Whole Slide Imaging: A Crash Course

The Digital Pathology Association recently released a white paper that provides a comprehensive overview of whole slide imaging, including the challenges and advantages of implementing this technology into existing workflows. You can read the full document here, but we’ve assembled the essential details in this article as a crash course on whole slide imaging.

What is Whole Slide Imaging?

The term “whole slide imaging” refers to the conversion of an entire microscope slide into a digital image that can be viewed on a computer screen. Whole slide images are captured using a “whole slide scanner”, which is essentially a high-end microscope with a built-in camera that is specifically designed to efficiently capture these images. The scanner captures whole slide images in a series of smaller “tiles” that are digitally “stitched” together into a high-resolution image of the entire slide. This allows researchers and pathologists to view these images on a computer screen with the same magnification with which they would view a slide under a microscope. There are many advantages of whole slide images versus maintaining a library of glass slides, but there are also challenges to consider when implementing whole slide imaging technologies.

Challenges Presented by Whole Slide Imaging

Whole slide images are extremely high-resolution, allowing scientists to differentiate individual cells at high magnification. This also means that the size of these image files can be very large, which can make them difficult to share. Image compression can be useful in reducing file sizes to make them less prohibitive, but compress too much and valuable information used for research or patient diagnosis can be lost. Cloud-based image management platforms such as ImageDx™ offer a good solution to combating the challenges of sharing large images.

Triplex whole slide image of breast carcinoma at magnification x5, x10, x20, and x40, respectively.

Whole slide images can be analyzed using different computational tools, but the quality of the data is limited by the quality of the image, the quality of the staining, and even the quality of the tissue itself. It is important to have multiple quality control checks throughout the process of sectioning tissue, staining tissue, and capturing images to ensure that any analysis will output reliable results.

Whole slide imaging is still relatively new, and is in the early stages of being widely integrated into pathology workflows. As with any new technology, there is a cost to purchasing the necessary equipment, training people to use that equipment, and incorporating this new equipment into existing processes (for example, including quality control steps throughout a workflow). For any organization interested in using whole slide imaging, this is an initial hurdle that must be overcome. Companies such as Reveal Biosciences offer whole slide imaging services, providing high quality whole slide images to clients without the need for the client to purchase equipment or train staff.  Services such as this can save clients significant time and money.

Advantages of Whole Slide Imaging

One major difficulty in relying upon traditional glass microscope slides is that it takes effort and storage space to organize and preserve them. Regardless of how well-preserved they are, they can break or degrade in quality over time. Important diagnostic information is often included within these slides, and this information is lost as the slide degrades. This is a non-issue with whole slide imaging; these images require next to no physical storage space, and the staining/tissue quality is forever preserved at the time of scanning. While we already discussed the challenges of sharing large image files, whole slide images are easier to share than glass slides, which need to be physically shipped between locations. This eliminates the risk of breakage during transportation and allows slides to be shared between locations much more rapidly. In the field of pathology, this enables patient samples to be easily shared with a specialist, even if there are no specialists located nearby.

Example of a whole slide image with annotations to highlight regions of interest.

Whole slide imaging also facilitates new tools for viewing and organizing microscope slides on a computer. Digital images can be navigated faster than a slide under a microscope, and scientists can add annotations directly onto the image to point out regions of interest. The image files themselves can be categorized in much more intuitive ways, reducing the time it takes to synthesize information across multiple microscope slides. These image viewing tools are also excellent for presentation and education purposes within fields such as pathology, allowing presenters to quickly point out regions of interest and allowing educators to standardize their curriculum with representative example images.

Whole slide image without mask (above the red line) and with mask (below the red line) used for computational analysis.

Computational analysis of whole slide images allows objective, quantitative data to drive important decisions in research and pathology. With a strong set of reference data, deep neural networks can be trained to process whole slide images and act as a tool to aid pathologists and researchers. Without whole slide images, these decisions would be more subjective and potentially inconsistent.

Whole Slide Imaging at Reveal Biosciences

With all of these advantages, it is clear that whole slide imaging is the future. Reveal specializes in developing deep learning-based models to generate quantitative data from whole slide images.  This data can be used for research or clinical applications.  We include multiple quality control checkpoints within our workflow to ensure the highest-quality images and data. Our image management platform, ImageDx™, makes it easier than ever for us to share whole slide images and data with our clients.

Contact us to learn how we can apply these technologies to your research.


Zarella, Mark D., et al. “A Practical Guide to Whole Slide Imaging: A White Paper From the Digital Pathology Association.” Archives of Pathology & Laboratory Medicine 143.2 (2018): 222-234.

By: Jeremy Warner, Scientific Marketing Associate, Reveal Biosciences