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Table of Contents Recent Releases Issue 41Issue • April24 • 2017 TABLE OF CONTENTS RECENT RELEASES Editor's Note ............................................................................... 1 KITWARE AND COLLABORATORS MAKE 1.0 RELEASE OF MATERIALS TOMOGRAPHY Recent Releases ......................................................................... 1 PLATFORM Kitware worked with researchers to make the first major Novel Mechanism Segments Anatomical Structures for 3D release of Tomviz, an open-source platform that processes Printing ....................................................................................... 3 data for materials tomography. Tomviz aligns, reconstructs, segments, visualizes, and analyzes three-dimensional tomo- GeoJS Draws Better Lines ......................................................... 7 graphic data through a reproducible pipeline. Kitware News .............................................................................. 9 The release followed the conclusion of Phase II of a Department of Energy Small Business Innovation Research project. For the project, Kitware partnered with Cornell EDITOR'S NOTE University and collaborated with members of other academic institutions to develop a multithreaded application architec- As winter turned to spring, we experienced some changes ture and an extensive Python environment in the platform. of our own at Kitware. For starters, we re-designed our “We created a responsive, graphical solution that processes website. The re-design not only consolidated content and and analyzes complex scientific data in a manner that may navigation options, but it revitalized the look of our pages. otherwise span multiple applications and programming Our website now runs on WordPress, scales better on cell environments,” said Marcus Hanwell, a technical leader at phones and tablets, and provides additional visualizations Kitware. Hanwell is a member of the Tomviz development and information on areas of focus. Please have a look at team who served as the principal investigator on the project. https://www.kitware.com. Let us know what you think! Since January, we also grew our team; we saw long-time employees jump into new roles; and we moved our office location in Santa Fe, New Mexico. To aid our communities, we collected pet supplies such as toys, food, and blankets. In addition, we sold paper hearts for Ronald McDonald House Charities. Our Kitware Gives Back team is already working on upcoming initiatives. For specifics, please read our blog at https://blog.kitware.com. This year, we are a silver sponsor of Computer Vision and Pattern Recognition (CVPR). Members of our computer vision team will set up a booth (242) at the event in July 2017. Multiple team members are event chairs. Senior Director of Computer Vision Anthony Hoogs is a general chair, and Assistant Director of Computer Vision Matt Turek is a corporate relations chair. We have more details in an event listing at https://blog.kitware.com/events/computer- vision-and-pattern-recognition-cvpr-2017. Tomviz shows an animation of a nanotube from Robert Hovden. Tomviz comes ready for download as open-source binaries for CMAKE UPS SUPPORT FOR CUDA, CSHARP, major operating systems like Windows, macOS, and Linux. To AND C++ begin the pipeline, Tomviz imports projection images from Kitware released version 3.8 of its open-source solution for transmission electron microscopes in industry-standard file cross-platform software development, CMake. The release formats such as Tagged Image File Format (TIFF), Medical upgraded support for CUDA, CSharp (C#), and C++, promot- Research Council (MRC), and Electron Microscopy Datasets ing both CUDA and C# to first-class programming languages. (EMD). While the platform can automatically align these Likewise, the release further simplified project compilation images, it enables users to manually adjust the tilt and rota- with the addition of C++11, C++14, and C++17 target-based tion of the axis. feature flags. These flags extend the existingtarget_ command. Kitware published detailed “Throughout the pipeline, Tomviz remains highly interac- compile_features notes on CMake 3.8 on its blog at https://blog.kitware.com/ tive,” said Robert Hovden, a former postdoctoral researcher cmake-3-8-0-available-for-download. To download CMake, at Cornell University and a founder of the Tomviz develop- please visit https://cmake.org/download. ment team. “Tomviz runs data operators in background threads, so users can continue to work with the platform PARAVIEW GETS MORE ANIMATED while it executes operations.” The ParaView 5.3 release included new plug-ins. One plug- in, , adjusts the gradient, contours, and details The platform builds on the capabilities of the Insight VTKmFilters in visualizations on many-core systems. Another plug-in, Segmentation and Registration Toolkit, the Visualization , animates streamlines. Toolkit, and ParaView. Through hardware-accelerated StreamLinesRepresentation rendering techniques, for example, Tomviz lets users alter visualization parameters such as the opacity, lighting, color, and orientation of volumes and geometries. Tomviz not only provides different rendering modes, but it contains multiple tools for analysis. One tool, a ruler, measures the lengths of objects in images. Tomviz also computes surface area, volume, and other labeled object attributes, which it displays in a spreadsheet that users can save. In addition to tabular data, Tomviz allows users to save its state with all data pipeline settings. Users can share and modify these settings to help others follow the necessary steps to reproduce results. Tomviz saves results as movies or exports them on the web as HTML files. To foster open dissemination, the Tomviz development team made live A screenshot captures the use of the examples publicly available on GitHub. These examples StreamLinesRepresentation plug-in. utilize images or the latest Web Graphics Library (WebGL) To reduce aliasing artifacts when ParaView renders lines, rendering techniques. wireframes, etc., the release turned on the Fast Approximate This material is based upon work supported by the Anti-Aliasing (FXAA) algorithm by default. The release also Department of Energy under Office of Science Award updated the integration of ParaView and OSPRay through Number DE-SC0011385. This report was prepared as an support for OSPRay 1.1.2. For more information, please visit account of work sponsored by an agency of the United States https://blog.kitware.com/paraview-5-3-0-release-notes. Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any war- GIRDER 2.2 TUNES DATA MANAGEMENT Girder 2.2 became available as open-source software. The ranty, express or implied, or assumes any legal liability or release polished the user interface on the administrative responsibility for the accuracy, completeness, or usefulness configuration page. It also presented a file-like interface for of any information, apparatus, product, or process disclosed, files in Girder assetstores. In addition, the release augmented or represents that its use would not infringe privately owned support for file formats in the DICOM viewer plug-in, it built rights. Reference herein to any specific commercial product, in support for Box as an Open Authorization (OAuth) pro- process, or service by trade name, trademark, manufacturer, vider, it incorporated support for static-only dependencies or otherwise does not necessarily constitute or imply its between plug-ins for web client code, it introduced a mode endorsement, recommendation, or favoring by the United that boosts upload performance, and it refined download States Government or any agency thereof. The views and performance in the Secure File Transfer Protocol (SFTP) opinions of authors expressed herein do not necessarily server. To download Girder, please go to https://github.com/ state or reflect those of the United States Government or girder/girder/releases/tag/v2.2.0. any agency thereof. 2 NOVEL MECHANISM SEGMENTS ANATOMICAL STRUCTURES FOR 3D PRINTING Csaba Pinter, Andras Lasso, and Gabor Fichtinger (Queen's University) A fundamental task in most aspects of medical image Unfortunately, representing and processing anatomical computing is segmentation, i.e., delineation of anatomical structures present major difficulties. These difficulties include structures of interest for further processing and quantifica- operation, as it may be necessary to perform conversion. tion. Segmentation can be manual, it can be semi-automatic Another difficulty is identity, since it is important to keep (through the initialization of an algorithm with limited track of the origin (provenance) of the structures and what input), or it can be fully automatic (through an autonomous they represent. A third difficulty is validity: Representations algorithm). A multitude of software tools and algorithms may change after conversions, so invalid data must remain exist for each type of segmentation, and segmentation has inaccessible at all times. Coherence serves as an additional served as the subject of extensive research in the field of point of difficulty. As structure sets typically correspond to medical image computing. the same entity (i.e., the patient), the in-memory objects that relate to the structures need to form a unified whole. Most commonly, three-dimensional (3D) binary volumes (labelmaps) store segmentation results. Each volume simply 3D Slicer [2] is one of the most popular open-source platforms indicates whether
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