Reproducibility verification is essential to the practice of scientific method. Researchers report their findings, which are strengthened as other independent groups in community share similar outcomes. In many fields where software has become a fundamental tool for capturing and analyzing data, this requirement reproducibility implies that reliable comprehensive platforms tools should be made available community. The will empower them public verify, through practice, observations reported...

This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is open source C++ software library that provides basic components needed to develop applications. It intended for fast prototyping and development The was developed through a collaboration between academic industry partners. Because designed safety-critical applications, team has adopted lightweight processes emphasizes safety robustness while, at same time, supporting geographically separated developers. A...

This paper presents a new algorithm for the fast, shared memory multi-core computation of augmented merge trees on triangulations. In contrast to most existing parallel algorithms, our technique computes trees. augmentation is required enable full extent tree based applications, including data segmentation. Our approach completely revisits traditional, sequential re-formulate as set independent local tasks Fibonacci heaps. results in superior time performance practice, well thanks OpenMP...

This paper presents a new algorithm for the fast, shared memory multi-threaded computation of contour trees on tetrahedral meshes. In contrast to previous algorithms, our technique computes augmented tree. Such an augmentation is required enable full extent tree based applications, including instance data segmentation. Our approach relies range-driven domain partitioning. We show how exploit such partitioning rapidly compute forests. also forests can be efficiently turned into output report...

This paper presents a new algorithm for the fast, shared memory, multi-core computation of augmented contour trees on triangulations. In contrast to most existing parallel algorithms our technique computes trees, enabling full extent tree based applications including data segmentation. Our approach completely revisits traditional, sequential re-formulate all steps as set independent local tasks. includes procedure Fibonacci heaps join and split two intermediate structures used compute tree,...

An open source lesion sizing toolkit has been developed with a general architecture for implementing segmentation algorithms and reference algorithm segmenting solid part-solid lesions from lung CT scans. The detects four three-dimensional features corresponding to the wall, vasculature, boundary edges, low density background parenchyma. These form boundaries propagation zones that guide evolution of subsequent level set algorithm. User input is used determine an initial seed point users may...

In scientific visualization, data are becoming more and important usually implies a cooperative effort. Moreover experts geographically distributed, therefore they need collaborative tools to work efficiently. To solve this limitation, prospective action has been recently initiated, with the development of web based application for interaction on two innovating technologies: WebGL WebSocket. demonstrate approach, prototype developed Visible Patient project. paper we present architecture...

Visualization and image processing of medical datasets has become an essential task for clinical diagnosis support as well treatment planning. In order to enable a physician use evaluate algorithms within setting, easily applicable software prototypes with dedicated user interface are essential. However, substantial programming knowledge is still required today when using powerful open source libraries such the Toolkit (VTK) or Insight (ITK). Moreover, these toolkits provide only limited...

Magentic Reasonance Imaging for mouse phenotype study is one of the important tools to understand human diseases.In this paper, we present a fully automatic pipeline process morphometric brain analysis.The method based on atlas-based tissue and regional segmentation, which was originally developed brain.To evaluate our method, conduct qualitative quantitative validation as well compare b-spline fluid registration methods components in pipeline.The includes visual inspection, shape volumetric...

In the recent years, scientific community has been focusing on management and dissemination of datasets. Challenged by rapid growth in number size data supported new governmental policies, sharing become a necessary step discovery. parallel, publishing companies have shifted their business to provide not only publications but also associated datasets readers. fact, industry investigating ways disseminate more importantly, present this readers meaningful manner. paper, we combination two...

This paper presents, to the best of our knowledge, first parallel algorithm for computation augmented Reeb graph piecewise linear scalar data. Such graphs have a wide range applications , including contour seeding and feature based segmentation. Our approach targets shared-memory multi-core workstations. For this, it completely revisits optimal, but sequential, algorithm, which is capable handing data in arbitrary dimension with optimal time complexity. We take advantage Fibonacci heaps...

We introduce an automated and accurate system for registering pre-operative 3D MR CT images with intraoperative ultrasound based on the vessels visible in both. The clinical goal is to guide radio-frequency ablation (RFA) of liver lesions using percutaneous even when are not directly ultrasound. locations desired RFA sites indicated images, those markings made appear within intra-operative images. present our current implementation, provide analyses its components, demonstrate performance.

We investigate the accuracy of intensity-based deformable image registration (DIR) for tumor localization in liver stereotactic body radiotherapy (SBRT). included 4DCT scans to capture breathing motion eight patients receiving SBRT metastases within a retrospective clinical study. Each patient had three fiducial markers implanted. The and were delineated mid-ventilation phase, their positions other phases estimated with registration. tested referenced sequential registrations strategies....

Respiratory motion leads to blur and artifacts in single-photon emission computed tomography (SPECT) images. This may be an issue some treatments such as liver radioembolization. The purpose of this work was reconstruct 4-D respiration-gated SPECT images using a data-driven approach. A respiratory signal extracted from list-mode data Laplacian eigenmaps used for retrospective phase gating. method evaluated on various datasets: Monte Carlo simulation patient acquisition, several acquisitions...

This paper presents an overview of several efforts towards reproducible research in the field medical imaging and visualization. In first section, components Open Science are presented: open access, data source. sec

Open source software has tremendous potential for improving the productivity of research labs and enabling development new medical applications. The Image-Guided Surgery Toolkit (IGSTK) is an open toolkit based on ITK, VTK, FLTK, uses cross-platform tools CMAKE DART to support common operating systems such as Linux, Windows, MacOS. IGSTK integrates basic components needed in surgical guidance applications provides a platform fast prototyping robust image-guided This paper gives overview...

In this paper, we present MIDAS, a web-based digital archiving system that processes large collections of data. Medical imaging research often involves interdisciplinary teams, each performing separate task, from acquiring datasets to analyzing the processing results. Moreover, number and size continue increase every year due recent advancements in acquisition technology. As result, many laboratories centralize their data rely on distributed computing power. We created repository based...

The ICT revolution of the last decade impacts scientific publishing and changes format in which articles are delivered how results research communicated.With researchers increasingly generating referencing 3D data their articles, ability to accurately visualize that online publications has become extremely important.To address growing demands visualization across various domains journals, Elsevier Kitware launched a project develop infrastructure supporting different formats, techniques,...