Quantifying Anatomical Shape with Slicersalt

SOURCEA PUBLICATION FOR SOFTWARE DEVELOPERS Issue 44 Quantifying Anatomical Shape p.3 with SlicerSALT CONTENTS Kitware Source contains information on open source software. Since 2006, its articles have shared first-hand experiences from Kitware team members and those outside the company’s offices who use and/or develop platforms such as CMake, the Visualization Toolkit, ParaView, the Insight Segmentation and Registration Toolkit, Resonant and the Kitware Image and Video Exploitation and Retrieval toolkit. Readers who wish to share their own experiences or subscribe to the publication can connect with the Kitware Source editor at [email protected]. Kitware Source comes in multiple forms. Kitware mails hard p.3 copies to addresses in North America, and it publishes each issue as a series of posts on https://blog.kitware.com. GRAPHIC DESIGNER QUANTIFYING ANATOMICAL Steve Jordan SHAPE WITH SLICERSALT EDITORS Sandy McKenzie Mary Elise Dedicke GRAND OPENING PHOTOGRAPHER p.5 Elizabeth Fox Photography This work is licensed under an Attribution 4.0 International 3D SLICER AND VIRTUAL (CC BY 4.0) License. INSECT DISSECTION Kitware, ParaView, CMake, KiwiViewer and VolView are registered trademarks of Kitware, Inc. All other trademarks are property of their respective owners. COVER CONTENT Stanford Bunny image generated with SlicerSALT’s Shape Analysis Module. See “Quantifying Anatomical Shape with p.8 SlicerSALT,” which begins on page three, for Stanford bunny meshes. KITWARE NEWS 2 QUANTIFYING ANATOMICAL SHAPE WITH SLICERSALT Beatriz Paniagua Two years ago, the National Institute of Biomedical Imaging and Bioengineering funded an initiative to create open source software to enable biomedical researchers to generate shape analysis measurements from their medical images. This software is called Slicer Shape AnaLysis Toolbox (SlicerSALT). It is designed to re-engineer state-of-the-art shape modeling and analysis research code into a robust, bundled toolkit. More specifically, SlicerSALT aims to enhance the intuitiveness and ease of use of research code for shape analysis studies. It also aims to help researchers find changes in shape with higher statistical power. This article demonstrates how to use SlicerSALT to compute a spherical harmonic representation of a random object of spherical topology (the Stanford bunny). The data for the example is available through the link below, and SlicerSALT is available as source code and as binary distributions for all major platforms (e.g., Linux Redhat/CentOS, Windows and MacOS). Links to the source code and distributions reside on salt.slicer.org. Example Data: http://bit.ly/kwsource-slicersalt-example-data Stanford Bunnies SlicerSALT’s Shape Analysis Module densely samples landmarks based on the geometric properties of spherical shapes. It was used to create the screenshot to the right that shows corresponding meshes of two Stanford bunnies: an original and another with a cut ear. Shape Analysis Module contains SPherical HARmonics-Point Distribution Model (SPHARM- PDM). SPHARM-PDM is a hierarchical, global, multi-scale boundary description that can only represent objects of spherical topology that are based in spherical harmonics. SPHARM-PDM can be computed from binary segmentations or surfaces. Screenshot showing corresponding meshes of two Stanford bunnies. In SlicerSALT, the binary segmentations or surfaces are pre-processed by a filter to ensure they have spherical topology. More specifically, the filter smoothes and fills small interior holes. The pre-processed inputs are then converted to quadrilateral surface meshes. From the meshes, SlicerSALT computes spherical parameterization with area-preserving, distortion minimizing spherical mapping. SlicerSALT implements this mapping to fit a spherical harmonics basis, which it uses to compute a SPHARM description for each input dataset. SlicerSALT then samples the SPHARM description to generate triangulated surfaces (or SPHARM-PDM representations) via icosahedron subdivision. These representations have geometric correspondence between structures, as they contain analogous points in similar parts of their geometry. In medical applications, SPHARM-PDM representations of the same anatomical structure can be used to quantify shape differences. SlicerSALT, for example, can use such representations to quantify a defect of a known magnitude between two models. In the case of the Stanford bunnies, the defect is a cut ear. 3 Quantifying Anatomical Shape With Slicersalt / Issue 44 SlicerSALT comparing the Stanford bunnies. In particular, two modules in SlicerSALT compute and visualize point-to-point correspondent vectors that quantify the localized differences between shapes. These modules are Model to Model Distance and Shape Population Viewer. For the Stanford bunnies example, SlicerSALT finds that the ear of one bunny was cut roughly three millimeters. This simple example illustrates the precision of SlicerSALT’s quantification methods, which can be used to measure shape defects in anatomy in the presence of disease or treatment. SlicerSALT analyzing the ear of a Stanford bunny. Acknowledgement Research reported in this publication was supported by the National Institute Of Biomedical Imaging and Bioengineering of the National Institutes of Health under Award Number R01EB021391. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Meet the Author Beatriz Paniagua is a technical leader on the medical computing team at Kitware, where she leads craniomaxillofacial and musculoskeletal image analysis projects as well as morphometry analysis projects. Her main research interests are computational anatomy and the translational aspects of science. 4 3D SLICER AND VIRTUAL INSECT DISSECTION Hollister Herhold Insects are arguably the most successful terrestrial life form. With an evolutionary history stretching over 400 million years, the world’s oceans remain the sole domain without a significant insect presence. Numbering somewhere around 1.5 million species, their vast diversity remains largely unparalleled. Scientists have been studying the structure, or morphology, of insects for hundreds of years. The overwhelming majority of studies, however, concentrate only on external anatomy. Investigation of internal structures has usually required one of two techniques: dissection, which distorts the position of internal organs by cutting into and prying open the exoskeleton; or serial sectioning, an extremely labor-intensive process where an insect is embedded in clear epoxy and thinly sliced, one section at a time, to show internal anatomy. New imaging modalities, in particular micro-CT scanning, have ushered in a renaissance in insect morphology. Here at the American Museum of Natural History in New York, our micro-CT scanner in the museum’s interdisciplinary Microscopy and Imaging Facility allows us to peer into areas previously unstudied. Lasioglossum, a genus of sweat bee, with abdominal air sacs shown. From Herhold et al., American Museum Novitates 3920, Feb 2019. Volume rendered in 3D Slicer. During an investigation of bee anatomy, we came across some unexpectedly large muscles in the abdomens of some “sweat bees,” so called because of their habit of occasionally drinking sweat off desert hikers. Muscles are found in the abdomens, the typically bulbous hind ends, of nearly all insects. These muscles are usually thin and flat, arranged along the inside of the body wall, and are used to pull segments together for abdominal pumping— basically, what looks like insect breathing. What was seen in these bees, however, were large, cylindrical muscles, arranged to pull top-to-bottom—a structure often seen in the thorax (the middle part where the legs and wings attach) for powering the wings, except these were in the abdomen. The actual purpose of these newly discovered muscles is a subject of ongoing research. 5 3D Slicer and Virtual Insect Dissection / Issue 44 Large dorsoventral, or top-to-bottom, muscles seen in a cutaway of Dieunomia nevadensis, a sweat bee. Dorsal-longitudinal muscles (dlm), oblique muscles (om), dorsal-ventral muscles (dvm) and spiracles (sp) are highlighted. From Herhold et al., American Museum Novitates 3920, Feb 2019. Volume rendered in 3D Slicer, muscle color added in Adobe Photoshop. High-resolution, volumetric datasets of insect internal structures are only as useful as the tools used for analysis. Voxel sizes for insect scanning are quite a bit smaller than the typical human-sized scan; for example, the 16 species scanned for the bee study ranged from 4.8 microns to 19.4 microns. We have been using 3D Slicer in our analysis pipeline since 2016. In addition to its vast array of packaged functionality, we have taken advantage of the Python scripting capabilities of 3D Slicer to develop custom analysis tools for various studies, such as area and volume measurement and plotting. Tube removal is an essential yet simple technique. Insects are typically placed in a plastic Eppendorf tube for scanning. Scan data includes the sample holder as well as the specimen. Removal of the tube is necessary to successfully volume-render the insect, otherwise the result is a great-looking, high-resolution image of an Eppendorf tube. Masking and cropping of the dataset is done using a “fill between slices” technique, where the desired sample area is marked at representative slices spaced throughout the volume along the head-to-tail axis of the insect. Approximately

Load more