John M. Schreiner

Inter-surface mapping

We consider the problem of creating a map between two arbitrary triangle meshes. Whereas previous approaches compose parametrizations over a simpler intermediate domain, we directly create and optimize a continuous map between the meshes. Map distortion is measured with a new symmetric metric, and is minimized during interleaved coarse-to-fine refinement of both meshes. By explicitly favoring low inter-surface distortion, we obtain maps that naturally align corresponding shape elements. Typically, the user need only specify a handful of feature correspondences for initial registration, and even these constraints can be removed during optimization. Our method robustly satisfies hard constraints if desired. Inter-surface mapping is shown using geometric and attribute morphs. Our general framework can also be applied to parametrize surfaces onto simplicial domains, such as coarse meshes (for semi-regular remeshing), and octahedron and toroidal domains (for geometry image remeshing). In these settings, we obtain better parametrizations than with previous specialized techniques, thanks to our fine-grain optimization.

High-Quality Extraction of Isosurfaces from Regular and Irregular Grids

Isosurfaces are ubiquitous in many fields, including visualization, graphics, and vision. They are often the main computational component of important processing pipelines (e.g., surface reconstruction), and are heavily used in practice. The classical approach to compute isosurfaces is to apply the Marching Cubes algorithm, which although robust and simple to implement, generates surfaces that require additional processing steps to improve triangle quality and mesh size. An important issue is that in some cases, the surfaces generated by Marching Cubes are irreparably damaged, and important details are lost which can not be recovered by subsequent processing. The main motivation of this work is to develop a technique capable of constructing high-quality and high-fidelity isosurfaces. We propose a new advancing front technique that is capable of creating high-quality isosurfaces from regular and irregular volumetric datasets. Our work extends the guidance field framework of Schreiner et al. to implicit surfaces, and improves it in significant ways. In particular, we describe a set of sampling conditions that guarantee that surface features will be captured by the algorithm. We also describe an efficient technique to compute a minimal guidance field, which greatly improves performance. Our experimental results show that our technique can generate high-quality meshes from complex datasets

Direct (Re)Meshing for Efficient Surface Processing

We propose a novel surface remeshing algorithm. While many remeshing algorithms are based on global parametrization or local mesh optimization, our algorithm is closely related to surface reconstruction techniques and it requires no explicit parameterization. Our approach is based on the advancing‐front paradigm, and it can be used to both incrementally remesh the complete surface, or simply to remesh a portion of it with a high‐quality mesh. It is accurate, fast, robust, and suitable for use with interactive mesh processing applications that require local remeshing. We show a number of applications, including matching the resolution of meshes when doing Boolean operations such as unions and intersections. We also show how to adapt the algorithm to blend and merge mixed‐mode objects — for example, to compute the union of a point‐set surface and a triangle mesh.

Revisiting Histograms and Isosurface Statistics

Recent results have shown a link between geometric properties of isosurfaces and statistical properties of the underlying sampled data. However, this has two defects: not all of the properties described converge to the same solution, and the statistics computed are not always invariant under isosurface-preserving transformations. We apply Federers Coarea Formula from geometric measure theory to explain these discrepancies. We describe an improved substitute for histograms based on weighting with the inverse gradient magnitude, develop a statistical model that is invariant under isosurface-preserving transformations, and argue that this provides a consistent method for algorithm evaluation across multiple datasets based on histogram equalization. We use our corrected formulation to reevaluate recent results on average isosurface complexity, and show evidence that noise is one cause of the discrepancy between the expected figure and the observed one.

Edge Transformations for Improving Mesh Quality of Marching Cubes

Marching Cubes is a popular choice for isosurface extraction from regular grids due to its simplicity, robustness, and efficiency. One of the key shortcomings of this approach is the quality of the resulting meshes, which tend to have many poorly shaped and degenerate triangles. This issue is often addressed through post processing operations such as smoothing. As we demonstrate in experiments with several datasets, while these improve the mesh, they do not remove all degeneracies, and incur an increased and unbounded error between the resulting mesh and the original isosurface. Rather than modifying the resulting mesh, we propose a method to modify the grid on which Marching Cubes operates. This modification greatly increases the quality of the extracted mesh. In our experiments, our method did not create a single degenerate triangle, unlike any other method we experimented with. Our method incurs minimal computational overhead, requiring at most twice the execution time of the original Marching Cubes algorithm in our experiments. Most importantly, it can be readily integrated in existing Marching Cubes implementations, and is orthogonal to many Marching Cubes enhancements (particularly, performance enhancements such as out-of-core and acceleration structures).

Hardware-Assisted Point-Based Volume Rendering of Tetrahedral Meshes

Medical image registration is a difficult problem. Not only a registration algorithm needs to capture both large and small scale image deformations, it also has to deal with global and local image intensity variations. In this paper we describe a new multiresolution elastic image registration method that challenges these difficulties in image registration. To capture large and small scale image deformations, we use both global and local affine transformation algorithms. To address global and local image intensity variations, we apply an image intensity standardization algorithm to correct image intensity variations. This transforms image intensities into a standard intensity scale, which allows highly accurate registration of medical images.Unstructured volume grids are ubiquitous in scientific computing, and have received substantial interest from the scientific visualization community. In this paper, we take a point-based approach to rendering unstructured grids. In particular, we present a novel method of approximating these irregular elements with point-based primitives amenable to existing hardware acceleration techniques. To improve interactivity to large datasets, we have adapted a level-of-detail strategy. We use a well-known quantitative metric to analyze the image quality achieved by the final rendering.

A mill based instrument and software system for dissecting slide-mounted tissue that provides digital guidance and documentation.

BackgroundDissection of specific Areas Of Interest (AOIs) of slide-mounted tumor samples is often used to enrich for cancer cells in order to generate better signal to noise ratios in subsequent biochemical characterization. Most clinical laboratories utilize manual dissection for practical reasons and to avoid the expense and difficulties of laser microdissection systems. Unfortunately, manual methods often lack resolution and process documentation. The goal of this project was to design a dissection system for slide-mounted tissue with better precision than manual methods that also provides digital image guidance and electronic process documentation.MethodsAn instrument that is essentially a micro tissue mill was developed. It employs a specialized disposable mill bit that simultaneously dispenses liquid, cuts tissue from the slide surface, and aspirates the liquid along with the displaced tissue fragments. A software package was also developed that is capable of transferring digitally annotated AOIs between images of serially cut tissue sections to guide dissection and generate an electronic record of the process.ResultsThe performance of this “meso” dissection system was tested using post dissection visual examination for resolution and accuracy, fluorescence based DNA quantitation for recovery efficiency, and dissection of closely situated mouse-human tissue sections followed by PCR amplification for purity determination. The minimum resolution is a dissected circle smaller than 200 microns in diameter, edge dissection accuracy is tighter than 100 microns, recovery efficiency appears greater than 95%, and recovery purity is greater than 99% relative to a different tissue located 100 microns from the dissection boundary. The system can dissect from both paraffinized and deparaffinized FFPE tissue sections that are mounted on plain glass slides, and it is compatible with DNA, RNA, and protein isolation.ConclusionsThe mesodissection system is an effective alternative to manual dissection methods and is applicable for biomarker analysis of anatomical pathology samples, where enrichment of AOIs from the tissue section is helpful, but pure cell populations are not required.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Chromosome structure is thought to be crucial for proper functioning of the nucleus. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. We begin by applying Oligopaint probes and the single-molecule localization microscopy methods of OligoSTORM and OligoDNA-PAINT to image 8 megabases of human chromosome 19, discovering that chromosomal regions contributing to compartments can form distinct structures. Intriguingly, our data also suggest that homologous maternal and paternal regions may be differentially organized. Finally, we integrate imaging data with Hi-C and restraint-based modeling using a method called integrative modeling of genomic regions (IMGR) to increase the genomic resolution of our traces to 10 kb. One Sentence Summary Super-resolution genome tracing, contact maps, and integrative modeling enable 10 kb resolution glimpses of chromosome folding.