Stack or trash? Quality assessment of virtual slides

Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of these Whole Slide Images (WSI) has become a crucial issue. At this time, the quality of a WSI is verified a posteriori by a technician or by a pathologist. There is however a significant amount of WSI that are too insufficient in quality (blurred, bad colors, poor contrast.) to be used for diagnoses. These slides have then to be scanned again with delay thus slowing down the diagnostic workflow. To address this problem, we chose to design a method of quality assessment followed by reacquisition, as opposed to a process of enhancement or restoration [1,2]. Such process indeed too frequently results in the degradation of image quality, a key factor in medical diagnosis. The quality of a flat image can be defined by several quantifiable parameters such as color, brightness, and contrast. One of the most important parameters, yet difficult to assess, is the focus sharpness (i.e. the level of focus blur) [3]). Quality assessment of WSI is much more complex than that of flat images because of their intrinsic structure made of multiple magnification levels (pyramidal structure) and resolutions above the gigapixel. One study [4] has shown the possibility of comparing the tiles’ contrast and entropy in two WSI obtained with two different scanners digitizing the same slide. Another work [5] assessed the focus sharpness of the tiles of a WSI with the generation of a focus assessment map of the WSI at a given magnification level. However, both these methods still require a human eye to assess if the WSI must be accepted or discarded after the scan. We describe here a fast method to automatically assess quality and to accept or discard WSI at the time of acquisition.