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Pathology practice is entering a period of widespread adoption of digital workflows, as near real-time access to "digital slides" provides opportunities to greatly improve clinical results and accelerate research.

Image source: Huron Digital Pathology.

As Liron Pantanowitz, professor of pathology and biomedical informatics at the University of Pittsburgh Medical Center recently described, digital pathology is used in image analysis, education, remote pathology, centralized services, archiving, workflow efficiency, sub-specialty practice, and computational pathology. Aspect provides benefits.

However, Pantanowitz also warned that the digital workflow must be executed correctly, which first requires the successful realization of the digitization of the slide by scanning the entire slide. Handle this part correctly and it will positively benefit the rest of the pathology workflow.

Let's take a look at the seven most prominent pitfalls encountered throughout the slide scan and potential solutions to overcome them.

Most slide scanners expect a standard 1" x 3" slide to place a barcode on the top of the slide, so it is designed to read the barcode at that specific location. But sometimes, multiple barcodes are superimposed on each other, making the slides too thick to fit into the slide handling mechanism. Or, there may be multiple barcodes at multiple locations on the slide. Both of these situations may result in the need for time-consuming manual intervention.

Solution: Find a more convenient slide rack and image-based barcode capture. Look for a slide scanner that can handle changes in the thickness of the slide in case you need to place the barcode on top of another. For example, the slide holder on Huron Digital Pathology’s TissueScope LE™ scanner can handle thicker slides. In addition, the scanner uses image-based barcode capture, so barcodes can be read anywhere on the slide.

During the preparation of the slides, the slides may be damaged or broken. They can still be scanned, but special care must be taken. The slides may have to be scanned separately, which undermines the automation expected in digital pathology.

In many scanners, when the slide passes through the scanner during image acquisition, the slide handling mechanism may actually destroy the slide. This not only damages the slides, but also requires maintenance of the scanner to remove the damaged slides and glass. This is obviously an operational hazard for laboratory personnel.

Solution for trap #2 and #3: look for a harmless slide holder. Choose a scanner that can accommodate imperfect slides without affecting throughput to ensure the integrity of the slides. The TissueScope LE120 slide holder has a unique clamping system that can accept broken or chipped slides. And because it is tray-based, the scanner does not actually touch the slides, thus ensuring the safety of precious specimens and fragile glass.

Figure 1. Huron Digital Pathology slide rack to ensure the safety of slides. 

Most slide scanners are automated, and are usually designed to accommodate original prepared slides with little change. In fact, this is often not the case. Therefore, laboratory staff need to be extra careful to reduce the variability in the preparation process, because this will affect the success of image acquisition, and rescanning is costly to the efficiency of the workflow.

For example, take the Advanced Optical Microscope Facility (AOMF) in Toronto, Canada's largest microscope facility. General Manager James Jonkman and his staff actively guide those responsible for preparing the slides to follow these strict procedures to ensure the best results:

Solution: Find a suitable slide holder and use the scan preview. A little extra installation medium shouldn't ruin your day, so look for a scanner that can handle difficult slides without compromising throughput. In addition, if available, please use the preview function of the scanner to ensure that the scan settings are captured correctly. Make sure that your scanner can fully control the area of ​​interest, focus area, and other factors to ensure a successful scan.

Figure 2. Huron's interface makes users more capable of handling difficult slides. Image source: Huron Digital Pathology.

As Pitfall #4 shows, scan preview and settings are critical steps to ensure that all slides are properly imaged. However, this step can be very time consuming, consuming 10-20% of scanner throughput every day. Your expensive investment (medium-to-high-throughput slide scanner) does not acquire images, but sits idle. In addition, when spending on shooting low-resolution preview images, the functions of these cameras are often wasted. So, how can a digital pathology workflow increase throughput without sacrificing image quality?

Solution: Improve scanner throughput by uninstalling scan preview and settings. If the workflow can separate the preview acquisition from the final image acquisition, the imaging system will be optimally utilized to maximize throughput. Huron Digital Pathology's TissueSnap™ is used with TissueScope LE120 to achieve this.

Figure 3. TissueSnap is connected to the LE slide scanner to maximize throughput. Image source: Huron Digital Pathology.

When TissueScope LE120 is scanning, TissueSnap can capture preview images of slides that have not been scanned. The preview image is immediately sent to the user interface of the main scanner. As the scanner continues to acquire high-resolution images, the next batch of slides can be simultaneously previewed and set up without interruption.

In addition to separating image settings from high-throughput scanning, TissueSnap also has compact size and network capabilities, which means it can be placed almost anywhere in the laboratory. Various TissueSnap preview stations placed in different locations can provide data for a single high-throughput scanner to improve workflow.

After the image acquisition is complete, the digital slide may go through a series of other stages: image viewing, image management, image sharing, and image analysis. When the digital slide passes through this cycle, it may interact with different software systems, which may have different degrees of integration with image acquisition. For example, image analysis software may prefer a different file format than viewing software. The risk here is the additional investment in software development, the additional cost of a proprietary image viewer, or, at worst, incompatibility.

Solution: Open. Look for scanners that output in a non-proprietary file format. For example, TissueScope LE has created a BigTIFF, which can be read by almost all image management and image analysis software, making it fast and easy to integrate. This gives you a lot of freedom to easily mix and match hardware and software components and reduce costs.

Figure 4. TissueScope LE120 with 1” x 3”, 2” x 3” and 5” x 7” slide holders. Image source: Huron Digital Pathology.

Although most slides are standard sizes (approximately 1” x 3”), in some cases—especially in research areas—the tissue can be much larger. This is especially true for the entire loaded brain, breast, and prostate tissue. So, how do you deal with these larger slides?

Solution: Flexible. Choose a scanning solution that can accommodate multiple slide sizes. For example, Huron's TissueScope can accommodate standard and double-wide slides, as well as slides of any size up to 6” x 8”.

Huron Digital Pathology, headquartered in Waterloo, Ontario, Canada, has 20 years of designing precision imaging instruments. Our end-to-end digital full slice imaging solution for digital pathology includes our award-winning TissueScope™ digital slice scanner; TissueView™ image viewing, sharing and management platform; and our workflow enhancement accessories, including us Innovative TissueSnap™ preview scanning station.

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Last update: May 18, 2020 at 6:47 am

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Huron Digital Pathology. 2020. Seven pitfalls of full slide scanning. News-Medical, accessed December 14, 2021, https://www.news-medical.net/whitepaper/20170104/The-Seven-Pitfalls-of-Whole-Slide-Scanning.aspx.

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