can also display the output from gel How it works within an image to compare signal and documentation systems. The JCB Data- The JCB DataViewer makes any pub- background. Three-dimensional data Viewer is compatible with an extensive lished image as accessible to readers as can be viewed either as individual sec- list of proprietary fi le types (see Table I), if they had acquired it. The user can in- tions or as a two-dimensional projection which are rendered into JPEG images teract with the data in a variety of ways; of the maximum intensities from the for all images, users can rescale the im- complete stack. In addition, image © 2008 Hill. This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No ages and adjust the intensity range of metadata, such as rendering details, di- Mirror Sites license for the fi rst six months after the the display, just like they normally do mensions, and acquisition conditions publication date (see http://www.jcb.org/misc/terms. with their own image display software. shtml). After six months it is available under a Creative are readily available. The reader can Commons License (Attribution–Noncommercial–Share thus access a maximum amount of in- Alike 3.0 Unported license, as described at http:// Correspondence to Emma Hill: [email protected] formation from published images, far creativecommons.org/licenses/by-nc-sa/3.0/). The Rockefeller University Press $30.00 J. Cell Biol. Vol. 183 No. 6 969–970 www.jcb.org/cgi/doi/10.1083/jcb.200811132 JCB 969 THE JOURNAL OF CELL BIOLOGY Table I. File types supported by the JCB DataViewer at the time of publication verify the fi gures presented in a JCB article with the original data from the acquisition Supported format File extensions apparatus represents the next step in our on- Bio-Rad .pic going commitment to image data integrity Bitmap .pic ( Rossner and Yamada, 2004 ). Although we DeltaVision .dv, .r3d, .r3d_d3d don ’ t require our authors to submit their Digital Imaging and Communications in Medicine .dicom, .dic, .dcm original data to the JCB DataViewer , we en- Amersham Biosciences GEL .gel courage it, as providing them ensures com- Graphics Interchange Format .gif Image Cytometry Standard .ics, .ids plete transparency. We are not just asking to Bitplane Imaris .ims see a larger section of a microscope fi eld or Improvision Tiff .tif a larger piece of a blot, but the actual data Joint Photographic Experts Group .jpeg, .jpg fi les acquired by authors (that have not had Leica “ lei ” Format .lei a whiff of Photoshop!). As we have done for Leica Image Format .lif the past six years, we will continue to screen Li-Cor L2D .l2d MetaMorph .stk all assembled fi gures in JCB articles for evi- Nikon NIS-Elements .nd2 dence of manipulation. Olympus FluoView FV1000 .oib, .oif Openlab Raw .raw Who can upload their data Openlab LIFF .liff to the JCB DataViewer ? PerkinElmer UltraView .tif, 0.2, 0.3, etc. As of December 1, 2008, all submitting au- PICT (Macintosh Picture) .pict thors have the option to upload their data to Portable Gray Map .pgm the JCB DataViewer . Authors submitting Portable Network Graphic .png Prairie Technologies TIFF .png new manuscripts to the JCB will indicate Tagged Image File Format .tif, .tiff during the submission process whether Visitech XYS .xys they have original data they wish to upload. Zeiss LSM .lsm The Editorial Offi ce will then send instruc- Zeiss AxioVision .zvi tions on how to do so. These data will be peer reviewed alongside the article. that can be viewed in a web browser. tion information, to enhance the search In addition, over the past few weeks, We will add support for other formats potential. we have invited authors who recently pub- as they become prevalent. An up-to- lished in the JCB to upload the original date list of all supported formats can be Data sharing data corresponding to their articles. All found here: http://jcb-dataviewer.rupress For several years, major funding agen- such retrospectively uploaded data have .org/jcb/page/imageformats/ . cies have stipulated that the original data not been peer reviewed. A disclaimer to generated using their research funds this effect will be posted prominently on What ’ s in it for our authors? must be made available to the public. For the JCB DataViewer website. We encour- The JCB DataViewer not only benefi ts many types of data, such as protein struc- age authors to continue the retrospective readers, but also the authors of our papers. tures, sequence data, or microarray and upload of data for papers already published All uploaded original data can be accessed gene expression data, there are estab- in the Journal. If you published a paper in directly from the published article at lished databases for complying with this the JCB that was submitted before Decem- http://www.jcb.org . This truly harnesses stipulation. The same has not been true ber 1, 2008 and would like to upload your the power of the Internet; it enables au- for image data — until now. original data, please contact us. thors to better showcase their data and to While a manuscript is under review, The JCB DataViewer is the next better substantiate the conclusions drawn uploaded data will only be visible to a pa- logical step in publishing image data and in their JCB article. Such transparency en- per ’ s authors and reviewers. Once a paper sets a new standard for making primary hances the value of the science presented, is published, the associated original data data accessible. We are convinced that it as readers have all of the information nec- will be made available to all readers, will be a useful tool for cell biologists essary to evaluate authors ’ interpretations. whether or not they have a subscription to and will facilitate and improve the com- A further benefi t to the author is the cre- the JCB . As with all material submitted to munication of scientifi c data. Try it out as ation of an archive of all of the primary the JCB , the copyright to the submitted a user and benefi t from it as an author! data that accompany an article. data remains with the author. At this time, Data submitted to the JCB Data- uploaded data fi les will not be available References Viewer will become part of a searchable for others to download; viewers will only Rossner , M. , and K.M. Yamada . 2004 . What ’ s in a database, which we provide as a resource have access to the rendered JPEG images. picture? The temptation of image manipula- for the community. Authors are encour- tion. J. Cell Biol. 166 : 11 – 15 . aged to input legends with details be- Data integrity Swedlow , J.R. , I. Goldberg , E. Brauner, and P.K. Sorger . 2003 . Informatics and quantitative yond those provided in the article itself, The JCB DataV iewer is also an important analysis in biological imaging. Science . such as precise methodology or acquisi- tool to ensure data integrity. The ability to 300 : 100 – 102 . 970 JCB • VOLUME 183 • NUMBER 6 • 2008

Journal

The Journal of Cell BiologyPubmed Central

Published: Dec 15, 2008

There are no references for this article.