Anatomy Directly from Imagery: General-Purpose, Scalable, and Open-Source Machine Learning Approaches
Shireen Youssef Elhabian
The form (or shape) and function relationship of anatomical structures is a central theme in biology where abnormal shape changes are closely tied to pathological functions. Morphometrics has been an indispensable quantitative tool in medical and biological sciences to study anatomical forms for more than 100 years. Recently, the increased availability of high-resolution in-vivo images of anatomy has led to the development of a new generation of morphometric approaches, called statistical shape modeling (SSM), that take advantage of modern computational techniques to model anatomical shapes and their variability within populations with unprecedented detail. SSM stands to revolutionize morphometric analysis, but its widespread adoption is hindered by a number of significant challenges, including the complexity of the approaches and their increased computational requirements, relative to traditional morphometrics. Arguably, however, the most important roadblock to more widespread adoption is the lack of user-friendly and scalable software tools for a variety of anatomical surfaces that can be readily incorporated into biomedical research labs. The goal of this proposal is thus to address these challenges in the context of a flexible and general SSM approach termed particle-based shape modeling (PSM), which automatically constructs optimal statistical landmark-based shape models of ensembles of anatomical shapes without relying on any specific surface parameterization. The proposed research will provide an automated, general-purpose, and scalable computational solution for constructing shape models of general anatomy.
In Aim 1, we will build computational and machine learning algorithms to model anatomies with complex surface topologies (e.g., surface openings and shared boundaries) and highly variable anatomical populations.
In Aim 2, we will introduce an end-to-end machine learning approach to extract statistical shape representation directly from images, requiring no parameter tuning, image pre-processing, or user assistance.
In Aim 3, we will provide intuitive graphical user interfaces and visualization tools to incorporate user-defined modeling preferences and promote the visual interpretation of shape models. We will also make use of recent advances in cloud computing to enable researchers with limited computational resources and/or large cohorts to build and execute custom SSM workflows using remote scalable computational resources. Algorithmic developments will be thoroughly evaluated and validated using existing, fully funded, large-scale, and constantly growing databases of CT and MRI images located on-site. Furthermore, we will develop and disseminate standard workflows and domain-specific use cases for complex anatomies to promote reproducibility. Efforts to develop the proposed technology are aligned with the mission of the National Institute of General Medical Sciences (NIGMS), and its third strategic goal: to bridge biology and quantitative science for better global health through supporting the development of and access to computational research tools for biomedical research. Our long-term goal is to increase the clinical utility and widespread adoption of SSM, and the proposed research will establish the groundwork for achieving this goal.Public Health Relevance
This project will develop general-purpose, scalable, and open-source statistical shape modeling (SSM) tools, which will present unique capabilities for automated anatomy modeling with less user input. The proposed technology will introduce a number of significant improvements to current SSM approaches and tools, including the support for challenging modeling problems, inferring shapes directly from images (and hence bypassing the segmentation step), parallel optimizations for speed, and new user interfaces that will be much easier and scalable than the current tools. The proposed technology will constitute an indispensable resource for the biomedical and clinical communities that will enable new avenues for biomedical research and clinical investigations, provide new ways to answer biologically related questions, allow new types of questions to be asked, and open the door for the integration of SSM with clinical care.