An interactive tool for ROI extraction and compression on whole slide images

In this paper, we presented an integrated graphical user interface (GUI) tool, which supports interactive regions of interest (ROIs) extraction from whole slide imagery and provides lossless compression of the ROIs extracted, leading to over 40 times compression on the original image. As a case study to demonstrate the usefulness of this tool, we applied a simple block-matching technique to detect malaria infected cells from a whole slide image based on a template provided by the user, who can control the percentage of the extracted pixels by varying the acceptable similarity threshold. The tool allowed us to conduct a comparative study on the efficiencies of several compression methods (including Bzip2, Winzip and Shape-Adaptive JPEG 2000) on image subsets that are continuously variable. This case study provides new insights into the interactions between the geometry of ROIs and the amount of compression achievable on medical images.