Matthew J. McAuliffe

Medical Image Processing, Analysis and Visualization in clinical research

Imaging has become an essential component in many fields of medical and laboratory research and clinical practice. Biologists study cells and generate 3D confocal microscopy data sets; virologists generate 3D reconstructions of viruses from micrographs; radiologists identify and quantify tumors from MRI and CT scans; and neuroscientists detect regional metabolic brain activity from PET and functional MRI scans. Analysis of these diverse image types requires sophisticated computerized quantification and visualization tools. Until recently, 3D visualization of images and quantitative analysis could only be performed using expensive UNIX workstations and customized software. Today, much of the visualization and analysis can be performed on an inexpensive desktop computer equipped with the appropriate graphics hardware and software. This paper introduces an extensible, platform-independent, general-purpose image processing and visualization program specifically designed to meet the needs of an Internet-linked medical research community. The application, named MIPAV (Medical Image Processing, Analysis and Visualization), enables clinical and quantitative analysis of medical images over the Internet. Using MIPAVs standard user interface and analysis tools, researcher and clinicians at remote sites can easily share research data and analyses, thereby enhancing their ability to study, diagnose, monitor and treat medical disorders.

Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy

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.

Volumetric Neuroimage Analysis Extensions for the MIPAV Software Package

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.

Sharing Heterogeneous Data: The National Database for Autism Research

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.

Whole cell segmentation in solid tissue sections

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

Dual-view plane illumination microscopy for rapid and spatially isotropic imaging

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.

Using global unique identifiers to link autism collections

OBJECTIVE To propose a centralized method for generating global unique identifiers to link collections of research data and specimens. DESIGN The work is a collaboration between the Simons Foundation Autism Research Initiative and the National Database for Autism Research. The system is implemented as a web service: an investigator inputs identifying information about a participant into a client application and sends encrypted information to a server application, which returns a generated global unique identifier. The authors evaluated the system using a volume test of one million simulated individuals and a field test on 2000 families (over 8000 individual participants) in an autism study. MEASUREMENTS Inverse probability of hash codes; rate of false identity of two individuals; rate of false split of single individual; percentage of subjects for which identifying information could be collected; percentage of hash codes generated successfully. RESULTS Large-volume simulation generated no false splits or false identity. Field testing in the Simons Foundation Autism Research Initiative Simplex Collection produced identifiers for 96% of children in the study and 77% of parents. On average, four out of five hash codes per subject were generated perfectly (only one perfect hash is required for subsequent matching). DISCUSSION The system must achieve balance among the competing goals of distinguishing individuals, collecting accurate information for matching, and protecting confidentiality. Considerable effort is required to obtain approval from institutional review boards, obtain consent from participants, and to achieve compliance from sites during a multicenter study. CONCLUSION Generic unique identifiers have the potential to link collections of research data, augment the amount and types of data available for individuals, support detection of overlap between collections, and facilitate replication of research findings.

Photoreceptor-derived activin promotes dendritic termination and restricts the receptive fields of first-order interneurons in Drosophila

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.

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

ABSTRACT Lymphotoxin alpha (LTα) 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 LTα 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 LTα-deficient mouse strain (neo-free LTα KO [LTαΔ/Δ]). Unlike the “conventional” LTα−/− mice, new LTαΔ/Δ 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 LTαΔ/Δ mice expressed TNF normally at both the mRNA and protein levels as opposed to conventional LTα KO mice, which showed substantial decreases in TNF. Additionally, the spleens of the neo-free LTα KO mice displayed several features resembling those of LTβ KO mice rather than conventional LTα KO animals. The phenotype of the new LTαΔ/Δ mice indicates that LTα plays a smaller role in lymphoid organ maintenance than previously thought and has no direct role in the regulation of TNF expression.

Free Software Tools for Atlas-based Volumetric Neuroimage Analysis

We describe new and freely available software tools for measuring volumes in subregions of the brain. The method is fast, flexible, and employs well-studied techniques based on the Talairach-Tournoux atlas. The software tools are released as plug-ins for MIPAV, a freely available and user-friendly image analysis software package developed by the National Institutes of Health. Our software tools include a digital Talairach atlas that consists of labels for 148 different substructures of the brain at various scales.