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Jon Ward

Jon Ward
Microscopes Intl. LLC

January 7, 2016

Blog
Deep Zoom Images

Large Image Viewer for Microscopists

Deep Zoom is a technology developed for efficiently transmitting and viewing very large images. It allows you to pan around and zoom in and out of large, high resolution images. It is fast because it only downloads the parts of the image currently displayed. Other parts are downloaded as you pan to (or zoom into them). Animations hide jerkiness in transitions and make the whole experience fairly smooth. Deep Zoom operates in a fashion that is very similar to that of Google Maps.

Deep Zoom started life at a company called Seadragon Software which was acquired by Microsoft in the mid 2000's. The technology was incorporated into Silverlight and appears to be used by Microsoft in various other applications Deep Zoom Composer. An open source project, Open Seadragon, is the basis for the Deep Zoom implementation offered by Microscopes International.

What are Deep Zoom Images?

You can think of Deep Zoom images as pyramidal sets of small image tiles that can be transmitted quickly. The tiles at the bottom layer of the pyramid are mapped pixel-for-pixel to the original large image. Tiles at each higher level are mapped at one-half the resolution of the level below. This progression continues to the top of the pyramid which is the zoomed-out representation of the whole image.

How are Deep Zoom Images Used?

There are several scenarios where Deep Zoom images are particularly useful. We envision Deep Zoom to be a review tool for microscopists and researchers who need to look at specific areas of an image that is captured from a standard glass slide as viewed through a microscope.

Converting Existing Images for Deep Zoom

There are several different ways to convert images into Deep Zoom image sets. For microscopy, a great resource is OpenSlide.org. OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides) and convert them into Deep Zoom image sets. OpenSlide supports various formats including Aperio (.svs, .tif.), Hamamatsu (.vms, .vmu, .npdi), Leica (.scn), and Philips (.tiff.)

Why is Deep Zoom Necessary?

Unfortunately, there are limitations to using whole-slide images. Often, these are very, very large, high-resolution images. Using standard computer software can be challenging because the tools are typically designed for images that can comfortably be uncompressed into RAM or a swap file. Whole-slide images routinely exceed the available RAM and can occupy tens of gigabytes.

In addition, there is no universal data format for whole-slide images, so each vendor implements its own formats, libraries, and viewers. Vendors do not always document their formats completely. And, since a vendor’s library or viewer is the only way to view a particular whole-slide image, doctors and researchers can be unnecessarily tied to a particular vendor. Finally, few (if any) vendors provide libraries and viewers for non-Windows platforms. Some have adopted a server approach, pushing tiles through a web server, or using Java applets, but these approaches have shortcomings in high-latency or non-networked environments. There are image formats like TIFF that support images composed of tiles. However, image viewer support for these TIFF features is not required and is not included in many TIFF viewers.

Deep Zoom provides a consistent viewer (a web browser) and image format that is easily transported to different viewers. The Deep Zoom image sets are no smaller than whole-slide images, but they are easily stored and shared using traditional sharing technologies (flash drive, Dropbox, iCloud Drive, Google Drive, and so on).

Is there an Easy Way to Scan Slides and Create Deep Zoom Images?

Yes. The uScopeMXII Digital Microscope from Microscopes International natively creates Deep Zoom image sets you can share on your company intranet or internet sites. No additional software or external applications are required.

The uScopeMXII comes in a variety of configurations with 20x (0.4NA), 40x (0.65NA), and 60x (0.85NA) objectives. It is portable and interfaces with your PC or laptop using only a single USB interface. User-defined filter sequences allow you to apply multi-step image processing enhancements (brightness, contrast, look-up tables, gamma control, sharpness, smoothing, and flat field correction) to captured images.

According to Mr. Oliver Kim, editor in chief of MicrobeHunter Microscopy Magazine, "Digitizing large areas of a slide at high resolution has never been easier. The uScope is a digital microscope which captures high resolution overlapping images of a slide and combines it into a final stitched image. Is virtual microscopy starting to find its way into the home-lab and into the education sector?" We certainly think so!

So, take a look at some of the deep zoom images above and tell us your thoughts. Is Deep Zoom a viable technology for your lab? How do you currently share your scanned slide images for review?


Jon

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