Arctique: An artificial histopathological dataset unifying realism and controllability for uncertainty quantification

Uncertainty Quantification (UQ) is crucial for reliable image segmentation. Yet, while the field sees continual development of novel methods, a lack of agreed-upon benchmarks limits their systematic comparison and evaluation: Current UQ methods are typically tested either on overly simplistic toy datasets or on complex real-world datasets that do not allow to discern true uncertainty. To unify both controllability and complexity, we introduce Arctique, a procedurally generated dataset modeled after histopathological colon images. We chose histopathological images for two reasons: 1) their complexity in terms of intricate object structures and highly variable appearance, which yields challenging segmentation problems, and 2) their broad prevalence for medical diagnosis and respective relevance of high-quality UQ. To generate Arctique, we established a Blender-based framework for 3D scene creation with intrinsic noise manipulation. Arctique contains 50,000 rendered images with precise masks as well as noisy label simulations. We show that by independently controlling the uncertainty in both images and labels, we can effectively study the performance of several commonly used UQ methods. Hence, Arctique serves as a critical resource for benchmarking and advancing UQ techniques and other methodologies in complex, multi-object environments, bridging the gap between realism and controllability. All code is publicly available, allowing re-creation and controlled manipulations of our shipped images as well as creation and rendering of new scenes.

BioTracker: An Open-Source Computer Vision Framework for Visual Animal Tracking

The study of animal behavior increasingly relies on (semi-) automatic methods for the extraction of relevant behavioral features from video or picture data. To date, several specialized software products exist to detect and track animals' positions in simple (laboratory) environments. Tracking animals in their natural environments, however, often requires substantial customization of the image processing algorithms to the problem-specific image characteristics. Here we introduce BioTracker, an open-source computer vision framework, that provides programmers with core functionalities that are essential parts of a tracking software, such as video I/O, graphics overlays and mouse and keyboard interfaces. BioTracker additionally provides a number of different tracking algorithms suitable for a variety of image recording conditions. The main feature of BioTracker is however the straightforward implementation of new problem-specific tracking modules and vision algorithms that can build upon BioTracker's core functionalities. With this open-source framework the scientific community can accelerate their research and focus on the development of new vision algorithms.