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Cell["Medical Image Analysis Prototyping", "Subtitle"],
Cell["Bart M. ter Haar Romeny & Markus A. van Almsick", "Author"],
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Eindhoven University of Technology
Department of Biomedical Engineering
Biomedical Image Analysis Group
B.M.terHaarRomeny@tue.nl \
\>", "Affiliation"],
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"This paper describes a new international collaborative initiative for the \
assembly of a high level medical image analysis toolkit, based on ",
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", to do efficient design and development of advanced computer vision \
algorithms for computer-aided diagnosis. ",
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" has come to a point that the combined symbolic and numeric power makes it \
a versatile and efficient framework for prototyping of complex algorithms."
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This is a first announcement, and call for interest and participation.\
\>", "Text"]
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Cell["Introduction", "Section"],
Cell["\<\
Medical images are made in huge quantities. The advent of the possibility to \
make 'slices' of patients at high resolution in a non-invasive way has \
revolutionized the making of medical diagnoses. Currently, 80% of all \
diagnoses in Western hospitals are based on and/or are supported by medical \
images.\
\>", "Text"],
Cell["\<\
It is also big business. Today, about one third of all capital investments in \
a modern hospital are done for medical imaging. Magnetic Resonance Imaging \
(MRI) scanners, Computed Tomography (CT) scanners, angiography suites, \
cardiovascular imaging suites, mammography, ultrasound, just to name a few \
imaging modalities. Hospitals become fully digital in an increasingly fast \
pace. It is estimated that in the US and Europe about 75% of the images are \
acquired directly in a digital form, and are stored in a so-called Picture \
Archiving and Communication System (PACS). A typical 1000 bed university \
hospital produces about 10 Terabyte of imaging data per year (this number \
increases 10-15% per year) and is required to store these for 10 years. \
Lightboxes hardly exist anymore. They are replaced by digital workstations \
(hundreds to thousands per hospital), that today mainly do image logistics \
and tele-radiology, but where a strong need for advanced processing \
emerges.\
\>", "Text"],
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"The MRI scanner is the one of the most versatile tomographic scanning \
systems, and is capable of measuring a wide range of physical properties of \
tissues. CT scanners recently made a full comeback in speed and resolution. \
Most CT scanners sold today are multi-slice scanners, i.e. they acquire \
attenuation data of the X-rays with multiple rows of detectors, typically \
4-64. A CT scan of the lung can easily be 2000 slices, with ",
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Cell["The need for computer-assisted diagnosis algorithms", "Section"],
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"The amount of images becomes so overwhelming, that computer assistance in \
the diagnostic process is strongly needed. This new field, \"Computer Aided \
Diagnosis\" has recently seen some remarkable successes, leading to \
commercial activity (see e.g. ",
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"). The computer analyses the images, and reports the location and type of \
the suspected lesion by means of a circle or marker on the original image, as \
an attention sign for the medical professional. In specific cases, such as in \
the detection of microcalcifications, masses and stellate tumors in \
mammography, the computer assisted diagnosis was 15-20% more sensitive than \
expert reading."
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"Currently, there are marked developments in the fields of large scale \
screening activities, i.e. automated lung nodule detection [2], automated \
analysis of retinal vessel leakage in screening for diabetes (see e.g. ",
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"), automated detection of colon polyps (which may develop into a cancer) \
in virtual endoscopy, automated melanoma detection in skin cancer screening, \
and the above mentioned areas in mammography. Many new fields are currently \
explored, such as follicle detection for fertility assessment [6], hand bone \
measurements for bone-age determination, etc. See for the recent developments \
the proceedings of the important conferences in this field, such as ",
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The big question is how to develop the sophisticated image analysis \
algorithms needed. These computer vision methods need a highly mathematical \
approach, in which differential geometry, partial differential equations, \
statistics, linear algebra, etc. play a crucial role.\
\>", "Text"],
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" has rarely be considered for this task, as, many years ago, it used to be \
slow and memory intensive. This has considerably changed since version 4, and \
with the current versions the rapid prototyping, the design of the algorithm \
before they are put into a commercial or specialized application, has become \
extremely efficient in ",
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"[3]. In Eindhoven we have now 3 years of extensive experience in the role \
of ",
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" in our research on Biomedical Image Analysis, and in the education of \
students [4] (see also the accompanying paper at this conference). The \
strategy of 'here is paper: read it, understand it, and make an \
implementation in ",
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Cell["\<\
Most current Digital Image Processing toolkits are rather basic, and contain \
the elementary operations on images, such as filters, geometric \
transformations, histogram operations, mathematical morphology and edge \
detection. There is however a great need for a toolkit with high level \
building blocks for CAD and quantitative extraction of parameters. We list a \
short list of exemplary needs:\
\>", "Text"],
Cell["\<\
- registration methods for intra- and multi-modality image matching
- texture analysis and statistical pattern recognition tools
- model based (atlas) shape recognition methods
- edge-preserving enhancement methods for denoising
- retrieval methods for similar images in huge databases
- robust analysis of optic flow dynamics, e.g. in dynamic heart wall \
studies\
\>", "Text"]
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MathVisionTools is a library of such high level functions, which is initiated \
and managed by Eindhoven University of Technology. We have started \
\>", "Text"],
Cell["\<\
See for a more extensive technical description the accompanying paper by M.A. \
van Almsick at this conference [8].
So far, the package contains:\
\>", "Text"],
Cell["\<\
- an extensive package for doing high order differential geometry on images \
of any dimension;
- a series of versatile conversion routines from specific image formats from \
medical devices (Kretz ultrasound, Biorad microscopy, MRL high field \
microscopy) to the universal DICOM format;
- multi-modality image registration routines;
- multi-scale optic flow detection on 2D-time image sequences [9];
- multi-scale edge focusing techniques for robust segmentation [6];
- active shape and active appearance algorithms for shape variability \
analysis;
- deblurring Gaussian noise [11];
- maximum intensity projection of black/white and color images;
- detection of stellate tumors in mammography (based on [10]);
- geometry-driven diffusion techniques for enhancement by edge-preserving \
smoothing;
- and many in development.\
\>", "Text"],
Cell[TextData[{
"Many of the functions included are based on the many functions released in \
the recent textbooks on multi-scale image analysis [1, 12], and the output of \
a wide range of successful student projects at Eindhoven University [4] (see \
also ",
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"- keep a central moderated base of computer-aided diagnosis functions, \
available through GetURL and Web-",
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";\n- organize periodically dedicated workshops between collaborating \
developer institutes;\n- make available a huge web repository with a wide \
variety of (anonymized) medical images for testing and mutual comparisons. \
Our contacts with university hospitals are excellent;\n- set up a common GUI \
by means of the new GUI toolkit in ",
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";\n- validation of our algorithms between collaborating members, and \
exchange the results;\n- collaboration and exchange with the NLM Segmentation \
and Registration Toolkit (",
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On the longer term, this may lead to (commercial) webservices for interested \
medical parties to have their images given a second opinion diagnosis for a \
small fee per image.\
\>", "Text"],
Cell[TextData[{
StyleBox["Mathematica",
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" is an excellent tool for image analysis prototyping, but may not be the \
best tool for operations on huge datasets. As medical images become larger \
and larger, this is a point of serious concern. MathVisionTools is ",
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" intended to be a industrial quality and speed toolkit, but a research \
tool for efficient and fast design and prototyping. We will include many \
existing pieces of code in C++, Java and Matlab by ",
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" inclusion. The developments of hardware graphics cards support for close \
to real-time calculations on huge datasets for a very low cost are exciting. \
MathVisionTools focuses on the core business of proper CAD: the development \
of high quality, high level, mathematically well underpinned, image analysis \
",
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We call for participation by interested institutes and companies. \
Participation will be on an exchange basis. The code will be made available \
to the partners only in the first stage of the project. During the project we \
will develop in conjunction a strategy how to distribute the code to the \
world. The code will be included in the common package after publication in \
the scientific literature by the authors.\
\>", "Text"],
Cell["Please contact:", "Text"],
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StyleBox["Prof. Bart M. ter Haar Romeny, Dipl. Ing. Markus van Almsick",
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"\nEindhoven University of Technology\nDepartment of Biomedical Engineering\
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+31-40-2475537\nFax +31-40-2472740\nEmail: ",
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"[",
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"] B. M. ter Haar Romeny, \"Front-End Vision and Multi-Scale Image \
Analysis. Multi-Scale Computer Vision Theory and Applications, written in ",
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"\". Dordrecht: Kluwer Academic Publishers, 2003."
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"] Bram van Ginneken, Bart M. ter Haar Romeny, Max A. Viergever, \
\"Computer-aided diagnosis in chest radiography: a survey\", IEEE \
Transactions on Medical Imaging, vol. 20, no. 12, 2001, pp. 1228-1241. ",
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"[",
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"] B.M. ter Haar Romeny, M.A. van Almsick, \"Rapid prototyping of \
biomedical image analysis applications with Mathematica\". Proc. Medicon \
2004, Ischia, Italy. ",
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"[",
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"] B. M. ter Haar Romeny, L. M. J. Florack, \"Front-End Vision, a \
Multiscale Geometry Engine\". Proc. First IEEE International Workshop on \
Biologically Motivated Computer Vision (BMCV2000), May 15-17, 2000, Seoul, \
Korea. Lecture Notes in Computer Science vol. 1811, pp. 297-307, \
Springer-Verlag, Heidelberg, Germany, 2000. ",
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"[",
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"] ",
"B. M. ter Haar Romeny, B. Titulaer, S. Kalitzin, G. Scheffer, F. Broekmans \
and E. te Velde, \"Computer assisted human follicle analysis for fertility \
prospects with 3D ultrasound\", Proceedings Intern. Conf. on Information \
processing in Medical Imaging (IPMI '99), vol. 1613, Lecture Notes in \
Computer Science, Springer-Verlag, Heidelberg, 1999. ",
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"[",
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"] A. Suinesiaputra, L. M. J. Florack, J. J. M. Westenberg, B. M. ter Haar \
Romeny, J. H. C. Reiber, and B. P. F. Lelieveldt. \"Optic flow computation \
from cardiac MR tagging using a multiscale differential method-a comparative \
study with velocity-encoded MRI\". In Proceedings of the Sixth International \
Conference on Medical Image Computing and Computer-Assisted \
Intervention-MICCAI 2003 (Montr\[EAcute]al, Canada, November 2003), pages \
483-490. "
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"[",
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"] M. A. van Almsick, B. M. ter Haar Romeny, \"MathVisionTools, the design \
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Conference 2004, Urbana-Champaign."
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Cell[TextData[{
"[",
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"] W. J. Niessen, B. M. ter Haar Romeny, L. M. J. Florack, and M. A. \
Viergever, \"A general framework for geometry-driven evolution equations,\" \
International Journal of Computer Vision, vol. 21, no. 3, pp. 187-205, 1997. \
"
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Cell[TextData[{
"[",
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"] N. Karssemeijer, G. M. te Brake, \"Detection of Stellate Distortions in \
Mammograms\", IEEE Tr. on Medical Imaging, vol. 15, no. 5, 611-619, Oct. \
1996. ",
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A. Viergever, \"Deblurring Gaussian blur,\" in Proceedings Mathematical \
Methods in Medical Imaging II, vol. 2299, (San Diego, CA), pp. 139-148, SPIE, \
July, 25-26 1994. "
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