RESUMEN
We present GyVe, an interactive visualization tool for understanding structure in sparse three-dimensional (3D) point data. The scientific goal driving the tool's development is to determine the presence of filaments and voids as defined by inferred 3D galaxy positions within the Horologium-Reticulum supercluster (HRS). GyVe provides visualization techniques tailored to examine structures defined by the intercluster galaxies. Specific techniques include: interactive user control to move between a global overview and local viewpoints, labelled axes and curved drop lines to indicate positions in the astronomical RA-DEC-cz coordinate system, torsional rocking and stereo to enhance 3D perception, and geometrically distinct glyphs to show potential correlation between intercluster galaxies and known clusters. We discuss the rationale for each design decision and review the success of the techniques in accomplishing the scientific goals. In practice, GyVe has been useful for gaining intuition about structures that were difficult to perceive with 2D projection techniques alone. For example, during their initial session with GyVe, our collaborators quickly confirmed scientific conclusions regarding the large-scale structure of the HRS previously obtained over months of study with 2D projections and statistical techniques. Further use of GyVe revealed the spherical shape of voids and showed that a presumed filament was actually two disconnected structures.
RESUMEN
The Virtual Pediatric Airways Workbench (VPAW) is a patient-centered surgical planning software system targeted to pediatric patients with airway obstruction. VPAW provides an intuitive surgical planning interface for clinicians and supports quantitative analysis regarding prospective surgeries to aid clinicians deciding on potential surgical intervention. VPAW enables a full surgical planning pipeline, including importing DICOM images, segmenting the airway, interactive 3D editing of airway geometries to express potential surgical treatment planning options, and creating input files for offline geometric analysis and computational fluid dynamics simulations for evaluation of surgical outcomes. In this paper, we describe the VPAW system and its use in one case study with a clinician to successfully describe an intended surgery outcome.
Asunto(s)
Imagenología Tridimensional/métodos , Modelos Biológicos , Enfermedades Respiratorias/diagnóstico por imagen , Enfermedades Respiratorias/cirugía , Cirugía Asistida por Computador/métodos , Interfaz Usuario-Computador , Simulación por Computador , Femenino , Enseñanza Mediante Simulación de Alta Fidelidad/métodos , Humanos , Masculino , Pediatría/métodos , Cuidados Preoperatorios/métodos , Sistema Respiratorio/diagnóstico por imagen , Sistema Respiratorio/cirugíaRESUMEN
In mitosis, the pericentromere is organized into a spring composed of cohesin, condensin, and a rosette of intramolecular chromatin loops. Cohesin and condensin are enriched in the pericentromere, with spatially distinct patterns of localization. Using model convolution of computer simulations, we deduce the mechanistic consequences of their spatial segregation. Condensin lies proximal to the spindle axis, whereas cohesin is radially displaced from condensin and the interpolar microtubules. The histone deacetylase Sir2 is responsible for the axial position of condensin, while the radial displacement of chromatin loops dictates the position of cohesin. The heterogeneity in distribution of condensin is most accurately modeled by clusters along the spindle axis. In contrast, cohesin is evenly distributed (barrel of 500-nm width × 550-nm length). Models of cohesin gradients that decay from the centromere or sister cohesin axis, as previously suggested, do not match experimental images. The fine structures of cohesin and condensin deduced with subpixel localization accuracy reveal critical features of how these complexes mold pericentric chromatin into a functional spring.
Asunto(s)
Adenosina Trifosfatasas/metabolismo , Proteínas de Ciclo Celular/metabolismo , Proteínas Cromosómicas no Histona/metabolismo , Proteínas de Unión al ADN/metabolismo , Mitosis/genética , Complejos Multiproteicos/metabolismo , Saccharomyces cerevisiae/genética , Huso Acromático/genética , Centrómero/genética , Cromatina/genética , Simulación por Computador , Cinetocoros , Microtúbulos , Proteínas Nucleares/genética , Saccharomyces cerevisiae/crecimiento & desarrollo , Proteínas Reguladoras de Información Silente de Saccharomyces cerevisiae/genética , Sirtuina 2/genética , CohesinasRESUMEN
Fluorescence microscopy provides a powerful method for localization of structures in biological specimens. However, aspects of the image formation process such as noise and blur from the microscope's point-spread function combine to produce an unintuitive image transformation on the true structure of the fluorescing molecules in the specimen, hindering qualitative and quantitative analysis of even simple structures in unprocessed images. We introduce FluoroSim, an interactive fluorescence microscope simulator that can be used to train scientists who use fluorescence microscopy to understand the artifacts that arise from the image formation process, to determine the appropriateness of fluorescence microscopy as an imaging modality in an experiment, and to test and refine hypotheses of model specimens by comparing the output of the simulator to experimental data. FluoroSim renders synthetic fluorescence images from arbitrary geometric models represented as triangle meshes. We describe three rendering algorithms on graphics processing units for computing the convolution of the specimen model with a microscope's point-spread function and report on their performance. We also discuss several cases where the microscope simulator has been used to solve real problems in biology.