Managing Spatial Selections With Contextual Snapshots

Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data

Inspection of tissues using a light microscope is the primary method of diagnosing many diseases, notably cancer. Highly multiplexed tissue imaging builds on this foundation, enabling the collection of up to 60 channels of molecular information plus cell and tissue morphology using antibody staining. This provides unique insight into disease biology and promises to help with the design of patient-specific therapies. However, a substantial gap remains with respect to visualizing the resulting multivariate image data and effectively supporting pathology workflows in digital environments on screen. We, therefore, developed Scope2Screen, a scalable software system for focus+context exploration and annotation of whole-slide, high-plex, tissue images. Our approach scales to analyzing 100GB images of 109 or more pixels per channel, containing millions of individual cells. A multidisciplinary team of visualization experts, microscopists, and pathologists identified key image exploration and annotation tasks involving finding, magnifying, quantifying, and organizing regions of interest (ROIs) in an intuitive and cohesive manner. Building on a scope-to-screen metaphor, we present interactive lensing techniques that operate at single-cell and tissue levels. Lenses are equipped with task-specific functionality and descriptive statistics, making it possible to analyze image features, cell types, and spatial arrangements (neighborhoods) across image channels and scales. A fast sliding-window search guides users to regions similar to those under the lens; these regions can be analyzed and considered either separately or as part of a larger image collection. A novel snapshot method enables linked lens configurations and image statistics to be saved, restored, and shared with these regions. We validate our designs with domain experts and apply Scope2Screen in two case studies involving lung and colorectal cancers to discover cancer-relevant image features.

CAST: Effective and Efficient User Interaction for Context-Aware Selection in 3D Particle Clouds

We present a family of three interactive Context-Aware Selection Techniques (CAST) for the analysis of large 3D particle datasets. For these datasets, spatial selection is an essential prerequisite to many other analysis tasks. Traditionally, such interactive target selection has been particularly challenging when the data subsets of interest were implicitly defined in the form of complicated structures of thousands of particles. Our new techniques SpaceCast, TraceCast, and PointCast improve usability and speed of spatial selection in point clouds through novel context-aware algorithms. They are able to infer a user's subtle selection intention from gestural input, can deal with complex situations such as partially occluded point clusters or multiple cluster layers, and can all be fine-tuned after the selection interaction has been completed. Together, they provide an effective and efficient tool set for the fast exploratory analysis of large datasets. In addition to presenting Cast, we report on a formal user study that compares our new techniques not only to each other but also to existing state-of-the-art selection methods. Our results show that Cast family members are virtually always faster than existing methods without tradeoffs in accuracy. In addition, qualitative feedback shows that PointCast and TraceCast were strongly favored by our participants for intuitiveness and efficiency.