Medical Image Processing Software
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Management of Large Sets of Image Data Capture, Databases, Image Processing, Storage, Visualization Karol Kozak
Management of large sets of image data Capture, Databases, Image Processing, Storage, Visualization Karol Kozak Download free books at Karol Kozak Management of large sets of image data Capture, Databases, Image Processing, Storage, Visualization Download free eBooks at bookboon.com 2 Management of large sets of image data: Capture, Databases, Image Processing, Storage, Visualization 1st edition © 2014 Karol Kozak & bookboon.com ISBN 978-87-403-0726-9 Download free eBooks at bookboon.com 3 Management of large sets of image data Contents Contents 1 Digital image 6 2 History of digital imaging 10 3 Amount of produced images – is it danger? 18 4 Digital image and privacy 20 5 Digital cameras 27 5.1 Methods of image capture 31 6 Image formats 33 7 Image Metadata – data about data 39 8 Interactive visualization (IV) 44 9 Basic of image processing 49 Download free eBooks at bookboon.com 4 Click on the ad to read more Management of large sets of image data Contents 10 Image Processing software 62 11 Image management and image databases 79 12 Operating system (os) and images 97 13 Graphics processing unit (GPU) 100 14 Storage and archive 101 15 Images in different disciplines 109 15.1 Microscopy 109 360° 15.2 Medical imaging 114 15.3 Astronomical images 117 15.4 Industrial imaging 360° 118 thinking. 16 Selection of best digital images 120 References: thinking. 124 360° thinking . 360° thinking. Discover the truth at www.deloitte.ca/careers Discover the truth at www.deloitte.ca/careers © Deloitte & Touche LLP and affiliated entities. Discover the truth at www.deloitte.ca/careers © Deloitte & Touche LLP and affiliated entities. -
A 3D Interactive Multi-Object Segmentation Tool Using Local Robust Statistics Driven Active Contours
A 3D interactive multi-object segmentation tool using local robust statistics driven active contours The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Gao, Yi, Ron Kikinis, Sylvain Bouix, Martha Shenton, and Allen Tannenbaum. 2012. A 3D Interactive Multi-Object Segmentation Tool Using Local Robust Statistics Driven Active Contours. Medical Image Analysis 16, no. 6: 1216–1227. doi:10.1016/j.media.2012.06.002. Published Version doi:10.1016/j.media.2012.06.002 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:28548930 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Med Image Anal. Author manuscript; available in PMC 2013 August 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Med Image Anal. 2012 August ; 16(6): 1216–1227. doi:10.1016/j.media.2012.06.002. A 3D Interactive Multi-object Segmentation Tool using Local Robust Statistics Driven Active Contours Yi Gaoa,*, Ron Kikinisb, Sylvain Bouixa, Martha Shentona, and Allen Tannenbaumc aPsychiatry Neuroimaging Laboratory, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115 bSurgical Planning Laboratory, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115 cDepartments of Electrical and Computer Engineering and Biomedical Engineering, Boston University, Boston, MA 02115 Abstract Extracting anatomical and functional significant structures renders one of the important tasks for both the theoretical study of the medical image analysis, and the clinical and practical community. -
Inviwo — a Visualization System with Usage Abstraction Levels
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, VOL X, NO. Y, MAY 2019 1 Inviwo — A Visualization System with Usage Abstraction Levels Daniel Jonsson,¨ Peter Steneteg, Erik Sunden,´ Rickard Englund, Sathish Kottravel, Martin Falk, Member, IEEE, Anders Ynnerman, Ingrid Hotz, and Timo Ropinski Member, IEEE, Abstract—The complexity of today’s visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for instance by providing a data flow network editor. Unfortunately, these abstractions result in several issues, which need to be circumvented through an abstraction-centered system design. Often, a high level of abstraction hides low level details, which makes it difficult to directly access the underlying computing platform, which would be important to achieve an optimal performance. Therefore, we propose a layer structure developed for modern and sustainable visualization systems allowing developers to interact with all contained abstraction levels. We refer to this interaction capabilities as usage abstraction levels, since we target application developers with various levels of experience. We formulate the requirements for such a system, derive the desired architecture, and present how the concepts have been exemplary realized within the Inviwo visualization system. Furthermore, we address several specific challenges that arise during the realization of such a layered architecture, such as communication between different computing platforms, performance centered encapsulation, as well as layer-independent development by supporting cross layer documentation and debugging capabilities. Index Terms—Visualization systems, data visualization, visual analytics, data analysis, computer graphics, image processing. F 1 INTRODUCTION The field of visualization is maturing, and a shift can be employing different layers of abstraction. -
Anatomical Models from Imaging Data
Prof. Steven S. Saliterman Department of Biomedical Engineering, University of Minnesota http://saliterman.umn.edu/ Magnetic Resonance Imaging (MRI) ◦ Human max. is 3T (Tesla) – resolution of 250µm x 250µm 0.5mm. ◦ High spatial resolution µMRI, 7-10T, 5-200µm. ◦ Magnetic nanoparticles. Computed tomography (CT)– Computer Axial Tomography ◦ Typical resolution of 0.24 – 0.3mm. ◦ µCT, resolution of 1-200µm. Ultrasound ◦ Resolution of 1mm x 1.mm x 0.2mm. PET – Positron emission tomography SPECT – Single photon emission computed tomography Optical Coherence Tomography (OCT) Traditional optical techniques. Prof. Steven S. Saliterman Prof. Steven S. Saliterman Mayo Foundation for Medical Education and Research Prof. Steven S. Saliterman CT scan/PET Scan/ Combined Mayo Foundation for Medical Education and Research Prof. Steven S. Saliterman Purpose ◦ To delineate and isolate anatomical features within an imaging database- e.g. bone, cartilage, soft tissue, edema; muscle, lung, brain & other organs, and tumors. Method ◦ Extract images from DICOM files (ITK-Snap, Onis) and possible deindentifying them for HIPPA regulations (DICOMCleaner). ◦ Segmentation Software (ITK-Snap, Materialise Mimics, Materialise 3- matic). Pre-segmentation Phase - identify parts of image as foreground and background. Active Contour Phase - manual and semiautomatic methods. ◦ Editing and fixing mesh files (.STL) - Autodesk Meshmixer. ◦ Slicer software – Simplify3D and Repetier. G-coding for the specific bioprinter - e.g. Slic3R (printer customized interface to control what happens in a sequence of control steps.) Prof. Steven S. Saliterman Sagittal or Median Parasagittal (Yellow) Transverse or Axial Frontal or Coronal Prof. Steven S. Saliterman Image, Wikipedia Manual Segmentation… Prof. Steven S. Saliterman Prof. Steven S. Saliterman Prof. Steven S. Saliterman Prof. -
A Client/Server Based Online Environment for the Calculation of Medical Segmentation Scores
A Client/Server based Online Environment for the Calculation of Medical Segmentation Scores Maximilian Weber, Daniel Wild, Jürgen Wallner, Jan Egger Abstract— Image segmentation plays a major role in medical for medical image segmentation are often very large due to the imaging. Especially in radiology, the detection and development broadly ranged possibilities offered for all areas of medical of tumors and other diseases can be supported by image image processing. Often huge updates are needed, which segmentation applications. Tools that provide image require nightly builds, even if only the functionality of segmentation and calculation of segmentation scores are not segmentation is needed by the user. Examples are 3D Slicer available at any time for every device due to the size and scope [8], MeVisLab [9] and MITK [10], [11], which have installers of functionalities they offer. These tools need huge periodic that are already over 1 GB. In addition, in sensitive updates and do not properly work on old or weak systems. environments, like hospitals, it is mostly not allowed at all to However, medical use-cases often require fast and accurate install these kind of open-source software tools, because of results. A complex and slow software can lead to additional security issues and the potential risk that patient records and stress and thus unnecessary errors. The aim of this contribution data is leaked to the outside. is the development of a cross-platform tool for medical segmentation use-cases. The goal is a device-independent and The second is the need of software for easy and stable always available possibility for medical imaging including manual segmentation training. -
An Open-Source Research Platform for Image-Guided Therapy
Int J CARS DOI 10.1007/s11548-015-1292-0 ORIGINAL ARTICLE CustusX: an open-source research platform for image-guided therapy Christian Askeland1,3 · Ole Vegard Solberg1 · Janne Beate Lervik Bakeng1 · Ingerid Reinertsen1 · Geir Arne Tangen1 · Erlend Fagertun Hofstad1 · Daniel Høyer Iversen1,2,3 · Cecilie Våpenstad1,2 · Tormod Selbekk1,3 · Thomas Langø1,3 · Toril A. Nagelhus Hernes2,3 · Håkon Olav Leira2,3 · Geirmund Unsgård2,3 · Frank Lindseth1,2,3 Received: 3 July 2015 / Accepted: 31 August 2015 © The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Results The validation experiments show a navigation sys- Purpose CustusX is an image-guided therapy (IGT) research tem accuracy of <1.1mm, a frame rate of 20 fps, and latency platform dedicated to intraoperative navigation and ultra- of 285ms for a typical setup. The current platform is exten- sound imaging. In this paper, we present CustusX as a robust, sible, user-friendly and has a streamlined architecture and accurate, and extensible platform with full access to data and quality process. CustusX has successfully been used for algorithms and show examples of application in technologi- IGT research in neurosurgery, laparoscopic surgery, vascular cal and clinical IGT research. surgery, and bronchoscopy. Methods CustusX has been developed continuously for Conclusions CustusX is now a mature research platform more than 15years based on requirements from clinical for intraoperative navigation and ultrasound imaging and is and technological researchers within the framework of a ready for use by the IGT research community. CustusX is well-defined software quality process. The platform was open-source and freely available at http://www.custusx.org. -
Medical Image Processing Software
Wohlers Report 2018 Medical Image Processing Software Medical image Patient-specific medical devices and anatomical models are almost always produced using radiological imaging data. Medical image processing processing software is used to translate between radiology file formats and various software AM file formats. Theoretically, any volumetric radiological imaging dataset by Andy Christensen could be used to create these devices and models. However, without high- and Nicole Wake quality medical image data, the output from AM can be less than ideal. In this field, the old adage of “garbage in, garbage out” definitely applies. Due to the relative ease of image post-processing, computed tomography (CT) is the usual method for imaging bone structures and contrast- enhanced vasculature. In the dental field and for oral- and maxillofacial surgery, in-office cone-beam computed tomography (CBCT) has become popular. Another popular imaging technique that can be used to create anatomical models is magnetic resonance imaging (MRI). MRI is less useful for bone imaging, but its excellent soft tissue contrast makes it useful for soft tissue structures, solid organs, and cancerous lesions. Computed tomography: CT uses many X-ray projections through a subject to computationally reconstruct a cross-sectional image. As with traditional 2D X-ray imaging, a narrow X-ray beam is directed to pass through the subject and project onto an opposing detector. To create a cross-sectional image, the X-ray source and detector rotate around a stationary subject and acquire images at a number of angles. An image of the cross-section is then computed from these projections in a post-processing step. -
Avizo Software for Industrial Inspection
Avizo Software for Industrial Inspection Digital inspection and materials analysis Digital workflow Thermo Scientific™ Avizo™ Software provides a comprehensive set of tools addressing the whole research-to-production cycle: from materials research in off-line labs to automated quality control in production environments. 3D image data acquisition Whatever the part or material you need to inspect, using © RX Solutions X-ray CT, radiography, or microscopy, Avizo Software is the solution of choice for materials characterization and defect Image processing detection in a wide range of areas (additive manufacturing, aerospace, automotive, casting, electronics, food, manufacturing) and for many types of materials (fibrous, porous, metals and alloys, ceramics, composites and polymers). Avizo Software also provides dimensional metrology with Visual inspection Dimensional metrology Material characterization advanced measurements; an extensive set of programmable & defect analysis automated analysis workflows (recipes); reporting and traceability; actual/nominal comparison by integrating CAD models; and a fully automated in-line inspection framework. With Avizo Software, reduce your design cycle, inspection times, and meet higher-level quality standards at a lower cost. + Creation and automation of inspection and analysis workflows + Full in-line integration Reporting & traceability On the cover: Porosity analysis and dimensional metrology on compressor housing. Data courtesy of CyXplus 2 3 Avizo Software for Industrial Inspection Learn more at thermofisher.com/amira-avizo Integrating expertise acquired over more than 10 years and developed in collaboration with major industrial partners in the aerospace, Porosity analysis automotive, and consumer goods industries, Avizo Software allows Imaging techniques such as CT, FIB-SEM, SEM, and TEM, allow detection of structural defects in the to visualize, analyze, measure and inspect parts and materials. -
Respiratory Adaptation to Climate in Modern Humans and Upper Palaeolithic Individuals from Sungir and Mladeč Ekaterina Stansfeld1*, Philipp Mitteroecker1, Sergey Y
www.nature.com/scientificreports OPEN Respiratory adaptation to climate in modern humans and Upper Palaeolithic individuals from Sungir and Mladeč Ekaterina Stansfeld1*, Philipp Mitteroecker1, Sergey Y. Vasilyev2, Sergey Vasilyev3 & Lauren N. Butaric4 As our human ancestors migrated into Eurasia, they faced a considerably harsher climate, but the extent to which human cranial morphology has adapted to this climate is still debated. In particular, it remains unclear when such facial adaptations arose in human populations. Here, we explore climate-associated features of face shape in a worldwide modern human sample using 3D geometric morphometrics and a novel application of reduced rank regression. Based on these data, we assess climate adaptations in two crucial Upper Palaeolithic human fossils, Sungir and Mladeč, associated with a boreal-to-temperate climate. We found several aspects of facial shape, especially the relative dimensions of the external nose, internal nose and maxillary sinuses, that are strongly associated with temperature and humidity, even after accounting for autocorrelation due to geographical proximity of populations. For these features, both fossils revealed adaptations to a dry environment, with Sungir being strongly associated with cold temperatures and Mladeč with warm-to-hot temperatures. These results suggest relatively quick adaptative rates of facial morphology in Upper Palaeolithic Europe. Te presence and the nature of climate adaptation in modern humans is a highly debated question, and not much is known about the speed with which these adaptations emerge. Previous studies demonstrated that the facial morphology of recent modern human groups has likely been infuenced by adaptation to cold and dry climates1–9. Although the age and rate of such adaptations have not been assessed, several lines of evidence indicate that early modern humans faced variable and sometimes harsh environments of the Marine Isotope Stage 3 (MIS3) as they settled in Europe 40,000 years BC 10. -
Getting Started First Steps with Mevislab
Getting Started First Steps with MeVisLab 1 Getting Started Getting Started Copyright © 2003-2021 MeVis Medical Solutions Published 2021-05-11 2 Table of Contents 1. Before We Start ................................................................................................................... 10 1.1. Welcome to MeVisLab ............................................................................................... 10 1.2. Coverage of the Document ........................................................................................ 10 1.3. Intended Audience ..................................................................................................... 11 1.4. Conventions Used in This Document .......................................................................... 11 1.4.1. Activities ......................................................................................................... 11 1.4.2. Formatting ...................................................................................................... 11 1.5. How to Read This Document ..................................................................................... 12 1.6. Related MeVisLab Documents ................................................................................... 12 1.7. Glossary (abbreviated) ............................................................................................... 13 2. The Nuts and Bolts of MeVisLab ........................................................................................... 15 2.1. MeVisLab Basics ...................................................................................................... -
Customized Product Design Based on Medical Imaging
INTERNATIONAL DESIGN CONFERENCE - DESIGN 2012 Dubrovnik - Croatia, May 21 - 24, 2012. CUSTOMIZED PRODUCT DESIGN BASED ON MEDICAL IMAGING G. Harih, B. Dolšak and J. Kaljun Keywords: product design, customization, medical imaging, reverse engineering, innovation 1. Introduction Design is a very complex task even for an experienced designer. Only designer who are capable of creative and analytical thinking combined can solve complex design problems. Technological innovation pushes the creativity to new limits and therefore designers are forced to design new products with new functionality within ever shorter time to market deadlines [Ye et al. 2008]. Computer Aided Engineering (CAE) software, especially Computer Aided Design (CAD) software has made great progress recently. Thereby the designer has comprehensive tools to meet the expectations of the company, although the creative and innovative thinking cannot be stimulated through this software. Products are usually mass produced in order to keep the production costs at lowest level and are therefore designed to suit a wide population. However there has been an increased market demand of customized products which incorporate whole product customization or customized parts [Merle et al. 2010]. Major part of companies or institutions who utilize customization can be attributed to medical applications (medical prosthesis, implants, splints, etc). Recent extensive development in various technologies such as medical imaging, 3D scanners and rapid prototyping has impacted also customization within luxury products and in products where high stresses an exceptional performance is expected such as high performance tools and gear, professional sports equipment and military equipment. In order to produce a customized part, the designer has an even more complex design process to overcome. -
3D Medical Image Segmentation in Virtual Reality
3D Medical Image Segmentation in Virtual Reality Shea B. Yonker, Oleksandr O. Korshak, Timothy Hedstrom, Alexander Wu, Siddharth Atre, Jürgen P. Schulze University of California San Diego, La Jolla, CA Abstract inside, all by using their hands like they would in the real world. The possible achievements of accurate and intuitive 3D In fact, our application goes beyond simulating what one could image segmentation are endless. For our specific research, we do in the real world by allowing the user to reach into the data aim to give doctors around the world, regardless of their set as if it is a hologram. computer knowledge, a virtual reality (VR) 3D image Finally, to more particularly examine one aspect of the segmentation tool which allows medical professionals to better data, our program allows for segmentation of this 3D image. For visualize their patients' data sets, thus attaining the best humans, looking at an image and deciphering foreground vs. understanding of their respective conditions. background is in most cases trivial. Whereas for computers, it We implemented an intuitive virtual reality interface that can be one of the most difficult and computationally taxing can accurately display MRI and CT scans and quickly and problems. For this reason, we will introduce several precisely segment 3D images, offering two different segmentation solutions, each of which is tailored to a specific segmentation algorithms. Simply put, our application must be application of medical imaging. able to fit into even the most busy and practiced physicians' workdays while providing them with a new tool, the likes of Related Work which they have never seen before.