The Giga-pixel Challenge: Full Resolution Image Analysis – Without Losing the Big Picture An open-source approach for multi-scale analysis and visualization of slide-scanner data

The amount of image data in a slide scanner image is usually in the giga-pixel range, inducing challenges for image analysis and visualization. At the same time, in order to maximize the information gained in these experiments and integrate expert knowledge with quantitative measurements, it is crucial to maintain the connection between high-resolution per-cell and per-region metrics with lower resolution relational metrics. We present a free and open-source framework for full resolution image analysis of large images, e.g. slide scanner data, with the possibility of visual examination and interaction at multiple resolutions. The interface enables seamless zooming and panning, with the option to toggle multiple layers, such as segmentation masks and classification results, on or off. We make use of the strength and flexibility of existing state-of-the-art opensource software for visualization, creating resolution pyramids, image registration and image analysis. Keywords—multi-scale image analysis, slide scanner data, open source