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Richard Rainbolt

Richard Rainbolt
Microscopes Intl. LLC

August 18, 2017

Blog
How Fast Do You Need to Scan?

Quickly Scanning Slides with the uScope Whole Slide Scanner

One of the most common questions we are asked about the uScope family of whole slide scanners is, "How fast does it scan a slide?" There is a simple answer to that question and there is a complex (but far more accurate) answer.

So, How Fast Does the uScope Scan a Slide?

Under ten (10) minutes at 20x. That's our stock answer. In reality, scan times are closer to eight (8) minutes. But, of course, there is much more to it than simply a number of minutes.

What Magnification is Used?

Objective magnification is a huge determining factor in scan speed. The reason is simple, higher magnification puts less image area on the camera, so more images must be captured. We use a 20x objective as the baseline for speed calculations. It's pretty easy to calculate scan speed differences once you know the objective magnification.

  • A 40x objective shows half the width and height of a 20x objective. So, it takes 4 times longer to scan with a 40x objective than it does with a 20x objective.
  • A 60x objective shows one-third the width and height of a 20x objective. So, it takes 9 times longer to scan with a 60x objective than it does with a 20x objective.

By the same token, scanning with a 10x objective would be about 4 times faster than scanning with a 20x objective.

How Big is a Slide?

Nearly all whole slide scanner manufacturers (us included) use an area of 15mm x 15mm (225mm2) as the scan region of a "whole slide". This is roughly the area under a square cover slip. It seems like a reasonable definition to use for the purpose of determining a scan time specification.

For the uScopeMXII and uScopeHXII this is equivalent to roughly 2,800 fields at 20x. And, it takes about six (6) minutes to scan that many fields. I know I said ten minutes above. So, you're probably wondering where the other four minutes went?

Post Processing

We use a technology called Deep Zoom to build and display large images. It is a Microsoft technology that's pervasive in applications and on the web (take a look at openseadragon and openslide). After scanning a slide, the uScope Navigator software optionally processes the individual field images and combines them into a Deep Zoom image set. This generally takes under four (4) minutes for a 15mm x 15mm scan—so, about ten (10) minutes in total.

Post processing involves several steps, such as:

  • Applying image filters (that you customize to fit your needs) to the scanned image fields,
  • Analyzing every field in the scan for image processing,
  • Applying image processing to each field in the scan (to improve image flatness or expand contrast, for example),
  • Combining fields into a large image,
  • Saving image tiles. This is required to create the Deep Zoom Image which is displayed using the Deep Zoom viewer.

There are a few parts of this process that can be optimized (depending on your requirements). If you don't need to filter or process the scanned images, those steps can be skipped.

Starting with uScope Navigator v4.3 (available September 2017), image fields may be combined as the slide is scanned. This will speed up post processing. In most cases, only the step of saving the Deep Zoom tiles is required.

Of course, if you have no need for a large image, you can skip the post processing and Deep Zoom Image generation entirely.

Other Factors

There are several other factors that contribute to the scan speed that you can control.

Focus Method

One of the largest contributors to scan speed (or lack, thereof) is how each field is focused. The uScope Navigator Software offers several focus methods to choose from. Each has its own advantages and caveats, which can affect image quality and scan time. Ultimately, you are the best person to decide the balance between image quality and scan speed.

  • Initial Focus
    The initial focus method allows you to set the initial focus (a single focus point) that is used for the entire scan. This is the fastest way to scan a slide. It is best used with tissue samples that are extremely thin (where focus doesn't change across the slide) or with specimens that are extremely thick (like insects) where general focus of the whole scan is desirable.
  • Fast Stack
    The fast stack focus method is similar to the initial focus method. After setting the initial focus the uScope Navigator Software captures a very few images above and below your focus point (typically one above and one below at your discretion) and chooses the best focused image. This is a very fast way to scan and it is often the best choice for pathology labs whose slide preparation yields four (4) microns thick sections.
  • Exhaustive Stack
    The exhaustive focus method is the slowest but most accurate. It should be used when best focus is critical. The uScope Navigator Software captures a very deep stack (typically 10 microns deep) of images of each field. The best-focused image is selected based on a contrast detection algorithm. This method is the best choice for thick sections or sections that are very inconsistent.
  • Predictive Focus
    The predictive focus method is the second fastest way to scan. This method is what we use for timing our scans. It provides the best trade-off between focus and scan time. When this focus method is used, the uScope Navigator Software collects focus points from within your region of interest. It creates a focus map of the specimen and captures each field at the predicted focus point.

The parameters for each focus method are completely user-configurable. You can experiment to determine the settings that work best for your slides, workflow, and performance requirements.

Scanning Multiple Regions

Many slides have multiple regions to scan that are spread out over the surface of the slide. Scanning a large area that's mostly empty is not a fast way to scan. Often, selecting and scanning each region separately is faster than scanning a large, mostly empty, area of the slide.

Conclusion

There are many factors that contribute to scan speed and performance. Hopefully, we have given you some insight into what speeds up scans and what slows them down.

Now, it's your turn to help us out. Tell us what you think are the real requirements for scanning speed.

Contact Microscopes International or speak with your local distributor.
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