Center for Scientific Computation in Imaging




As part of the recently completed NSF-funded Shape Analysis for Phenomics with 3D Imaging Data (SAPID) award (DBI-1147260), we have developed new quantitative image analysis methods for application with high-resolution volumetric CT and MRI imaging data acquired from biological specimens for evolutionary biology research. These methods include our spherical wave decomposition (SWD) approach which provides a general computational method for segmenting and characterizing the geometric shape of individual specimens or anatomical structures (Yopak et al, 2016), and our Symplectomorphic Registration using Entropy Spectrum Pathways (SYMREG-ESP) approach which provides a robust new approach for non-linear registration of multi-modality multi-subject volumetric image data (Galinsky & Frank, 2018). One of the major innovations of SYMREG-ESP is that it facilitates mapping of whole bodies, or anatomical structures, from multiple specimens into a single reference frame to allow direct comparison of their shape. Together, these methods are incorporated into the SAPID Toolkit (STK) which is a set of software tools that facilitate the characterization and quantitative statistical analysis of morphological variation in volumetric imaging datasets.

Current support for software development at CSCI includes the NSF- funded INSPIRE: Quantitative Estimation of Space-Time processes in volumetric data (QUEST) award (ACI-1550405). This project involves the development of a user interface to facilitate the broader use of new spatial-temporal data analysis methods that we developed for the analysis of both neuroimaging data (QUEST-NI) and meteorology data acquired from Doppler radar (QUEST-WX). Since structural features (in brain and weather) are also required to be characterized and registered, both of these software applications now incorporate the STK products. QUEST-NI and QUEST-WX software applications are currently still under development but are available for download by researchers on request (see below).

Software Products

The STK analysis tools (SWD, SYMREG-ESP) can be found in the Morphology tools in the QUEST-NI software application. The current QUEST-NI and QUEST-WX applications, though in a state of continuing development as we integrate extensions to our novel methods, provide an easy-to-use, front-end visualization application for performing all of the shape, connectivity, and registration computations on 3D digital specimens.

Information regarding the the QUEST-NI and QUEST-WX software can be found here: