Polymorph segmentation representation for medical image computing. (April 2019)

• Record Type: Journal Article
• Authors: Pinter, Csaba; Lasso, Andras; Fichtinger, Gabor
• Is Part Of: Computer methods and programs in biomedicine. Volume 171(2019)
• Page Start: 19
• Page End: 26
• Publication Date: 2019-04
• Subjects: Segmentation -- Software library -- Open-source -- 3D Slicer -- Voxelization -- DICOM; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2019.02.011
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: A software library called PolySeg is developed to facilitate dynamic management of segmented structures in different representations. PolySeg provides automatic conversions between numerous representations (e.g. labelmap, surface) to support analysis workflows or interactive editing. Segment Editor in the open-source 3D Slicer platform provides easy-to-use manual and semi-automatic segmentation features. Abstract: Background and objective: Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects. Methods: A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in the Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions. Results: The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications. Conclusions: A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software's BSD-style open-source license allows complete freedom of use of the library.