In JoVE (1)

Other Publications (25)

Articles by Matthew McAuliffe in JoVE

 JoVE Neuroscience

Analyzing Dendritic Morphology in Columns and Layers

1Section on Neuronal Connectivity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), 2Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health (NIH), 3Biomedical Imaging Research Services Section, Center for Information Technology, National Institutes of Health (NIH)

JoVE 55410

Other articles by Matthew McAuliffe on PubMed

Assessing Prostate Volume by Magnetic Resonance Imaging: a Comparison of Different Measurement Approaches for Organ Volume Analysis

Investigative Radiology. Apr, 2005  |  Pubmed ID: 15770143

We sought to evaluate the capabilities of different magnetic resonance imaging (MRI)-based methodologies for measuring prostate volume.

Whole Cell Segmentation in Solid Tissue Sections

Cytometry. Part A : the Journal of the International Society for Analytical Cytology. Oct, 2005  |  Pubmed ID: 16163696

Understanding the cellular and molecular basis of tissue development and function requires analysis of individual cells while in their tissue context.

Novel Lymphotoxin Alpha (LTalpha) Knockout Mice with Unperturbed Tumor Necrosis Factor Expression: Reassessing LTalpha Biological Functions

Molecular and Cellular Biology. Jun, 2006  |  Pubmed ID: 16705172

Lymphotoxin alpha (LTalpha) can exist in soluble form and exert tumor necrosis factor (TNF)-like activity through TNF receptors. Based on the phenotypes of knockout (KO) mice, the physiological functions of LTalpha and TNF are considered partly redundant, in particular, in supporting the microarchitecture of the spleen and in host defense. We exploited Cre-LoxP technology to generate a novel neomycin resistance gene (neo) cassette-free LTalpha-deficient mouse strain (neo-free LTalpha KO [LTalphaDelta/Delta]). Unlike the "conventional" LTalpha-/- mice, new LTalphaDelta/Delta animals were capable of producing normal levels of systemic TNF upon lipopolysaccharide (LPS) challenge and were susceptible to LPS/D-galactosamine (D-GalN) toxicity. Activated neutrophils, monocytes, and macrophages from LTalphaDelta/Delta mice expressed TNF normally at both the mRNA and protein levels as opposed to conventional LTalpha KO mice, which showed substantial decreases in TNF. Additionally, the spleens of the neo-free LTalpha KO mice displayed several features resembling those of LTbeta KO mice rather than conventional LTalpha KO animals. The phenotype of the new LTalphaDelta/Delta mice indicates that LTalpha plays a smaller role in lymphoid organ maintenance than previously thought and has no direct role in the regulation of TNF expression.

Radio Frequency Ablation Registration, Segmentation, and Fusion Tool

IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society. Jul, 2006  |  Pubmed ID: 16871716

The radio frequency ablation segmentation tool (RFAST) is a software application developed using the National Institutes of Health's medical image processing analysis and visualization (MIPAV) API for the specific purpose of assisting physicians in the planning of radio frequency ablation (RFA) procedures. The RFAST application sequentially leads the physician through the steps necessary to register, fuse, segment, visualize, and plan the RFA treatment. Three-dimensional volume visualization of the CT dataset with segmented three dimensional (3-D) surface models enables the physician to interactively position the ablation probe to simulate burns and to semimanually simulate sphere packing in an attempt to optimize probe placement. This paper describes software systems contained in RFAST to address the needs of clinicians in planning, evaluating, and simulating RFA treatments of malignant hepatic tissue.

Technologies for Guidance of Radiofrequency Ablation in the Multimodality Interventional Suite of the Future

Journal of Vascular and Interventional Radiology : JVIR. Jan, 2007  |  Pubmed ID: 17296700

Several new image-guidance tools and devices are being prototyped, investigated, and compared. These tools are introduced and include prototype software for image registration and fusion, thermal modeling, electromagnetic tracking, semiautomated robotic needle guidance, and multimodality imaging. The integration of treatment planning with computed tomography robot systems or electromagnetic needle-tip tracking allows for seamless, iterative, "see-and-treat," patient-specific tumor ablation. Such automation, navigation, and visualization tools could eventually optimize radiofrequency ablation and other needle-based ablation procedures and decrease variability among operators, thus facilitating the translation of novel image-guided therapies. Much of this new technology is in use or will be available to the interventional radiologist in the near future, and this brief introduction will hopefully encourage research in this emerging area.

Cortical Atrophy is Relevant in Multiple Sclerosis at Clinical Onset

Journal of Neurology. Sep, 2007  |  Pubmed ID: 17361339

Increasing evidence suggests relevant cortical gray matter pathology in patients with Multiple Sclerosis (MS), but how early this pathology begins; its impact on clinical disability and which cortical areas are primarily affected needs to be further elucidated.

Volumetric Neuroimage Analysis Extensions for the MIPAV Software Package

Journal of Neuroscience Methods. Sep, 2007  |  Pubmed ID: 17604116

We describe a new collection of publicly available software tools for performing quantitative neuroimage analysis. The tools perform semi-automatic brain extraction, tissue classification, Talairach alignment, and atlas-based measurements within a user-friendly graphical environment. They are implemented as plug-ins for MIPAV, a freely available medical image processing software package from the National Institutes of Health. Because the plug-ins and MIPAV are implemented in Java, both can be utilized on nearly any operating system platform. In addition to the software plug-ins, we have also released a digital version of the Talairach atlas that can be used to perform regional volumetric analyses. Several studies are conducted applying the new tools to simulated and real neuroimaging data sets.

Extensive Cortical Inflammation is Associated with Epilepsy in Multiple Sclerosis

Journal of Neurology. Apr, 2008  |  Pubmed ID: 18227989

Epilepsy is three to six times more frequent in MS than in the general population. Previous studies based on conventional magnetic resonance (MR) imaging have suggested a possible correlation between cortical inflammatory pathology and epileptic seizures. However, pure intracortical lesions (ICLs) are unlikely to be demonstrated with conventional MR. We applied the double inversion recovery (DIR) sequence in relapsing remitting MS (RRMS) patients with or without epileptic seizures in order to clarify the relationship between ICLs and epilepsy in MS in vivo.

Using Global Unique Identifiers to Link Autism Collections

Journal of the American Medical Informatics Association : JAMIA. Nov-Dec, 2010  |  Pubmed ID: 20962132

To propose a centralized method for generating global unique identifiers to link collections of research data and specimens.

Defective Motion Processing in Children with Cerebral Visual Impairment Due to Periventricular White Matter Damage

Developmental Medicine and Child Neurology. Jul, 2012  |  Pubmed ID: 21232054

We sought to characterize visual motion processing in children with cerebral visual impairment (CVI) due to periventricular white matter damage caused by either hydrocephalus (eight individuals) or periventricular leukomalacia (PVL) associated with prematurity (11 individuals).

Sharing Heterogeneous Data: the National Database for Autism Research

Neuroinformatics. Oct, 2012  |  Pubmed ID: 22622767

The National Database for Autism Research (NDAR) is a secure research data repository designed to promote scientific data sharing and collaboration among autism spectrum disorder investigators. The goal of the project is to accelerate scientific discovery through data sharing, data harmonization, and the reporting of research results. Data from over 25,000 research participants are available to qualified investigators through the NDAR portal. Summary information about the available data is available to everyone through that portal.

Spatially Isotropic Four-dimensional Imaging with Dual-view Plane Illumination Microscopy

Nature Biotechnology. Nov, 2013  |  Pubmed ID: 24108093

Optimal four-dimensional imaging requires high spatial resolution in all dimensions, high speed and minimal photobleaching and damage. We developed a dual-view, plane illumination microscope with improved spatiotemporal resolution by switching illumination and detection between two perpendicular objectives in an alternating duty cycle. Computationally fusing the resulting volumetric views provides an isotropic resolution of 330 nm. As the sample is stationary and only two views are required, we achieve an imaging speed of 200 images/s (i.e., 0.5 s for a 50-plane volume). Unlike spinning-disk confocal or Bessel beam methods, which illuminate the sample outside the focal plane, we maintain high spatiotemporal resolution over hundreds of volumes with negligible photobleaching. To illustrate the ability of our method to study biological systems that require high-speed volumetric visualization and/or low photobleaching, we describe microtubule tracking in live cells, nuclear imaging over 14 h during nematode embryogenesis and imaging of neural wiring during Caenorhabditis elegans brain development over 5 h.

Segmentation and Quantitative Analysis of Individual Cells in Developmental Tissues

Methods in Molecular Biology (Clifton, N.J.). 2014  |  Pubmed ID: 24318825

Image analysis is vital for extracting quantitative information from biological images and is used extensively, including investigations in developmental biology. The technique commences with the segmentation (delineation) of objects of interest from 2D images or 3D image stacks and is usually followed by the measurement and classification of the segmented objects. This chapter focuses on the segmentation task and here we explain the use of ImageJ, MIPAV (Medical Image Processing, Analysis, and Visualization), and VisSeg, three freely available software packages for this purpose. ImageJ and MIPAV are extremely versatile and can be used in diverse applications. VisSeg is a specialized tool for performing highly accurate and reliable 2D and 3D segmentation of objects such as cells and cell nuclei in images and stacks.

Photoreceptor-derived Activin Promotes Dendritic Termination and Restricts the Receptive Fields of First-order Interneurons in Drosophila

Neuron. Feb, 2014  |  Pubmed ID: 24462039

How neurons form appropriately sized dendritic fields to encounter their presynaptic partners is poorly understood. The Drosophila medulla is organized in layers and columns and innervated by medulla neuron dendrites and photoreceptor axons. Here, we show that three types of medulla projection (Tm) neurons extend their dendrites in stereotyped directions and to distinct layers within a single column for processing retinotopic information. In contrast, the Dm8 amacrine neurons form a wide dendritic field to receive ∼16 R7 photoreceptor inputs. R7- and R8-derived Activin selectively restricts the dendritic fields of their respective postsynaptic partners, Dm8 and Tm20, to the size appropriate for their functions. Canonical Activin signaling promotes dendritic termination without affecting dendritic routing direction or layer. Tm20 neurons lacking Activin signaling expanded their dendritic fields and aberrantly synapsed with neighboring photoreceptors. We suggest that afferent-derived Activin regulates the dendritic field size of their postsynaptic partners to ensure appropriate synaptic partnership.

Discogenic Low Back Pain

Physical Medicine and Rehabilitation Clinics of North America. May, 2014  |  Pubmed ID: 24787335

Most lumbar disk herniations improve over time with or without medical treatment. Disk herniations and annular tears may not be symptomatic and are shown to exist in patients without any symptoms. In some patients, chronic low back pain may result from the syndrome of internal disk disruption. Treatment of chronic pain of diskal cause can be challenging and have varying results in terms of success. The diagnosis, cause, and treatment options are reviewed in this article.

Dual-view Plane Illumination Microscopy for Rapid and Spatially Isotropic Imaging

Nature Protocols. Nov, 2014  |  Pubmed ID: 25299154

We describe the construction and use of a compact dual-view inverted selective plane illumination microscope (diSPIM) for time-lapse volumetric (4D) imaging of living samples at subcellular resolution. Our protocol enables a biologist with some prior microscopy experience to assemble a diSPIM from commercially available parts, to align optics and test system performance, to prepare samples, and to control hardware and data processing with our software. Unlike existing light sheet microscopy protocols, our method does not require the sample to be embedded in agarose; instead, samples are prepared conventionally on glass coverslips. Tissue culture cells and Caenorhabditis elegans embryos are used as examples in this protocol; successful implementation of the protocol results in isotropic resolution and acquisition speeds up to several volumes per s on these samples. Assembling and verifying diSPIM performance takes ∼6 d, sample preparation and data acquisition take up to 5 d and postprocessing takes 3-8 h, depending on the size of the data.

Atlas Based AAM and SVM Model for Fully Automatic MRI Prostate Segmentation

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference. 2014  |  Pubmed ID: 25570593

Automatic prostate segmentation in MR images is a challenging task due to inter-patient prostate shape and texture variability, and the lack of a clear prostate boundary. We propose a supervised learning framework that combines the atlas based AAM and SVM model to achieve a relatively high segmentation result of the prostate boundary. The performance of the segmentation is evaluated with cross validation on 40 MR image datasets, yielding an average segmentation accuracy near 90%.

GPU Based Multi-histogram Volume Navigation for Virtual Bronchoscopy

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference. 2014  |  Pubmed ID: 25570698

An interactive navigation system for virtual bronchoscopy is presented, which is based solely on GPU based high performance multi-histogram volume rendering.

Evaluation and Nonsurgical Management of Rotator Cuff Calcific Tendinopathy

The Orthopedic Clinics of North America. Apr, 2015  |  Pubmed ID: 25771323

Rotator cuff calcific tendinopathy is a common finding that accounts for about 7% of patients with shoulder pain. There are numerous theories on the pathogenesis of rotator cuff calcific tendinopathy. The diagnosis is confirmed with radiography, MRI or ultrasound. There are numerous conservative treatment options available and most patients can be managed successfully without surgical intervention. Nonsteroidal anti-inflammatory drugs and multiple modalities are often used to manage pain and inflammation; physical therapy can help improve scapular mechanics and decrease dynamic impingement; ultrasound-guided needle aspiration and lavage techniques can provide long-term improvement in pain and function in these patients.

Intravascular Penetration Following Lumbar Transforaminal Epidural Injections Using the Infraneural Technique

Pain Medicine (Malden, Mass.). Aug, 2015  |  Pubmed ID: 25917778

Untwisting the Caenorhabditis Elegans Embryo

ELife. Dec, 2015  |  Pubmed ID: 26633880

The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software ( that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (Supplementary file 1) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

Location of Radicular Spinal Arteries in the Lumbar Spine from Analysis of CT Angiograms of the Abdomen and Pelvis

Pain Medicine (Malden, Mass.). Jan, 2016  |  Pubmed ID: 26332923

Reports of catastrophic neurologic injuries following lumbar transforaminal epidural steroid injections are rare but serious potential complications. The traditional method of performing lumbar transforaminal epidural steroid injections is in the "safe triangle" to avoid contact to the spinal nerve. Some authors advocate an alternative approach by placing the needle inferiorly in a region referred to as "Kambin's triangle" to avoid incurring arteries. This study aimed to determine the location of arteries within the L1-L4 intervertebral foramen in vivo, specifically if they lie within or in close proximity to the "safe triangle" or Kambin's triangle using CT angiograms of the abdomen and pelvis.

The NINDS Parkinson's Disease Biomarkers Program

Movement Disorders : Official Journal of the Movement Disorder Society. Jun, 2016  |  Pubmed ID: 26442452

Neuroprotection for Parkinson's disease (PD) remains elusive. Biomarkers hold the promise of removing roadblocks to therapy development. The National Institute of Neurological Disorders and Stroke has therefore established the Parkinson's Disease Biomarkers Program to promote discovery of PD biomarkers for use in phase II and III clinical trials.

Axial Superresolution Via Multiangle TIRF Microscopy with Sequential Imaging and Photobleaching

Proceedings of the National Academy of Sciences of the United States of America. Apr, 2016  |  Pubmed ID: 27044072

We report superresolution optical sectioning using a multiangle total internal reflection fluorescence (TIRF) microscope. TIRF images were constructed from several layers within a normal TIRF excitation zone by sequentially imaging and photobleaching the fluorescent molecules. The depth of the evanescent wave at different layers was altered by tuning the excitation light incident angle. The angle was tuned from the highest (the smallest TIRF depth) toward the critical angle (the largest TIRF depth) to preferentially photobleach fluorescence from the lower layers and allow straightforward observation of deeper structures without masking by the brighter signals closer to the coverglass. Reconstruction of the TIRF images enabled 3D imaging of biological samples with 20-nm axial resolution. Two-color imaging of epidermal growth factor (EGF) ligand and clathrin revealed the dynamics of EGF-activated clathrin-mediated endocytosis during internalization. Furthermore, Bayesian analysis of images collected during the photobleaching step of each plane enabled lateral superresolution (<100 nm) within each of the sections.

Checking Questionable Entry of Personally Identifiable Information Encrypted by One-Way Hash Transformation

JMIR Medical Informatics. Feb, 2017  |  Pubmed ID: 28213343

As one of the several effective solutions for personal privacy protection, a global unique identifier (GUID) is linked with hash codes that are generated from combinations of personally identifiable information (PII) by a one-way hash algorithm. On the GUID server, no PII is permitted to be stored, and only GUID and hash codes are allowed. The quality of PII entry is critical to the GUID system.

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