Optimizing Storage and Computational Efficiency: An Efficient Algorithm for Whole Slide Image Size Reduction

Abstract

ObjectiveTo efficiently store, transfer, and analyze whole slide imaging (WSI), we developed an image-processing algorithm to remove the unneeded background in a WSI and assemble tissue-containing parts into smaller WSIs without any change in tissue area image resolution. Patients and MethodsWe used histology slides of nondysplastic Barrett esophagus, low-grade dysplasia, and high-grade dysplasia, which were digitized using Aperio AT2 Scanner from January 1992 to September 2020. The algorithm involved converting color images to grayscale images, binarizing images by assigning zero to the background and 1 to the foreground, filling the holes and dilating the foreground masks, and extracting connected components. Using the coordinates of each component, the vertices of the smallest surrounding bounding box were calculated, and tissue-containing parts were cropped from the original slide. The smallest possible rectangle that encloses all bounding boxes containing tissue was found using the rectangle-packer package. ResultsThe algorithm resulted in a mean reduction of 7.11×. The performance of a previously developed deep learning model for the detection of Barrett esophagus dysplasia grade on the size-reduced WSIs was comparable with that on the original WSIs. ConclusionOur algorithm for WSI size reduction can assist researchers in storing, transferring, and analyzing WSIs while optimally using them in their workflow.