Towards Advanced Interactive Visualization for Virtual Atlases

Under embargo until: 2020-07-24An atlas is generally defined as a bound collection of tables, charts or illustrations describing a phenomenon. In an anatomical atlas for example, a collection of representative illustrations and text describes anatomy for the purpose of communicating anatomical knowledge. The atlas serves as reference frame for comparing and integrating data from different sources by spatially or semantically relating collections of drawings, imaging data, and/or text. In the field of medical image processing, atlas information is often constructed from a collection of regions of interest, which are based on medical images that are annotated by domain experts. Such an atlas may be employed, for example, for automatic segmentation of medical imaging data. The combination of interactive visualization techniques with atlas information opens up new possibilities for content creation, curation, and navigation in virtual atlases. With interactive visualization of atlas information, students are able to inspect and explore anatomical atlases in ways that were not possible with the traditional method of presenting anatomical atlases in book format, such as viewing the illustrations from other viewpoints. With advanced interaction techniques, it becomes possible to query the data that forms the basis for the atlas, thus empowering researchers to access a wealth of information in new ways. So far, atlas-based visualization has been employed mainly for medical education, as well as biological research. In this survey, we provide an overview of current digital biomedical atlas tasks and applications and summarize relevant visualization techniques. We discuss recent approaches for providing next-generation visual interfaces to navigate atlas data that go beyond common text-based search and hierarchical lists. Finally, we reflect on open challenges and opportunities for the next steps in interactive atlas visualization.acceptedVersio

Real-time super resolution contextual close-up of clinical volumetric data

Bibliography: p. 98-104Some pages are in colour

Real-Time Super Resolution Contextual Close-up of Clinical Volumetric Data

We present an illustrative visualization system for real-time and high quality rendering of clinical volumetric medical data. Our technique is inspired by a medical illustration technique for depicting contextual close-up views of selected regions of interest where internal anatomical features are rendered in high detail. Our method integrates four important components: decimation of original volume for interactivity, B-spline subdivision for super-resolution rendering, fast gradient quantization technique for feature extraction and GPU fragment shaders for gradient dependent rendering and transfer functions. Examples with clinical CT and MRI data demonstrate the capabilities of our system. Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: I.3.3 Picture/Image Generation J.3 [Computer Applications]: Life and Medical Sciences 1

Visible Ape Project: divulgando a anatomia dos grandes primatas através modelos 3D e ilustrações científicas

Com o surgimento de novas tecnologias, associada á ilustração do conhecimento científico, mecanismo de linguagem gráfica utilizado para comunicar ciência, e a constante procura de novos métodos de criação utilizando técnicas digitais, enquanto recursos documentais e didáticos - incluindo ilustração 3D – cada vez mais se constata que estes podem auxiliar numa melhor perceção e conhecimento sobre a natureza (sensibilizando e consciencializando). Neste trabalho, foram criados de raiz vários modelos 3D objetivos de alguns sistemas vitais com especial relevância para o sistema muscular do chimpanzé, bonobo, o Orangotango, gorila e gibão-comum, usando a aplicação de escultura tridimensional virtual Zbrush. Esses modelos servirão como base para modelar os sistemas musculares de outros grandes primatas. Ambos, modelos 3D e ilustração científica serão usados na plataforma “Visible Ape Project”. Este projeto foi criado com o objetivo de divulgar exclusivamente informações massivas e de pormenor sobre a anatomia e dos principais primatas, por meio de modelos cientificamente corretos e esteticamente apelativos (arquétipo 3D), a fim de transbordar as fronteiras da comunidade académica e atingir também um público não-especializado, mais generalizado, comunicando uma mensagem cientificamente elaborada e complexa, mas que, desta forma, resultará de mais fácil perceção, interpretação e assimilação.With the emergence of new technologies, associated with the illustration of scientific knowledge, graphic language mechanism used to communicate science, and the constant search for new methods of creation using digital techniques, as documental and didactic resources - including 3D illustration - increasingly become notes that these can help in a better perception and knowledge about nature (raising awareness and raising awareness). In this work, several objective 3D models of some vital systems were created from scratch, with special relevance to the muscular system of the chimpanzee, bonobo, the Orangutan, gorilla and common gibbon, using the application of three-dimensional virtual sculpture software Zbrush. These models will serve as a basis for modeling the muscle systems of other great apes. Both 3D models and scientific illustration will be used in the “Visible Ape Project” platform. This project was created with the objective of exclusively disclosing massive and detailed information about the anatomy and the main primates, through scientifically correct and aesthetically appealing models (3D archetype), in order to cross the boundaries of the academic community and also achieve a non-specialized, more generalized public, communicating a scientifically elaborated and complex message, but which, in this way, will result in easier perception, interpretation and assimilation.Projeto “Visible Ape Project”. Financiado pelo a National Science FundationMestrado em Biologia Aplicad

Focus+Context via Snaking Paths

Focus+context visualizations reveal specific structures in high detail while effectively depicting its surroundings, often relying on transitions between the two areas to provide context. We present an approach to generate focus+context visualizations depicting cylindrical structures along snaking paths that enables the structures themselves to become the transitions and focal areas, simultaneously. A method to automatically create a snaking path through space by applying a path finding algorithm is presented. A 3D curve is created based on the 2D snaking path. We describe a process to deform cylindrical structures in segmented volumetric models to match the curve and provide preliminary geometric models as templates for artists to build upon. Structures are discovered using our constrained volumetric sculpting method that enables removal of occluding material while leaving them intact. We find the resulting visualizations effectively mimic a set of motivating illustrations and discuss some limitations of the automatic approach