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SimITK: Visual Programming of the ITK Image-Processing Library within Simulink

Andrew W. L. Dickinson, Purang Abolmaesumi, David G. Gobbi, Parvin Mousavi
2014 Journal of digital imaging  
Compared to their pure-code equivalents, the workflows highlight ITK usability through an alternative visual interpretation of the code that abstracts away potentially confusing technicalities.  ...  Experience Program (NSERC-CREATE) for their assistance and support; Saba El-Hilo for her contributions towards the tutorials found on the project website; and Karen Li and Jing Xiang for their initial  ...  Acknowledgments We would like to acknowledge the Natural Sciences and Engineering Research Council (NSERC), Canadian Institute for Health Research (CIHR), and the NSERC Collaborative Research and Training  ... 
doi:10.1007/s10278-013-9667-7 pmid:24402456 pmcid:PMC3948930 fatcat:gttw4hu34neufizts75d7vi6e4

Image Segmentation, Registration and Characterization in R with SimpleITK

Richard Beare, Bradley Lowekamp, Ziv Yaniv
2018 Journal of Statistical Software  
ITK is an open source C++ toolkit that has been actively developed over the past 18 years and is widely used by the medical image analysis community.  ...  In this article we describe the SimpleITK R package. SimpleITK is a simplified interface to the insight segmentation and registration toolkit (ITK).  ...  Acknowledgments This work was supported by the Intramural Research Program of the U.S.  ... 
doi:10.18637/jss.v086.i08 pmid:30288153 pmcid:PMC6168008 fatcat:namgrlek7ncgvazbwwdv5skwpi

Joint Platforms and Community Efforts in Surgical Robotics Research

Árpád Takács, Sándor Jordán, Dénes Nagy, Péter Pausits, Tamás Haidegger, József K. Tar, Imre J. Rudas
2015 MACRo 2015  
In modern medical research and development, the variety of research tools has extended in the previous years.  ...  Exploiting the benefits of shared hardware platforms and software frameworks is crucial to keep up with the technological development rate.  ...  Insight Segmentation and Registration Toolkit Similarly to the VTK, the Insight Segmentation and Registration Toolkit (ITK) is an open-source, cross-platform system, mostly used in segmentation and image  ... 
doi:10.1515/macro-2015-0009 fatcat:2ev3iwlcrvc25gi7clggpx7dru

Automated Feature Extraction and Retrieval of Ultra Sound Kidney Images using Maxi-Min Approach

S. Manikandan, V. Rajamani
2010 International Journal of Computer Applications  
A general purpose medical image retrieval framework has been proposed with two subsystems namely enrollment and the query subsystem.  ...  As an attempt to design a new content based image retrieval methodology following the above framework, MAXI-MIN approach is implemented for the ultra sound kidney images for the retrieval process.  ...  Existing image processing tools like Khoros/Cantata/VisiQuest1, the Insight Toolkit (ITK)2, the Visualization Toolkit (VTK)3, or ImageJ4 provide a huge number of routines useful for feature extraction  ... 
doi:10.5120/844-1120 fatcat:mb32awylvfcs5hvr3od6ntr2yi

Extraction of Pulmonary Areas in Thoracic CT Images Including Pleural Effusion Using a Registration Method

Akinori TSUNOMORI, Hayaru SHOUNO, Shoji KIDO
2008 Medical Imaging Technology  
:塵肺症の segmentation for image retrieval using the Insight 臨床と画像 -アスベストーシスを中心に-.  ...  画像診断 Toolkit(ITK).  ... 
doi:10.11409/mit.26.338 fatcat:5epr5x4g7vcd5lz5ux65oehva4

BRISC—An Open Source Pulmonary Nodule Image Retrieval Framework

Michael O. Lam, Tim Disney, Daniela S. Raicu, Jacob Furst, David S. Channin
2007 Journal of digital imaging  
We have created a content-based image retrieval framework for computed tomography images of pulmonary nodules.  ...  When presented with a nodule image, the system retrieves images of similar nodules from a collection prepared by the Lung Image Database Consortium (LIDC).  ...  Armato III from the University of Chicago, local principal investigator for the Lung Image Data Consortium, for providing an explanation of their database.  ... 
doi:10.1007/s10278-007-9059-y pmid:17701069 pmcid:PMC2039863 fatcat:ik5t2ztdp5frhblidztrnpdtri

Interfaces and integration of medical image analysis frameworks: Challenges and opportunities

Kelsie Covington, Evan S. McCreedy, Min Chen, Aaron Carass, Nicole Aucoin, Bennett A. Landman
2010 2010 Biomedical Sciences and Engineering Conference  
In this initial effort, we focus on four platforms Medical Image Analysis and Visualization (MIPAV), Java Image Science Toolkit (JIST), command line tools, and 3D Slicer.  ...  platform is used for collaboration.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the NIH, CIT and under extramural grants 1R21NS064534-01A109 and R21-EB009900.  ... 
doi:10.1109/bsec.2010.5510850 pmid:21151892 pmcid:PMC2998761 fatcat:f5ko3kil3rfr3p66gxsdbw2c2a

Watershed Segmentation of Lung CT Scan Images for Early Diagnosis of Cancer

Shubhpreet Kaur, Gagandeep Jindal
2011 International Journal of Computer and Electrical Engineering  
These methods are based on the filters available in the 'Insight Segmentation and Registration Toolkit' (ITK).  ...  The achieved results support the use of the proposed algorithm for extraction of lung nodules from the image.  ...  Further obtained segments can be used for content based medical image retrieval as a diagnostic aid.  ... 
doi:10.7763/ijcee.2011.v3.431 fatcat:muyqepenijfoxlhrajfd3ex6li

Building generic anatomical models using virtual model cutting and iterative registration

Mei Xiao, Jung Soh, Oscar Meruvia-Pastor, Eric Schmidt, Benedikt Hallgrímsson, Christoph W Sensen
2010 BMC Medical Imaging  
Conclusions: Our method is very flexible and easy to use such that anyone can use image stacks to create models and retrieve a sub-region from it at their ease.  ...  such as the CAVE Automated Virtual Environment.  ...  We also thank the reviewers for their comments.  ... 
doi:10.1186/1471-2342-10-5 pmid:20144190 pmcid:PMC2830992 fatcat:frprsbo2kraljp7uj6hvalmcre

Automated generation of directed graphs from vascular segmentations

Brian E. Chapman, Holly P. Berty, Stuart L. Schulthies
2015 Journal of Biomedical Informatics  
Automated feature extraction from medical images is an important task in imaging informatics.  ...  The segmentations were acquired in a semi-automated fashion using existing segmentation tools.  ...  We identified n PT using image orientation information extracted from the headers of the original medical images.  ... 
doi:10.1016/j.jbi.2015.07.002 pmid:26165778 pmcid:PMC4547695 fatcat:qtzfxfcqa5gn5e2pdrfk3ioqia

Bioinformatics Solutions for Image Data Processing [chapter]

Pietro Cinaglia, Luciano Caroprese, Giuseppe Lucio Cascini, Francesco Dattola, Pasquale Iaquinta, Miriam Iusi, Pierangelo Veltri, Ester Zumpano
2018 Medical and Biological Image Analysis  
solutions and toolkits for medical imaging in order to suggest an overview of techniques and methods that can be applied for the imaging analysis in medicine.  ...  In recent years, the increasing use of medical devices has led to the generation of large amounts of data, including image data.  ...  It is part of the SciJavasoftware stack and in use by several projects including ImageJ2, ImgLib2, and the Insight Toolkit (ITK).  ... 
doi:10.5772/intechopen.76459 fatcat:kejwf2t3rrcjnccmad4d2jskwa

OIPAV: an Integrated Software System for Ophthalmic Image Processing, Analysis, and Visualization

Lichun Zhang, Dehui Xiang, Chao Jin, Fei Shi, Kai Yu, Xinjian Chen
2018 Journal of digital imaging  
Typical examples include Osirix [1] , 3D Slicer [2] and Paraview [3] , which are application system based on Visualization Toolkit (VTK) [4] and Insight Toolkit (ITK) [5] .  ...  In the layer of high-level libraries, a number of popular medical programming toolkits including ITK, DCMTK [8] , VTK and vtkINRIA3D [9] support base processing and visualization functions for higher  ... 
doi:10.1007/s10278-017-0047-6 pmid:30187316 fatcat:gwx63bm4argu5cb7vch6ewmdjy

Integrating Segmentation Methods From Different Tools Into a Visualization Program Using an Object-Based Plug-In Interface

Felix Fischer, M Alper Selver, Walter Hillen, Cüneyt Guzelis
2010 IEEE Transactions on Information Technology in Biomedicine  
This paper describes the implementation of an interface, which can be used to plug-in and then apply a segmentation method to a medical image series.  ...  The design allows access to insight registration and segmentation toolkit, Java, and MATLAB functionality together, eases sharing and comparing segmentation techniques, and serves as a visual debugger  ...  several different applications, such as insight registration and segmentation toolkit (ITK) [27] , MATLAB [9] , and Java.  ... 
doi:10.1109/titb.2010.2044243 pmid:20403791 fatcat:esl5nqq3zzgevjc4yiyi2wjjay

Imaging-based observational databases for clinical problem solving: the role of informatics

Alex A T Bui, William Hsu, Corey Arnold, Suzie El-Saden, Denise R Aberle, Ricky K Taira
2013 JAMIA Journal of the American Medical Informatics Association  
The development of these databases and ensuing models can aid in medical decision making and knowledge discovery and ultimately, transform the use of imaging to support individually-tailored patient care  ...  With the increased use of imaging and its progressive technical advances, the role of imaging informatics is now evolving-from one of managing images, to one of integrating the full scope of clinical information  ...  Acknowledgements The authors would like to thank Dr Hooshang Kangarloo for his insights and vision, which have guided the UCLA Medical Imaging Informatics Group over many years.  ... 
doi:10.1136/amiajnl-2012-001340 pmid:23775172 pmcid:PMC3822107 fatcat:itmeorvnfffk7leafwgcytc36e

Data preparation for artificial intelligence in medical imaging: A comprehensive guide to open-access platforms and tools

Oliver Diaz, Kaisar Kushibar, Richard Osuala, Akis Linardos, Lidia Garrucho, Laura Igual, Petia Radeva, Fred Prior, Polyxeni Gkontra, Karim Lekadir
2021 Physica medica (Testo stampato)  
The pillar supporting the development of reliable and robust AI algorithms is the appropriate preparation of the medical images to be used by the AI-driven solutions.  ...  Here, we provide a comprehensive guide for the necessary steps to prepare medical images prior to developing or applying AI algorithms.  ...  Acknowledgments This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 952103, from the Spanish Ministry (grant RTI2018-095232  ... 
doi:10.1016/j.ejmp.2021.02.007 pmid:33684723 fatcat:ygrrorchbrautnwlaixrqq25hy
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