07 August 2012

Virtual Nanoscopy Enables Large Scale Composite Images

The electron microscope is a type of microscope that uses a beam of electrons to illuminate and create an image of a target specimen. The electron microscope has a greater resolving power than a light powered optical microscope allowing it to view smaller objects in greater detail.

Electron microscopes are able to do this because electrons have wavelengths about 100,000 times shorter than photons (light). They can achieve better than 50 picometer resolution and magnifications of up to about 10,000,000x whereas ordinary, non-confocal light microscopes are limited by diffraction to about 200 nanometer resolution and useful magnifications below 2000x.

It uses electrostatic and electromagnetic "lenses" to control the electron beam and focus it to form an image. These lenses operate somewhat similar to the glass lenses of an optical microscope that form a magnified image by focusing light on or through the specimen. Electron microscopes are used to observe a wide range of biological and inorganic specimens including microorganisms, cells, large molecules, biopsy samples, metals, and crystals. Industrially, the electron microscope is often used for quality control and failure analysis.

Image: Advances in “virtual nanoscopy” enable the generation of large-scale composite images of biological tissues, as described in The Journal of Cell Biology (JCB) and made accessible through an upgrade to JCB’s JCB DataViewer web application. Users can “zoom in” from a high-resolution, composite image of a zebrafish embryo (top) to detailed images of tiny subcellular structures (bottom). Credit: © Williams et al, 2012

Virtual nanoscopy: Like 'Google Earth' for cell biologists

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, JCB's browser-based image presentation tool, now also makes these data publicly accessible for exploration and discovery.

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. and the Rockefeller University Press, 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).

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.

Video: Eva Nogales (UC Berkeley): Introduction to Electron Microscopy

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."


Rockefeller University Press
Open Microscopy Environment (OME)
JCB DataViewer
Glencoe Software, Inc
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