To What Extent Does Downsampling, Compression, and Data Scarcity Impact Renal Image Analysis?

Abstract

The condition of the Glomeruli, or filter sacks, in renal Direct Immunofluorescence (DIF) specimens is a critical indicator for diagnosing kidney diseases. A digital pathology system which digitizes a glass histology slide into a Whole Slide Image (WSI) and then automatically detects and zooms in on the glomeruli with a higher magnification objective will be extremely helpful for pathologists. In this paper, using glomerulus detection as the study case, we provide analysis and observations on several important issues to help with the development of Computer Aided Diagnostic (CAD) systems to process WSIs. Large image resolution, large file size, and data scarcity are always challenging to deal with. To this end, we first examine image downsampling rates in terms of their effect on detection accuracy. Second, we examine the impact of image compression. Third, we examine the relationship between the size of the training set and detection accuracy. To understand the above issues, experiments are performed on the state-of-the-art detectors: Faster R-CNN, R-FCN, Mask R-CNN and SSD. Critical findings are observed: (1) The best balance between detection accuracy, detection speed and file size is achieved at 8 times downsampling captured with a 40 χ objective; (2) compression which reduces the file size dramatically, does not necessarily have an adverse effect on overall accuracy; (3) reducing the amount of training data to some extents causes a drop in precision but has a negligible impact on the recall; (4) in most cases, Faster R-CNN achieves the best accuracy in the glomerulus detection task. We show that the image file size of 40 χ WSI images can be reduced by a factor of over 6000 with negligible loss of glomerulus detection accuracy.