Virtual nanoscopy: Like 'Google Earth' for cell biologists

August 06, 2012

Just as users of Google Earth can zoom in from space to a view of their own backyard, researchers can now navigate biological tissues from a whole embryo down to its subcellular structures thanks to recent advances in electron microscopy and image processing, as described in The Journal of Cell Biology (JCB). An upgrade to the JCB DataViewer (http://jcb-dataviewer.rupress.org), JCB's browser-based image presentation tool, now also makes these data publicly accessible for exploration and discovery.

Since the early days of cell biology, electron microscopy has revealed cellular structures in exquisite detail. The technique has always been limited, however, by the fact that it can only capture a tiny portion of the cell in a single image at high resolution, making it difficult for researchers to relate the structures they see to the cell as a whole, let alone to the tissue or organ in which the cell is located. Viewing samples at lower resolution, on the other hand, can reveal the larger picture of a cell or tissue, but researchers then lose the benefit of seeing fine details.

A team of scientists from Leiden University Medical Center in the Netherlands has addressed this problem by developing new tools for stitching together thousands of electron microscopy images into single, high-resolution images of biological tissues--a "Google Earth" for cell biologists--which can be explored using the newly enhanced JCB DataViewer.

Faas et al. describe their recent advances to a technique called "virtual nanoscopy" in the August 6th issue of JCB. The researchers were able to stitch together over 26,000 individual images to generate an almost complete electron micrograph of a zebrafish embryo encompassing 281 gigapixels in total at a resolution of 16 million pixels per inch. Using the JCB DataViewer, anyone can navigate the zebrafish image from the level of the whole, 1.5 millimeter-long embryo down to subcellular structures.

The ability to integrate information across cells and tissues will provide researchers with exceptional opportunities for future discoveries. But the image's large size and complexity meant that providing access to Faas et al.'s data necessitated a major upgrade to the JCB DataViewer, a browser-based image hosting platform originally launched in 2008 to promote the sharing of original data associated with JCB publications.

"If you can image it, you should be able to publish it," says JCB Executive Editor Liz Williams. As a journal, "JCB remains committed to developing cutting-edge tools for the presentation of the data that drive progress in the field of cell biology."
-end-
About The Journal of Cell Biology

Founded in 1955, The Journal of Cell Biology (JCB) is published by The Rockefeller University Press. All editorial decisions on manuscripts submitted are made by active scientists in conjunction with our in-house scientific editors. JCB content is posted to PubMed Central, where it is available to the public for free six months after publication. Authors retain copyright of their published works and third parties may reuse the content for non-commercial purposes under a creative commons license. For more information, please visit www.jcb.org.

About the JCB DataViewer

The JCB DataViewer is an image hosting and presentation platform for original image data associated with articles published in JCB. Developed in a collaboration between Glencoe Software, Inc. (www.glencoesoftware.com) and the Rockefeller University Press (www.rupress.org), the JCB DataViewer was the first browser-based viewer for multidimensional microscopy image data. It is based on open source software built by the Open Microscopy Environment (OME; http://openmicroscopy.org).

Faas, F.G.A., et al. 2012. J. Cell Biol. doi:10.1083/jcb.201201140

Williams, E.H., et al. 2012. J. Cell Biol. doi:10.1083/jcb.201207117

Rockefeller University Press

Related Cell Biology Articles from Brightsurf:

Deep learning on cell signaling networks establishes AI for single-cell biology
Researchers at CeMM have developed knowledge-primed neural networks (KPNNs), a new method that combines the power of deep learning with the interpretability of biological network models.

RNA biology provides the key to cell identity and health
Two papers in Genome Research by the FANTOM Consortium have provided new insights into the core regulatory networks governing cell types in different vertebrate species, and the role of RNA as regulators of cell function and identity.

Cell biology: Your number's up!
mRNAs program the synthesis of proteins in cells, and their functional lifetimes are dynamically regulated.

Cell biology -- maintaining mitochondrial resilience
Mitochondria cannot autonomously cope with stress and must instead call on the cell for help.

Cell biology: All in a flash!
Scientists of Ludwig-Maximilians-Universitaet (LMU) in Munich have developed a tool to eliminate essential proteins from cells with a flash of light.

A biology boost
Assistance during the first years of a biology major leads to higher retention of first-generation students.

Cell-free synthetic biology comes of age
In a review paper published in Nature Reviews Genetics, Professor Michael Jewett explores how cell-free gene expression stands to help the field of synthetic biology dramatically impact society, from the environment to medicine to education.

Scientists develop electrochemical platform for cell-free synthetic biology
Scientists at the University of Toronto (U of T) and Arizona State University (ASU) have developed the first direct gene circuit to electrode interface by combining cell-free synthetic biology with state-of-the-art nanostructured electrodes.

In a first for cell biology, scientists observe ribosome assembly in real time
A team of scientists from Scripps Research and Stanford University has recorded in real time a key step in the assembly of ribosomes -- the complex and evolutionarily ancient 'molecular machines' that make proteins in cells and are essential for all life forms.

Cell biology: Endocannabinoid system may be involved in human testis physiology
The endocannabinoid system (ECS) may be directly involved in the regulation of the physiology of the human testis, including the development of sperm cells, according to a study in tissue samples from 15 patients published in Scientific Reports.

Read More: Cell Biology News and Cell Biology Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.