Matthew Michael McCormick

Matthew Michael McCormick
Kitware, Inc. · Department of Medical Imaging

PhD

About

42
Publications
12,188
Reads
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660
Citations
Additional affiliations
July 2011 - present
Kitware, Inc.
Position
  • Technical Expert
July 2011 - July 2017
Kitware, Inc.
Position
  • Engineer
May 2005 - May 2011
University of Wisconsin–Madison
Position
  • Research Assistant

Publications

Publications (42)
Article
Stitching partially overlapping image tiles into a montage is a common requirement for materials microscopy. We developed ITKMontage, a new module for the open-source Insight Toolkit (ITK), capable of robustly and quickly generating extremely large, high-bit-depth montages within the memory constraints of standard workstations. The phase correlatio...
Conference Paper
Microfractures (cracks) are the third most common cause of tooth loss in industrialized countries. If they are not detected early, they continue to progress until the tooth is lost. Cone beam computed tomography (CBCT) has been used to detect microfractures, but has had very limited success. We propose an algorithm to detect cracked teeth that pair...
Article
p>Whole-slide histology images contain information that is valuable for clinical and basic science investigations of cancer, but extracting quantitative measurements from these images is challenging for researchers who are not image analysis specialists. In this paper, we describe HistomicsML2, a software tool for learn-by-example training of machi...
Preprint
Extracting quantitative phenotypic information from whole-slide images presents significant challenges for investigators who are not experienced in developing image analysis algorithms. We present new software that enables rapid learn-by-example training of machine learning classifiers for detection of histologic patterns in whole-slide imaging dat...
Conference Paper
Computed tomography (CT) images can potentially provide insights into bone structure for diagnosis of disorders and diseases. However, evaluation of trabecular bone structure and whole bone shape is often qualitative or semi-quantitative. This limits inter-study comparisons and the ability to detect subtle bone quality variations during early disea...
Conference Paper
Temporomandibular Joint (TMJ) Osteoarthritis (OA) is associated with significant pain and disability. It is really hard to diagnose TMJ OA during early stages of the disease. Subchondral bone texture has been observed to change in the TMJ early during TMJ OA progression. We believe that raw probability-distribution matrices describing image texture...
Article
Full-text available
ITK-SNAP is an interactive software tool for manual and semi-automatic segmentation of 3D medical images. This paper summarizes major new features added to ITK-SNAP over the last decade. The main focus of the paper is on new features that support semi-automatic segmentation of multi-modality imaging datasets, such as MRI scans acquired using differ...
Article
Full-text available
Objective: Ultrasound is an effective tool for rapid non-invasive assessment of cardiac structure and function. Determining the cardiorespiratory phases of each frame in the ultrasound video and capturing the cardiac function at a much higher temporal resolution is essential in many applications. Fulfilling these requirements is particularly chall...
Conference Paper
We aim to diagnose scoliosis using a self contained ultrasound device that does not require significant training to operate. The device knows its angle relative to vertical using an embedded inertial measurement unit, and it estimates its angle relative to a vertebrae using a neural network analysis of its ultrasound images. The composition of thos...
Conference Paper
To date, there is no single sign, symptom, or test that can clearly diagnose early stages of Temporomandibular Joint Osteoarthritis (TMJ OA). However, it has been observed that changes in the bone occur in early stages of this disease, involving structural changes both in the texture and morphometry of the bone marrow and the subchondral cortical p...
Article
This document describes a new remote module implemented for the Insight Toolkit (ITK), itkBoneMorphometry. This module contains bone analysis filters that compute features from N-dimensional images that represent the internal architecture of bone. The computation of the bone morphometry features in this module is based on well known methods. The tw...
Conference Paper
Full-text available
By using a laser projector and high speed camera, we can add three capabilities to an ultrasound system: tracking the probe, tracking the patient, and projecting information onto the probe and patient. We can use these capabilities to guide an untrained operator to take high quality, well framed ultrasound images for computer-augmented, point-of-ca...
Conference Paper
Full-text available
We present an algorithm to automatically estimate the diameter of the optic nerve sheath from ocular ultrasound images. The optic nerve sheath diameter provides a proxy for measuring intracranial pressure, a life threating condition frequently associated with head trauma. Early treatment of elevated intracranial pressures greatly improves outcomes...
Article
Full-text available
The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development...
Article
This document describes a new remote module implemented for the Insight Toolkit ITK, itkTextureFeatures. This module contains two texture analysis filters that are used to compute feature maps of N-Dimensional images using two well-known texture analysis methods. The two filters contained in this module are itkScalarImageToTextureFeaturesImageFilte...
Article
Full-text available
Strain quantifies local deformation of a solid body. In medical imaging, strain reflects how tissue deforms under load. Or, it can quantify growth or atrophy of tissue, such as the growth of a tumor. Additionally, strain from the transformation that results from image-to-image registration can be applied as an input to a biomechanical constitutive...
Article
Full-text available
A 3D Slicer (Fedorov et al. 2012) extension for ultrasound scan conversion during 2D and 3D image generationfor traditional B-mode imaging (Matthew M McCormick 2010), but also next-generation ultrasound imagemodalities like ultrasound spectroscopy (S. R. Aylward et al. 2016), acoustic radiation force imaging (ARFI)(Palmeri et al. 2016), acoustic ra...
Conference Paper
Current prostate cancer screening methods involve non-targeted needle biopsies and detection of clinically-insignificant lesions that receive excessive treatments, exposing patients to unnecessary adverse side effects and placing a burden on our health care systems. There is a strong clinical need for improved prostate imaging methods that are sens...
Article
Full-text available
This document describes a new class, itk::MorphologicalContourInterpolator, which implements a method proposed by Albu et al. in 2008. Interpolation is done by first determining correspondence between shapes on adjacent segmented slices by detecting overlaps, then aligning the corresponding shapes, generating transition sequence of one-pixel dilati...
Article
Full-text available
This document describes a new class, itk::RLEImage, which uses run-length encoding to reduce the memory needed for storage of label maps. This class is accompanied by all the iterators to make it a dropin replacement for itk::Image. By changing the image typedef to itk::RLEImage, many ITK image processing algorithms build without modification and w...
Conference Paper
Full-text available
We introduce the concept of "Ultrasound Spectroscopy". The premise of ultrasound spectroscopy is that by acquiring ultrasound RF data at multiple power and frequency settings, a rich set of features can be extracted from that RF data and used to characterize the underlying tissues. This is beneficial for a variety of problems, such as accurate tiss...
Article
The Insight Segmentation and Registration Toolkit (www.itk.org) has become a standard in academia and industry for medical image analysis. In recent years, the ITK developers’ community has focused on providing programming interfaces to ITK from Python, Java, and Javascript and making ITK available via leading applications such as Slicer and ImageJ...
Article
Full-text available
This document describes a new class, itk::RLEImage, which uses run-length encoding to reduce the memory needed for storage of label maps. This class is accompanied by all the iterators to make it a dropin replacement for itk::Image. By changing the image typedef to itk::RLEImage, many ITK image processing algorithms build without modification and w...
Article
Full-text available
We present a common framework, for registering images to an atlas and for forming an unbiased atlas, that tolerates the presence of pathologies such as tumors and traumatic brain injury lesions. This common framework is particularly useful when a sufficient number of protocol-matched scans from healthy subjects cannot be easily acquired for atlas f...
Conference Paper
Full-text available
Low-rank image decomposition has the potential to address a broad range of challenges that routinely occur in clinical practice. Its novelty and utility in the context of atlas-based analysis stems from its ability to handle images containing large pathologies and large deforma- tions. Potential applications include atlas-based tissue segmentation...
Poster
Full-text available
This poster was presented at SciPy 2014 conference. It describes a system for faster, straightforward cross-platform CPython builds across HPC, desktop, and mobile platforms with multiple build system generators and easy integration with C/C++/Fortran scientific computing libraries. Abstract While the Python language has seen multiple implementatio...
Article
Full-text available
Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of...
Article
Full-text available
Accurate subsample displacement estimation is necessary for ultrasound elastography because of the small deformations that occur and the subsequent application of a derivative operation on local displacements. Many of the commonly used subsample estimation techniques introduce significant bias errors. This article addresses a reduced bias approach...
Article
Full-text available
A hierarchical block-matching motion tracking algorithm for strain imaging is presented. Displacements are estimated with improved robustness and precision by utilizing a Bayesian regularization algorithm and an unbiased subsample interpolation technique. A modified least-squares strain estimator is proposed to estimate strain images from a noisy d...
Article
This document describes the latest efforts in integrating the Lesion Sizing Toolkit (LSTK) into ITK v4 as an external/remote module providing an Open Science dashboard website with a large open image archive of lung cancer CT images for LSTK development and testing.
Conference Paper
Full-text available
Publicly available scientific resources help establish evaluation standards, provide a platform for teaching and may improve reproducibility. Version 4 of the Insight ToolKit ( ITK $^{\text{4}}$) seeks to establish new standards in publicly available image registration methodology. In this work, we provide an overview and preliminary evaluation of...
Article
It has been postulated that up to 11 million "silent" strokes occur annually. While these patients are without classic neurologic deficits, they may exhibit cognitive decline. In this study, we examine the cognitive function of patients with carotid stenosis. Additionally, we evaluate a noninvasive measure of strain in pulsating carotid artery plaq...
Article
Full-text available
Absolute backscatter coefficients in tissue-mimicking phantoms were experimentally determined in the 5-50 MHz frequency range using a broadband technique. A focused broadband transducer from a commercial research system, the VisualSonics Vevo 770, was used with two tissue-mimicking phantoms. The phantoms differed regarding the thin layers covering...
Article
Full-text available
Noise artifacts due to signal decorrelation and reverberation are a considerable problem in ultrasound strain imaging. For block-matching methods, information from neighboring matching blocks has been utilized to regularize the estimated displacements. We apply a recursive Bayesian regularization algorithm developed by Hayton et al. [Artif. Intell....
Article
Full-text available
Two phantoms have been constructed for assessing performance of high-frequency ultrasound imagers. They also allow for periodic quality assurance tests and training technicians in the use of higher-frequency scanners. The phantoms contain eight blocks of tissue-mimicking material; each block contains a spatially random distribution of suitably smal...
Article
We have previously reported on the equivalent scatterer size, attenuation coefficient, and axial strain properties of atherosclerotic plaque ex vivo. Since plaque structure and composition may be damaged during a carotid endarterectomy procedure, characterization of in vivo properties of atherosclerotic plaque is essential. The relatively shallow d...
Article
Full-text available
In this paper, we explore two parameters or strain indices related to plaque deformation during the cardiac cycle, namely, the maximum accumulated axial strain in plaque and the relative lateral shifts between plaque and vessel wall under in vivo clinical ultrasound imaging conditions for possible identification of vulnerable plaque. These strain i...

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Cited By

Projects

Projects (5)
Project
Lists some of the strain estimation algorithms developed/published by our group.
Project
Develop noninvasive, ultrasound-based strain indices to screen and assess human subjects for arterial disease and vulnerable plaque deposition using Lagrangian carotid strain imaging.
Project