The New Repository on the Block

The Cell: An Image Library – CCDB

February 07, 2012

The need for data validation and accessibility has never been greater than it is today. We are inundated with information from a multitude of resources, but how can we easily evaluate the accuracy of that data? In the past, the peer review process provided this and was often run by publishers. However, now that people can self publish on the World Wide Web, we must take it upon ourselves to find those sources that are credible and dedicated to scientific accuracy. Broad scientific disciplines have found great benefit in the aggregation of data. The early protein sequence databases and the nucleotide databases have proven invaluable to their fields. While the microscopy imaging field is a little late to the game, mostly due to technical issues around storage of large image data sets, there is a new player in the field. The Cell: An Image Library-CCDB.

The value that The Cell brings

As a peer-reviewed database of microscopy image data, we provide the necessary oversight to ensure that only valid and credible data are presented in The Cell. This means you as a user can trust that what you are getting has not been inappropriately manipulated.

In addition, in the United States there are funding organizations that are already requiring that all data obtained under federally funded research be made publicly available. Imagine the effort and infrastructure needed for researchers to develop a website to present all their images that are not in their final paper. And consider the experience of users moving from site to site, each with its own navigation and search, trying to access the data they are interested in. By submitting their images to The Cell, researchers easily meet these requirements as well as providing their data along with others’ data in a simple-to-use, consistent system.

The Cell can also serve as an archive of all an experimenter’s microscopy data so that a lab and others can reference these data easily in the future. How much information is stored on hard   drives, buried under folders on a desk? The Cell can make that information available for others to query and save time and money repeating experiments that have already been done. The scientific process requires the sharing of results and The Cell provides the capability to share all results instead of just what appears in a final paper.

In addition, as a truly multimedial library The Cell has the capability to present additional videos that journals do not wish to host on their supplemental information sites. Since The Cell is a free resource, these extra videos will always be available.  

Fig. 1: A colorized scanning electron microscope picture of a nerve ending that has been broken open to reveal the synaptic vesicles (orange and blue) beneath the cell membrane. Courtesy of Tina Carvalho. www.cellimagelibrary.org/images/214
Fig. 2: Dorsal root ganglion cells from embryonic mice were cultured and stimulated to produce cyclooxygenase-2 (COX-2). Cultures were immuno-stained for neuron-associated tubulin (green), COX-2 (red) and DNA (blue). COX-2 is primarily expressed in neurons. Courtesy of Lawrence J Marnett. www.cellimagelibrary.org/images/38818
Fig. 3: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Courtesy of Dieter Brandner and Ginger Withers. cellimagelibrary.org/images/8476
Fig. 4: Intestinal epithelium from the adult midgut of Drosophila melanogaster were immuno-stained for the cell periphery (integrin, red), nuclei (DAPI, blue) and stem cells (green). Nuclei are not seen in the tiny stem cells. The system was used to determine the role of intestinal stem cells in establishing the size of the gut in response to changes in food availability. Courtesy of Lucy O'Brien David Bilder. cellimagelibrary.org/images/39686

The features that The Cell offers

In addition to the value The Cell offers the researcher as mentioned above, this database also has a wide array of features for users, be they researchers, educators, students, or the public.

The Cell utilizes the Web Image Browser (WIB). The WIB is an easy to use, intuitive way to explore high-resolution images. It gives the user the capability to zoom and see the great detail present in these images. Using The Cell’s other Detailed Viewer, the user can also explore 4D images, those that are both a Z series and a time series.

Additionally for users, there are free accounts that also contain some useful features. With a free account the user can define Areas of Interest, and upon returning to The Cell, these Areas of Interest are updated with recent images so that the user has a customized homepage. An account also provides the ability to tag photos to certain photoboxes for easy reference  later. The user can create and define as many of these as needed or desired.

The Cell has some very exciting features planned for the future development of these current features. The user can “friend” other researchers and share photoboxes with them. Or perhaps an educator looking for a set of images to explain mitosis could share a photobox with other educators. In the future, Areas of Interest and Advanced Searches will be accessible by personal subscription, so that when images matching personal interests are entered into the system, an email will alert the user that new images are waiting.

Paramecium multimicronucleatum - Video of the Contractile Vacuole Complex. In vivo CVC filling/expulsion cycles. A CV in a compressed cell is observed in side view undergoing cycles of filling (diastole) and expulsion (systole) of its fluid content as the CV membrane fuses then separates from the plasma membrane and with one radial arm. Movies were taken by Dr. Tomomi Tani with differential interference contrast optics attached to a Leica inverted microscope. A Leica Fluotar x63 objective lens (NA = 0.7) was used. The video was taken by Tomomi Tani and Richard Allen.  cellimagelibrary.org/images/9692

The way to submit images

A resource such as this is as useful as the community makes it. The Cell needs participation from researchers not only to contribute to and use the library but also to provide feedback about what might be needed.

To start, The Cell needs images - and not just those already published (In fact there are often copyright encumbrances on those but The Cell does have arrangements with some publishers). For more information please see the Licensing Policy.

To submit images please use The Cell’s online upload capability for many of the more common data formats. Should there be data straight from the microscope or a format not handled by the online uploader, The Cell can almost certainly handle it with the DataRollup software. This process can also be used to submit large series of images as a batch. This software uses the Bio-Formats.

The way to join The Cell community

First and foremost, for any questions, comments or suggestions please contact David Orloff (dorloff@ascb.org), Senior Manager, Image Library.

To follow along with The Cell community and learn of new developments, please join one or more of these social media:
LinkedIn
Facebook  
Twitter 
Image of the Week

The ASCB welcomes feedback, including suggestions for the library’s improvements, at dorloff@ascb.org.

 

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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