Whole Slide Imaging Performance
Constantin S Friedman, Liza Rivera, Victor Brodsky. New York-Presbyterian Hospital/Weill Cornell Medical College, New York, NY
Background: Whole-slide scanning is becoming increasingly prevalent, but there is a lack of real-world data on the performance of whole-slide scanning systems. Our preliminary data had indicated that scan time (adjusting for the slides which need to be re-scanned and manual steps) at “20X” averages 5.18 minutes per slide and average file size was 498 megabytes; whereas at “40X” average time 27.58 minutes per slide, and average file size was 726 megabytes. As a scanning service was being implemented at NYP/Weill-Cornell, we analyzed scanner speed and workload for a larger sample of scanned slides, in order to enable institutions interested in scanning to define the time, personnel and storage requirements.
Design: Slides selected by attending pathologists were scanned using the Aperio Scanscope AT (2012); Console version 188.8.131.523. The slides comprised a mix of teaching slides, consult cases, and surgical pathology cases; the pathologists could choose to scan at “20x” (0.46 microns/pixel) or “40x” (0.22 microns/pixel).
Results: Over a 60-day period, 2433 slides were scanned; 2203 slides were scanned at “20x” and 230 were scanned at “40x”. The average time to scan each slide at “20x” was 3.76 min. Factoring in the observed 2.5% rescan rate increased the time to 3.86 minutes. Including the pre and post-scan manual steps, which averaged 1.55 minutes per slide, the total average time per “20x” slide was 5.41 minutes. The average time to scan each slide at “40x” was 20.38 min. Factoring in the observed 5.5% rescan rate increased the time to 21.50 minutes. Including the manual steps, the total average time per “40x” slide was 23.05 minutes. Scanning at “20x” resulted in an average file size of 560 megabytes, and scanning at 40x resulted in an average file size of 605 megabytes. An average of 40.55 slides per day were scanned, with a maximum of 154 slides.
Conclusions: The scan times and storage requirements for “20x” slides increased compared with our previous data, whereas those for “40x” slides decreased. The decrease in average “40x” file size may be attributable to a large number of immunostained biopsy slides resulting in better compression ratios. We had previously calculated that a 7 hour work day of 1 full-time employee (FTE), followed by 16 hours of machine scan time can result in a predicted maximum of 260 slides scanned at “20x”. Currently with 3.5 hours of daily FTE time 40.55 slides per day were scanned as we develop the scanning service. While scanning at “40x” significantly increased the scan time, having the attending pathologists choose the magnification resulted in only 10% of slides being scanned at “40x”.
Wednesday, March 6, 2013 1:00 PM
Poster Session VI # 262, Wednesday Afternoon