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The Cell: An Image Library – An Overview of an Award-winning Multimedia Site

Much more than just an archive, The Cell: An Image Library-CCDB (Cell Centered Database; ‘The Cell’) serves many additional purposes. Whilst many researchers use The Cell to organize their own images for research and archival purposes- the real value of The Cell is the ability to share those images with other researchers.

In many scientific fields, there is a great benefit in the aggregation of data. For example, protein and nucleic acid sequence databases have proven invaluable to their fields, and now, The Cell’s database of images and videos is also being used by the research community.  With a crisp interface and many additional features, The Cell has added significant value to the scientific community.

Research Value: don’t hide your images- share them!

It is shocking in this day and age to think of the value of all the biological images which have been captured, yet languish on hard drives or buried under heaps of folders on the desk of researchers and scientists worldwide! These valuable data are being kept (unintentionally it has to be said) from others who may benefit from these images. If each of us shared just a fraction of our images, then this could add to our collective knowledge and save everyone both time and money. Fellow scientists may not have to repeat that three day live-cell imaging experiment, they could see something new in your images, or even analyze the images for a different purpose. The Cell presents the ideal forum for presenting these images to the research community and the public. The images are peer-reviewed so users can be confident that they are seeing only the highest quality images with accurate metadata annotations.

As society increasingly embraces the open sharing of data, The Cell is becoming the central repository for all types of cell imaging. Built to accept almost any image file format for upload and offering downloads as jpeg, OME-TIF, and the originally uploaded format, The Cell is ideal as a centralized file distribution system. As new formats are generated by microscope manufacturers, these can easily be incorporated into The Cell.

There has been a recent requirement by funding agencies and private funders to ensure that all research generated under a grant be made publicly available – a task that would be difficult and expensive for individual research groups to fulfill, but which The Cell has been designed to accomplish.  From the perspective of the users, The Cell not only puts all the information in one place, but provides a consistent and easy to use searchable interface, which means you can readily view and download image data provided by numerous diverse research groups.

An ideal scenario would be for researchers to submit their best 20, 30 or 50 images along with their manuscript, but following publication, could make their entire set of images available to the research community. In addition to further supporting conclusions, this sharing allows other researchers to analyze these images for other purposes such as testing a new algorithm for pattern recognition.

Previously, providing access to videos has always presented a challenge to publishers. Not now though! Videos and animations are easily handled by The Cell. Just as no one would consider publishing a DNA sequence in a paper anymore (simply referencing the entity in GenBank), The Cell can serve this role for videos (and even entire experimental sets). This is particularly true if the publisher would like to publish one or more videos, but not those that would normally be in the supplemental materials.

Features- interact and customize

A number of features have been developed which aid researchers in using The Cell. To search the image database, which currently houses over 9000 images, a simple search box is provided at the top of every page. As you begin typing you will be prompted with suggested search terms found in the Library. There is also a very extensive advanced search with keywords and terms from the nine ontologies used to annotate sixteen different fields. In the future, users will be able to subscribe to these complex search parameters so that as new images matching the selected criteria are published in the Library, users will receive an email alert. Users can also browse by Cell Process, Cell Component, Cell Type, Organism, and Recent Images.

Images, videos, and animations can be downloaded from the site for offline use (although there are various licensing requirements which must be observed). Images can be downloaded in a variety of formats and many of them are in the public domain.

The Cell utilizes the Web Image Browser (WIB). The WIB is an intuitive and easy to use way to explore high-resolution images. The user has the capability to zoom-in to see the greater detail present in each one. Many of the images are in 3-D which includes the Z dimension. Some are also stacks of images through time, whilst others combine both the Z dimension and the time dimension to create 4-D images. Images can also be viewed by holding the time point constant and moving through space in the Z dimension. Therefore, images can be viewed quite elegantly with either the WIB or the ‘Detailed Viewer’.

Additional benefits are added when a user signs up for a free account.

Once logged in, users have the option of saving favorite images in customized ‘Photoboxes’ and defining ‘Areas of Interest’. These ‘Areas of Interest’ are then updated with images loaded into The Cell from the last 30 days, so with each log in, users have effectively customized their home page in The Cell. Future plans include being able to connect directly with researchers, and share folders with those researchers or the public.

A key aspect of The Cell is the interactive cell illustration on the homepage. Students and researchers alike have found this very useful in understanding aspects of the cell which are not their specialty. When users hover over the illustration, this in turn highlights the different organelles or features. Clicking on the interactive cell brings up a search results page which includes an interactive image of the organelle or feature, a brief explanation of that item and the five most commonly annotated biological processes and related molecular functions. Image results appear following the selection of any of these functions or processes.

This interactive illustration fills one of the key needs in connecting abstract conceptual knowledge as expressed in illustrations, and the reality of images seen in different microscopy modalities. Very few, if any, resources make this relationship as clear as The Cell does!

This feature has been launched for the Endoplasmic Reticulum, Golgi Apparatus, Microtubule Organizing Centers, Mitochondrion, and the Nucleus. Try it out here with the Mitochondrion.

How to submit images

Just as all large scientific and research databases rely on constant submissions from their community, so too does The Cell. Arrangements are already in place with various publishers regarding presenting images in The Cell (which in turn, links back to their articles), but scientists and researchers are always needed to submit images, just as the protein and nucleic acid sequences need sequence data. Researchers are encouraged to submit high quality images from all types of experiments, including unpublished and negative results. The Cell presents the opportunity to capture scientific efforts towards creating a true knowledge base.

There are a variety of ways to protect contributor’s rights. For more information please see the Licensing Policy. There are also two ways to submit your images, the Online Upload Tool and the easy to install DataRollup Software. The Online Upload Tool is a simple way to submit a few images from the more common data formats, and the DataRollup is for submissions of larger collections of images and those from the less common file formats. This software uses the Bio-Formats.

Join the community, make suggestions

If you have any questions regarding submitting images, or are a publisher which would like to work with us, please contact David Orloff ([email protected]), Director, Image Library. We welcome feedback and suggestions.

We have also created a number of tools to stay informed about The Cell, see our Image of the Week, communicate with other microscopy professionals, ask questions, and share images. Please join us via one or more of these social media:

LinkedIn
Facebook
Twitter
Image of the Week

Author Affiliations:

David Orloff: American Society for Cell Biology, Bethesda, MD, USA

Additional Authors:

Janet Iwasa, PhD, Harvard Medical School, Department of Cell Biology, Boston, MA, USA.

Caroline Kane, PhD, University of California, Molecular and Cell Biology, Berkeley, CA, USA.

This project is supported by Award Number RC2GM092708 from the National Institute of General Medical Sciences (NIGMS), U.S. National Institutes of Health, to the American Society for Cell Biology.

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