in december 2008 , the journal of cell biology ( jcb ) launched the jcb dataviewer , an online repository for original image data in the life sciences ( fig .
1 ) . to our knowledge , this system is the first open repository that enables routine archiving and sharing of original image datasets supporting published scientific articles .
one key attribute of the jcb dataviewer that distinguishes it from past and current data repositories is that the original binary data and metadata , additional information captured by acquisition software about an image , such as the instruments used , acquisition settings , image size , and resolution , are preserved and accessible by the community . as of this writing , the jcb dataviewer contains 6,446 multidimensional ( 5d ; including space , channel , and time ) images in support of 186 published articles .
the jcb dataviewer is a customized application based on the open source and open development open microscopy environment ( ome ) remote objects ( omero ) and bio - formats projects , released by the ome consortium ( http://openmicroscopy.org ) .
an example of original image data associated with this paper , viewed in the jcb dataviewer .
the image shows the following : a 3d stack of a fixed hela cell stained with dapi ( blue ) , anti - incenp ( red ) , and anti - tubulin ( green ) , recorded using a wide - field microscope ; a time - lapse video of a c. elegans embryo expressing gfp - tubulin , recorded using a multiphoton microscope ; a transmission electron microscope ( tem ) image of bacteriophages visualized using negative stain ; a 3d stack of a fixed hela cell stained with anti - tubulin , recorded using an omx 3d structured illumination microscope ; a tem image of rb bound to dna ; and a 5d image of gfp - coilin and yfp - histone h2b in a hela cell , recorded by wide - field microscopy ( platani et al . , 2000 ) .
note that available metadata differ substantially between the different images , depending on the metadata that are stored in the original files .
these images and their associated metadata are available at http://jcb - dataviewer.rupress.org / jcb / browse/2859/. one goal of the jcb dataviewer was to initiate the development of a functional , scientifically valuable online image repository . the first step was to make original data available alongside a publication , available for examination by reviewers and readers of a submitted or published manuscript .
currently , the jcb dataviewer allows access to original data for viewing , simple measurement , and review , but users can not download the original data files , and sophisticated image analysis and querying tools are not included in the application . in the next update , users will be able to download video versions of data stored in the jcb dataviewer , and original image data will be available in an open , standardized data format that preserves the original image metadata ( ome tagged image file format [ tiff ] ) .
authors will also retain access to their original data , thereby making the jcb dataviewer an archive where authors can store their own published data .
these updates represent one more step toward the development of a fully functional data repository .
the data in the jcb dataviewer are freely available to the public immediately upon publication , without a subscription to the jcb . in the future ,
as image repositories mature , we plan to merge the data held in the jcb dataviewer with whatever resources emerge as the definitive public repository of image data in the life sciences .
the jcb dataviewer is one of a growing number of image data repositories that are now available , each focused on providing access not only to results but also to some combination of sophisticated visualization , analysis , and mining of these complex data ( table i and fig .
each of these efforts has emphasized specific applications and functionality and reflects the simple fact that the diversity of scientific exploration and images can not yet be addressed by a single resource . however , there are ongoing efforts to align data models where possible , and perhaps most importantly , simplify submission and subsequent processing through the definition and use of file formats that support standardized metadata .
these are examples of real progress toward the goals that many have discussed and that have recently been reiterated ( cosepup , 2009 ; field et al . , 2009 ; schofield et al . ,
scientific image data repositories for cell and developmental biology slif , subcellular location image finder ; pslid , protein subcellular location image database . in development as of 2010 . recommendations for ome compliant image metadata .
the image and instrument elements from the ome data model , with attributes and hierarchies shown in diagrammatic form .
the image element contains core metadata that can be used for display and processing of the associated binary image data .
currently , an ome compliant image completes all of the metadata in the image element . by the end of 2010 , we aim to include the instrument element in the ome compliant specification .
the bio - formats library provides support for writing ome - xml either as a stand - alone file or within the header of an ome - tiff file .
updates to the ome data model are announced on the project s roadmap site ( http://ome-xml.org/roadmap ) . in summary ,
significant effort by peer - reviewed , competitively funded groups in the us and europe has produced image informatics tools that the research community uses .
the tools and resources are by no means finished , and our current status seems analogous to the state of the genomics resources in the mid-1980 s , when individual authors submitted their own sequence data to genbank , swissprot , and others .
the diversity of imaging platforms , experiments , techniques , and data makes this analogy only partially correct and undoubtedly makes the challenge of building and running scientifically useful image repositories harder .
regardless , the sophistication of centralized scientific image resources is growing , and as a result , so will the value they deliver to the scientific community . those resources that depend on submissions from the community
will require the development , adoption , and use of standardized file formats that support as rich a metadata structure as possible .
this is why the development and use of standardized image data and metadata formats are so important .
many laboratories have at least one sophisticated imaging system , and many large shared - use facilities provide access to an array of imaging systems . after many years of innovation and development ,
modern digital imaging systems enable temporally and spatially resolved , multichannel measurement and visualization of molecular and ion concentrations in cells and tissues . emerging imaging techniques such as multispectral , polarization , fluorescence lifetime , and fluorescence correlation are extending the complexity of analysis of biological cells and tissues .
however , most digital microscope imaging systems , whether commercial products or laboratory prototypes , are usually run by custom software that saves and processes data using a pff . in general , every new imaging platform comes with a new pff , so rapid advances in imaging simultaneously make data exchange and access more difficult . to realize the dream of open data access and sharing
, we first must solve the basic problem of accessing the data contained in pffs .
any solution will not directly lead to new scientific insights , but it is a prerequisite for submission to repositories and the discoveries they enable through reanalysis .
for example , if the data from cell - based phenotypic screens were available , they could be reanalyzed for aberrations that were not of interest to the investigators who did the original screen . generally speaking ,
image data are written in formats that include the binary data and the actual image measurement , along with some representation of the metadata : the size of the binary data , its dimensions , acquisition system settings , and any other information that the developer of the acquisition software considered useful . in our experience , storage of binary data in many commercial microscopy formats is based on common formats ( tiff , hdf5 , and ole2 , etc . ) or other formats that most software tools can read ( although there are some notable , extreme exceptions ) .
because standards are not yet agreed upon , microscope and imaging companies define their own metadata formats in their pffs , and these are often incompatible with those from competing companies .
since 2000 , the ome has been dedicated to building tools for specification , management , and sharing of biological light microscopy data ( swedlow et al . , 2003 , 2009 ;
2 ) , which covers most of the metadata in pffs from many sources and includes most of the fundamental imaging metadata in cell and developmental biology .
this specification , used within the context of a tiff file ( ome - tiff ) , provides a simple , easy to use format for microscope imaging data that can be used by any software that reads the tiff file format .
a popular tool ( > 13,000 installations worldwide ) is bio - formats , a software library that interfaces with a large number of software tools ( such as imagej ) , enables the reading of > 75 pffs , and supports output to ome - tiff .
for many years , the imaging community has expressed a desire to move away from the current ad hoc approach toward more defined standards for metadata representation ( goldberg et al . , 2005 ) . however , creating a reasonable standard takes years of community discussion and effort . for the standard to be successful ,
it must be widely used and functional enough to be worth the effort of conformance , and it takes time for the  snowball effect  to occur . given the diversity and rapid evolution of imaging applications in biology , we do nt believe that standards can be mandated by any one entity .
instead , we argue that standards for biological imaging must be supported and developed , and once they are valuable for scientific discovery and data sharing , and have demonstrated the ability to rapidly adapt to new technologies , the community must demand the support of these formats in the commercial platforms they purchase . under the umbrella of the ome , we have been collecting community feedback for several years now , and our recommendations for this process are detailed in box 1 .
recommendations for use of pffs image metadata must be associated with the binary image data , preferably as a single file .
microscope systems must not store metadata in proprietary databases that are available only on the data acquisition system .
metadata must be readable by third party software using a common , openly accessible software package or library .
pff developers must work with developers of open translation libraries to ensure their format is correctly interpreted .
if compression is supported , the user must be given the option of saving uncompressed or losslessly compressed images ( which allows the exact original data to be reconstructed after compression ) .
if compression or encryption is used , the algorithm and parameters must be stated and stored in the metadata .
commercial software programs must provide data export to an open metadata specification . to ensure that commercial software writes these formats correctly , open
public and charity funding for imaging systems must include a requirement that the system writes data in an open , accessible format , wherever possible .
when pffs must be used , new versions must be announced to the scientific community , and users and funding bodies must predicate their purchases on this type of support for the scientific community .
once a standardized repository is available , journals must require deposition of original data supporting scientific manuscripts . in some cases ,
however , in our experience with bio - formats , omero , and the jcb dataviewer , most of the data we have seen could be recorded in an open , standardized , multidimensional file format .
as the number of imaging systems and the rate of innovation grows , maintaining a tool like bio - formats , simply because commercial vendors do not use standardized file formats , becomes increasingly untenable .
reverse engineering is slow and inherently error prone , as metadata stored in pffs are decoded and translated . as popular as bio - formats is ,
it is time to reconsider the value pffs deliver for a specific commercial product against the costs , which are paid for by public and charity funding : lost time for scientific researchers , inhibited collaborations , and impeded access to data using the aforementioned emerging data repositories .
many scientific funding bodies now require the published output from the work they fund to be deposited in open access repositories .
the same open access principle should be extended to the data generated through their funding to enable broad dissemination and further analysis . as with other forms of data , there is no requirement to publish all images associated with a paper , just the ones that form the definitive representation of the reported discovery .
the ome , international society for advancement of cytometry ( http://www.isac-net.org ) , and digital imaging and communications in medicine ( http://medical.nema.org/dicom/ ) formats are all well developed , supported , and available for use .
it may be that no single format can satisfy every requirement or data type , but our experience demonstrates that the vast majority of the data used to support scientific publications can be properly stored in these formats .
we can support a range of open file formats with bio - formats , thus allowing interconversion between open file formats where necessary .
we have developed the ome metadata standards through extensive direct experience and discussion with the user and commercial developer communities .
we plan to use them as we progress to the development of a public repository but remain open to suggestions about how they can be improved .
as noted in the box 1 , the use and adoption of these file formats wo nt happen by itself , the community must work to drive their adoption .
individual scientists and their funding bodies must require support for these formats when they purchase or fund new imaging systems .
the argument for this concerted action is based on a simple , practical goal : scientific data , funded by the public and nonprofit charities , must be publicly available . over the next few years , the technical capabilities in image repositories will mature .
data to fill these repositories must be open , accessible , and ready for use .
 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 . 
Scientific image data repositories for the life sciences
Microscopy file formats
Future directions and recommendations