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JCB Virtual Nanoscopy Viewer is not "Google Earth" for Cell Biologists but is a Good Start
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JCB Virtual Nanoscopy Viewer is not "Google Earth" for Cell Biologists but is a Good Start

At the start of August 2012, the Journal of Cell Biology (JCB) proclaimed in a press release that their new JCB Data Viewer was a major breakthrough, and the equivalent of the mirror world “Google Earth” for cell biologists. Well, the capabilities of the viewer are a breakthrough all right, but they are not yet up to the standards expected of a mirror world program.

As those intimately familiar with VR will know, a mirror world is a virtual reality that recreates our world as closely as possible. A mirror to our world in the most literal sense. Google Earth being the most well known of these – an attempt to mirror the entire Earth.

The JCB data viewer on the other hand, thinks of the microscale. As a tool of use to cell biologists, it sounded too good to be true. A viewer able to mirror the full functionality of a cell so we can view it from any angle or depth we choose? That would truly revolutionise the field of study!

Of course such hopes are bound to be disappointed. The new viewer is nothing of the sort. Rather, it is a method to share data collected from various imaging methods, including the electron microscope, by means of a browser-based 3D-capable data viewer, which lets researchers from different labs share their data in a standard format that can be examined by other researchers, via JCBs website.

It has the capability to be a true mirror-world viewer for micro and nanoscale imagery, but it is not currently being used as such. Even so, it is far, far ahead of anything cell biology researchers had before.

The viewer is more a panorama generator than an actual VR interface.

All images uploaded to the journal as supplement to submitted manuscripts is archived as freely accessible material by JCB themselves. Sadly the viewer's capabilities are sorely limited, to simple zoom in, zoom out, and repositioning capabilities.

As the site itself puts it:

The JCB DataViewer is a web-based, multi-dimensional image data-viewing application. It is a tool for visualization and simple analysis of original image data files associated with JCB articles.

Image data uploaded by authors as a supplement to submitted manuscripts is archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software.

Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots.

It is little more than an image library system as things currently stand, and far from being a mirror world in its own right. Yet, as stated before, it has the capability to view files in as 3D environments. The problem is, nobody is uploading that kind of data as things are. The problem may not then lay with the software, but with the users not taking full advantage of it. Even so, there is more than meets the eye in many of the images displayed.

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 created the viewer as a means to address that problem by stitching thousands of electron microscopy images into single, high-resolution panoramas. 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.

They could then use the JCB DataViewer, anyone can navigate the zebrafish image from the level of the whole, 1.5 millimeter-long embryo down to subcellular structures. When you add in the possibility of seeing the displayed image in the full three dimensions, as a multitude of layers, each also nearly 300 gigapixels in size, it becomes clear that the tool is designed to image extremely massive datasets.

It is not a VR viewer, at least not yet. It is however, a massive increase in capability for handling huge datasets, for the average researcher. One which will scale to full 3D, as our data gathering and storing capabilities continue to increase.

References

Virtual Nanoscopy: Like “Google Earth” for Cell Biologists

JCB DataViewer

The JCB DataViewer scales up

Staff Comments

 


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