Core 3: Visualization and Analysis
The Resource has a mix of applied computer science and biomedical microscopy applications, producing specialized visualization and analysis tools targeted primarily at optical and scanned-probe microscopy systems. Our collaborators continue to provide challenging visualization and analysis problems that drive technique development and dissertations in computer science. Our focus on solving collaborators’ problems by providing computer-integrated tools continues to result in new visualization and analysis tools.
Advanced Visualization
An example simulation from the Virtual Cell project at the University of Connecticut displayed in the nDive tool. Four chemical species are shown in a volume display.
The difficulty with toolkits like the open-source Visualization ToolKit (VTK) from a scientist’s point of view is rather like the difficulty a computer scientist would have if given free access to an automotive shop: all the tools needed to fix a car are in there somewhere, but knowing which tools to use and how is beyond their experience. Our aim is to provide tools that are optimized to answer the specific questions posed by our collaborators in the belief that a tool that solves a particular problem is more likely to be of broader usefulness than a “generic” tool that is not optimized for usefulness on any particular problem. This requires drawing on an understanding of the available techniques, the characteristics of the human visual system, the characteristics of the data sets, and the questions being asked.
Our collaborators continue to provide data sets and questions that push the state of the art in 3D visualization. Problems generated from Radiology colleagues have produced two computer-science dissertation topics and tools of use for both micron-scale and organ-scale data sets. We have four ongoing projects in this area, with the longest-running one (ImageSurfer) maturing into a visualization and analysis tool and the two newest ones (nDive and FOR) providing publications and novel views into biomedical and microscopy data sets. We continue to apply cutting-edge computer graphics and interaction to biomedical problems in the Eve for Microscopy project.
3D Scalar Volume Visualization: ImageSurfer
Advanced Graphics and Interaction, including EVE for Microscopy
Image Analysis
Yeh, E., J. Haase, et al. (2008). "Pericentric Chromatin Is Organized into an Intramolecular Loop in Mitosis." Current Biology 18(2): 81-90.
The process of discovery is a sequence of hypothesis formation, experimentation, model development, and the comparison of models with experimental data. As soon as scientists have used novel visualization tools to form initial hypotheses, they immediately want quantitative tools to help them compare these models to the experiment data to see how well they fit.
Given the present focus of our Resource on physical interaction with actual molecules, and away from simulated interaction with molecules, our suite of analysis tools has turned to tools that can model the artifacts of their imaging systems (Microscope Simulator), extract quantitative motion from video sequences (Spot Tracker, Video Motion Extraction), and fit models of increasing complexity to their data (Microscope Simulator, Model Extraction, and Physical Simulation).