Web-based Stereo Rendering for Visualization and Annotation of Scientific Volumetric Data

摘要

Advancement in high-throughput microscopy technology such as the Knife-EdgeScanning Microscopy (KESM) is enabling the production of massive amounts of high-resolutionand high-quality volumetric data of biological microstructures. To fullyutilize these data, they should be efficiently distributed to the scientific research communitythrough the Internet and should be easily visualized, annotated, and analyzed.Given the volumetric nature of the data, visualizing them in 3D is important. However,since we cannot assume that every end user has high-end hardware, an approachthat has minimal hardware and software requirements will be necessary, such as astandard web browser running on a typical personal computer. There are several webapplications that facilitate the viewing of large collections of images. Google Mapsand Google Maps-like interfaces such as Brainmaps.org allow users to pan and zoom2D images efficiently. However, they do not yet support the rendering of volumetricdata in their standard web interface.The goal of this thesis is to develop a light-weight volumetric image viewer usingexisting web technologies such as HTML, CSS and JavaScript while exploiting theproperties of stereo vision to facilitate the viewing and annotations of volumetric data.The choice of stereogram over other techniques was made since it allows the usage ofraw image stacks produced by the 3D microscope without any extra computation onthe data at all. Operations to generate stereo images using 2D image stacks includedistance attenuation and binocular disparity. By using HTML and JavaScript that are computationally cheap, we can accomplish both tasks dynamically in a standardweb browser, by overlaying the images with intervening semi-opaque layers.The annotation framework has also been implemented and tested. In order forannotation to work in this environment, it should also be in the form of stereogramand should aid the merging of stereo pairs. The current technique allows users toplace a mark (dot) on one image stack, and its projected position onto the otherimage stack is calculated dynamically on the client side. Other extra metadata suchas textual descriptions can be entered by the user as well. To cope with the occlusionproblem caused by changes in the z direction, the structure traced by the user willbe displayed on the side, together with the data stacks. Using the same stereo-gramcreation techniques, the traces made by the user is dynamically generated and shownas stereogram.We expect the approach presented in this thesis to be applicable to a broaderscientific domain, including geology and meteorology.