Ultrafast Focus Detection for Automated Microscopy

Abstract: Technological advancements in modern scientific instruments, such as scanning electron microscopes (SEMs), have significantly increased data acquisition rates and image resolutions enabling new questions to be explored; however, the resulting data volumes and velocities, combined with automated experiments, are quickly overwhelming scientists as there remain crucial steps that require human intervention, for example reviewing image focus. We present a fast out-of-focus detection algorithm for electron microscopy images collected serially and demonstrate that it can be used to provide near-real-time quality control for neuroscience workflows. Our technique, \textit{Multi-scale Histologic Feature Detection}, adapts classical computer vision techniques and is based on detecting various fine-grained histologic features. We exploit the inherent parallelism in the technique to employ GPU primitives in order to accelerate characterization. We show that our method can detect of out-of-focus conditions within just 20ms. To make these capabilities generally available, we deploy our feature detector as an on-demand service and show that it can be used to determine the degree of focus in approximately 230ms, enabling near-real-time use.