Eng, Daniel C. (2008-12). Web-based Stereo Rendering for Visualization and Annotation of Scientific Volumetric Data. Master's Thesis. Thesis uri icon

abstract

  • Advancement in high-throughput microscopy technology such as the Knife-Edge Scanning Microscopy (KESM) is enabling the production of massive amounts of high-resolution and high-quality volumetric data of biological microstructures. To fully utilize these data, they should be efficiently distributed to the scientific research community through 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 approach that has minimal hardware and software requirements will be necessary, such as a standard web browser running on a typical personal computer. There are several web applications that facilitate the viewing of large collections of images. Google Maps and Google Maps-like interfaces such as Brainmaps.org allow users to pan and zoom 2D images efficiently. However, they do not yet support the rendering of volumetric data in their standard web interface. The goal of this thesis is to develop a light-weight volumetric image viewer using existing web technologies such as HTML, CSS and JavaScript while exploiting the properties 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 of raw image stacks produced by the 3D microscope without any extra computation on the data at all. Operations to generate stereo images using 2D image stacks include distance attenuation and binocular disparity. By using HTML and JavaScript that are computationally cheap, we can accomplish both tasks dynamically in a standard web browser, by overlaying the images with intervening semi-opaque layers. The annotation framework has also been implemented and tested. In order for annotation to work in this environment, it should also be in the form of stereogram and should aid the merging of stereo pairs. The current technique allows users to place a mark (dot) on one image stack, and its projected position onto the other image stack is calculated dynamically on the client side. Other extra metadata such as textual descriptions can be entered by the user as well. To cope with the occlusion problem caused by changes in the z direction, the structure traced by the user will be displayed on the side, together with the data stacks. Using the same stereo-gram creation techniques, the traces made by the user is dynamically generated and shown as stereogram. We expect the approach presented in this thesis to be applicable to a broader scientific domain, including geology and meteorology.
  • Advancement in high-throughput microscopy technology such as the Knife-Edge
    Scanning Microscopy (KESM) is enabling the production of massive amounts of high-resolution
    and high-quality volumetric data of biological microstructures. To fully
    utilize these data, they should be efficiently distributed to the scientific research community
    through 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 approach
    that has minimal hardware and software requirements will be necessary, such as a
    standard web browser running on a typical personal computer. There are several web
    applications that facilitate the viewing of large collections of images. Google Maps
    and Google Maps-like interfaces such as Brainmaps.org allow users to pan and zoom
    2D images efficiently. However, they do not yet support the rendering of volumetric
    data in their standard web interface.
    The goal of this thesis is to develop a light-weight volumetric image viewer using
    existing web technologies such as HTML, CSS and JavaScript while exploiting the
    properties 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 of
    raw image stacks produced by the 3D microscope without any extra computation on
    the data at all. Operations to generate stereo images using 2D image stacks include
    distance attenuation and binocular disparity. By using HTML and JavaScript that are computationally cheap, we can accomplish both tasks dynamically in a standard
    web browser, by overlaying the images with intervening semi-opaque layers.
    The annotation framework has also been implemented and tested. In order for
    annotation to work in this environment, it should also be in the form of stereogram
    and should aid the merging of stereo pairs. The current technique allows users to
    place a mark (dot) on one image stack, and its projected position onto the other
    image stack is calculated dynamically on the client side. Other extra metadata such
    as textual descriptions can be entered by the user as well. To cope with the occlusion
    problem caused by changes in the z direction, the structure traced by the user will
    be displayed on the side, together with the data stacks. Using the same stereo-gram
    creation techniques, the traces made by the user is dynamically generated and shown
    as stereogram.
    We expect the approach presented in this thesis to be applicable to a broader
    scientific domain, including geology and meteorology.

publication date

  • December 2008