Microscopes Intl. LLC
August 18, 2017
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.
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.
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.
By the same token, scanning with a 10x objective would be about 4 times faster than scanning with a 20x objective.
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?
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:
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.
There are several other factors that contribute to the scan speed that you can control.
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.
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.
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.
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.