For more information, please visit IMDI website for more information.

Using 3 publicly available anatomical whole-body atlases, Sprague-Dawley (SD) rat (Bai et al. 2006), MOBY mouse (Segars et al. 2004) and Digimouse (Dogdas et al. 2007), articulated versions of these atlases were built. To this end, major bones/bone groups were manually segmented for each atlas skeleton. Then, a kinematic model for each atlas was built: each joint position was identified and the corresponding Degrees of Freedom (DoFs) were specified, according to the joint type i.e., ball or hinge joint.

Within our research, the articulated MOBY atlas proved to be a very useful tool for whole-body segmentation of mice from low-contrast microCT (Baiker et al. 2010a, Khmelinskii and Baiker et al. 2010), multi-modality image combination (Wildeman et al. 2009, Khmelinskii et al. 2010) and follow-up studies (Baiker et al. 2010b) and proved to be a valuable tool for pre-clinical research.

For further information and details about articulated atlas construction and applications please refer to the following articles:

• A. Khmelinskii and M. Baiker, E. L. Kaijzel, J. Chen, J. H. C. Reiber and B. P. F. Lelieveldt. Articulated whole-body atlases for small animal image analysis: construction & applications. Mol. Imaging Biol, 2010, in press, (Khmelinskii and Baiker et al. 2010)
• M. Baiker, J. Milles, J. Dijkstra, T. Henning, A. W. Weber, I. Que, E. Kaijzel, C. W. G. M. Löwik, J. H. C. Reiber and B. P. F Lelieveldt. Atlas-based whole-body segmentation of mice from low-contrast Micro-CT data. Med. Image Anal., 2010,in press (Baiker et al. 2010a)
• M. Baiker, J. Dijkstra, J. Milles, C. W. G. M. Löwik, B. P. F. Lelieveldt, Paragios, N.; Duncan, J. & Ayache, N. (ed.). Handbook of Biomedical Imaging, “Atlas-based whole-body registration in mice”. Springer, N.Y., USA, 2010, in press (Baiker et al. 2010b)
• A. Khmelinskii, M. Baiker, X. J. Chen, J. H. C. Reiber, R. M. Henkelman, and B. P. F. Lelieveldt. Atlas-based organ & bone approximation for ex-vivo µMRI mouse data: a pilot study. IEEE Intl. Symp. on Biomedical Imaging. in press, 2010(Khmelinskii et al. 2010)
• M. H. Wildeman, M. Baiker, J. H. C. Reiber, C. W. G. M. Löwik, M. J. T. Reinders & B. P. F. Lelieveldt. 2D/3D registration of micro-CT data to multi-view photographs based on a 3D distance map. Proc. IEEE Intl. Symp. on Biomedical Imaging,2009, 987-990 (Wildeman et al. 2009)
• M. Baiker, J. Milles, A. M. Vossepoel, I. Que, E. L. Kaijzel, C. W. G. M. Löwik, J. H. C. Reiber, J. Dijkstra & B. P. F. Lelieveldt. Fully automated whole-body registration in mice using an articulated skeleton atlas. Proc. IEEE Intl. Symp. on Biomedical Imaging, 2007, 728-731 (Baiker et al. 2007)

Acknowledgement and citation

The presented modifications to the original atlases (the manually partitioned skeletons) are free for download for academic purposes. To this end, the online form has to be filled and subsequently the download page will be loaded.
The e-mail address will be used only for verification purposes. Also, please note that we do not provide access to the original atlases; the conditions of use for the MOBY, Digimouse, and SD Rat atlases vary, and are listed on the original atlas websites. We request that any publication using one of the articulated atlases cites either the reference [1] or [2] from the list above, along with the citation requested by the original atlas owners.

Download

The download packages include a labeled volume file (Amira am format, which can also be loaded in ImageJ), surface representations of individual bones of the segmented skeleton and the skin in the STL format, a list with joint coordinates and a small documentation. To apply for downloading the atlas files, please fill out thisform. You will then receive an email with further instructions.

Links and references to the original atlases

• MOBY Atlas
  • Segars, W. P.; Tsui, B. M. W.; Frey, E. C.; Johnson G. A. and Berr, S. S. Development of a 4D digital mouse phantom for molecular imaging research. Mol. Imag. Biol. 6(3):149-159, 2004.
  • For further information on the MOBY phantom, please contactpaul.segars@duke.edu.
• Digimouse Atlas
  • Dogdas, B.; Stout, D.; Chatziioannou, A. and Leahy, R. M. Digimouse: a 3D whole body mouse atlas from CT and cryosection data”. Phys. Med. Biol.52(3):577-587, 2007.
• SD Rat atlas
  • Wu, L.; Zhang, G.; Luo, Q. and Liu, Q. An image-based rat model for Monte Carlo organ dose calculations. Med. Phys. 35(8): 3759-3764, 2008.
  • Bai, X.; Yu, L.; Liu, Q.; Zhang, J.; Li, A.; Han, D.; et al. A high-resolution anatomical rat atlas. J. Anat. 209(5):707-708, 2006.

Contact information

• Martin Baiker - m.baiker@lumc.nl
• Artem Khmelinskii - a.khmelinskii@lumc.nl
• B. P. F. Lelieveldt - b.p.f.lelieveldt@lumc.nl

This page is taken from here.

76 attendees, 17 accepted full papers (5 from the Netherlands), 23 posters and a poster fast-forward session, 4 invited talks, 2 keynotes by respectively Prof.dr. Anders Ynnerman on their Virtual Autopsy work and Dr. Roland Bammer on camera-based motion-correction in MRI acquisition, and finally 1 social event in the Leipzig zoo and Kiwara Lodge. All the numbers, together with a strong scientific program, added up to a successful event that shall be continued in Linköping, Sweden in 2012, after which the workshop will take place on a yearly basis.  We would like to thank everyone involved and also our sponsors (DFG, Siemens, MeVis and Medis) for contributing to VCBM’s success!

The Diagnostic Image Analysis group at the Department of Radiology, Radboud University Nijmegen Medical Centre, is offering a PhD position.

Organization
The Diagnostic Image Analysis group is a research division of the Department of Radiology of the Radboud University Nijmegen Medical Centre. Nijmegen is the oldest Dutch city with a rich history and one of the liveliest city centers in the Netherlands. Radboud University Nijmegen Medical Centre (RUNMC) is a leading academic centre for medical science, education and health care with over 8,500 staff and 3,000 students.

The focus of the Diagnostic Image Analysis group is the development and validation of novel methods in a broad range of medical imaging applications. Research topics include image analysis, image segmentation, machine learning, and the design of decision support systems and application areas include breast imaging, prostate imaging, and lung imaging. Key to the success of the group is close cooperation with clinical partners and a disease oriented approach.Currently the group consists of 16 researchers, including 10 PhD students.

Job profile
Computer Aided Diagnosis (CAD) is a rapidly expanding field in medical imaging, and is aimed at developing applications to help radiologists to detect and diagnose disease. A PhD position is available for a researcher who will investigate new methods for the detection of abnormalities in chest computed tomography (CT) scans. Initially, the research will be focused on the detection of lung cancer. Lung cancer is the most deadly cancer and early detection with CT is one of the most promising strategies to reduce lung cancer mortality. Later in the project the goal may be extended to find other types of abnormalities in chest CT scans.

Embedding
This project will be carried out in close collaboration with Fraunhofer MEVIS (http://www.mevis.fraunhofer.de) in Bremen, Germany and MeVis Medical Solutions, based in Bremen, Germany and Pewaukee,Wisconsin, USA.

Requirements
You should be a creative and enthusiastic researcher with an MSc degree in Computer Science, Physics, Engineering or Biomedical Sciences. Good communication skills and expertise in software development, preferably in C++, are essential.

Terms of employment
You will be appointed as a PhD student with the standard salary and secondary conditions for PhD students in the Netherlands. Your performance will be evaluated after 1 year. If the evaluation is positive, the contract will be extended by 3 years. The research should result in a PhD thesis.

Information
For more information contact Dr. B. van Ginneken or Dr.ir. N. Karssemeijer.

Application
Send applications as a single pdf file to both b.vanginneken@rad.umcn.nl and n.karssemeijer@rad.umcn.nl. In this pdf file the following should be included: CV, list of followed courses and grades, letter of motivation, and preferably a reprint of your Master thesis or any publications in English you have written.

Faculty/department

Engineering, Mathematics and Computer Science
The faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) is known world wide for its high academic quality and social relevance of its research programs. The faculty’s excellent facilities accentuate its international position in teaching and research. The faculty offers an interdisciplinary setting for its 500 employees, 350 PhD students and 1700 undergraduates. Together they work on a broad range of technical innovations in the fields of sustainable energy, telecommunications, microelectronics, embedded systems, computer and software engineering, interactive multimedia and applied mathematics.
The Department of Mediamatics focuses on media and knowledge processing. The department consists of four groups: 1) Pattern Recognition and Bioinformatics Group: Processing, analysis, and interpretation of biological and biomedical data, Medical Image Processing, Computer Vision and Pattern Recognition 2) Multimedia Signal Processing Group: Processing, analysis, and interpretation of multimedia signals, Security and Privacy 3) Computer Graphics: Modelling, representation and visualization of 3D objects and scientific data; 4) Human Computer Interaction: Design, analysis, implementation and validation of human-machine systems and the application of AI techniques to enhance the interaction. Four important application domains are telecommunications, consumer electronics, industrial automation, and life/health sciences.

Job description
The PRB group actively participates in the Medical Delta consortium, a collaboration between TU Delft and two University Medical Center: Erasmus Medical Center and Leiden University Medical Center. Goal of medical delta is the development of novel technology that enhances health care in a broad sense. Within the Computer Vision and Pattern Recognition lab, there is a vacancy for a PhD student who will conduct research on the intersection between the fields of bio-informatics and bio-imaging. Bio informatics explores mechanisms of gene expression, metabolism, reaction, etc., within the cell, whereas bio-imaging increasingly enables imaging gene expression.

The goal of this project is to investigate methods to link gene expression data to biomedical imaging data. This may involve for instance linking anatomy derived in MRI images to gene expression atlases (phenotyping transgenic mice), or to protein expression in spectroscopy or microscopic data. Also, techniques to correlate features in multi-spectral imaging series form a part of this research project. Finally, methods to compare phenotypes in a group based on genetic differences are of interest. We are looking for a PhD student who can contribute to this research at the intersection between bioinformatics and bioimaging.  She/he is expected to cooperate intensively with imaging researchers at the Leiden University Medical Center, as well as with computer vision and bioinformatics researchers at the PRB group.

Requirements
The candidate should have a MSc degree in Computer Science or a related field and a background in digital image processing, and have affinity for biomedical research. Experience in biomedical image analysis and bio-informatics is an asset. Additionally, the candidate should have excellent spoken and written communication skills and programming skills (C, C++, Matlab).

Conditions of employment
This position has a temporary employment basis of three years. TU Delft offers an attractive benefits package, including a flexible work week, free high-speed Internet access from home, and the option of assembling a customized compensation and benefits package (the ‘IKA’). Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities.

Information and application
For more information about this position, please contact Dr. E. A. Hendriks, phone: +31 (0)15-2786269, e-mail: e.a.hendriks@tudelft.nl. To apply, please e-mail a detailed CV along with a letter of application by 17 April, 2009 to Mrs. J. Eddini, peno-ewi@tudelft.nl.

job_openings

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Position A

PhD student, Fluorescence guided Oncological surgery
(F/M)
(36 hours p/w)

The PhD student is part of a multi-disciplinary research team working on a novel way of cancer surgery using multi-spectral fluorescence imaging. Using fluorescent tumor-targeting probes, tumor tissue can be made visible during surgery with a novel multi-spectral imaging system. Potentially, this may provide the surgeon with a tool for more effective and complete removal of tumor tissue. Research goal for the PhD student is the development of algorithms for photon attenuation correction for light sources in biological tissues using optical images at multiple wavelengths. Research is carried out in close collaboration with molecular biologists and oncological surgeons as part of the MUSIS project funded by the Center for Translational Molecular Medicine (www.ctmm.nl). A strong background in physics is required, and experience with tissue optics and photon attenuation correction is preferred.

Position A:

•    Investigate tissue models of photon propagation based on response ratios in multiple wavelength ranges
•    Determine optimal acquisition wavelengths to enable attenuation correction for different fluorophores
•    Develop fast algorithms for attenuation correction based on this optimal wavelength configuration
•    Support the integration of these algorithms in a multi-spectral camera system for oncological surgery
•    Present the work in scientific papers and on international conferences
•    Complete a PhD thesis

We are looking for creative and enthusiastic scientists with an

•    M.Sc in Physics
•    Affinity and experience with biomedical research and medical image processing and visualization
•    Ability to solve problems on an abstract level, but also able to apply these solutions in (clinical) practice, in a pragmatic manner
•    Clear interest in the application and utilization of (bio)medical, technological research
•    Enthusiastic team-player
•    Attentive to detail and committed
•    Excellent communication and writing skills
•    Knowledge of Linux, Windows and matlab
•    Knowledge of C++ will be an advantage

We offer:

•    An intellectual challenge on a scientifically hot topic with a high potential impact on cancer surgery; this within an enthusiastic and successful research team;
•    An excellent software and hardware infrastructure based on the latest computer and camera technology;
•    The opportunity to collaborate closely with surgeons, radiologists, molecular biologists and medical industry
•    The assignment of the investigator will be on a project basis and initially for a period of 12 months followed by the remaining period of 3 years under the condition of a positive judgment over the first year.

For more information, please contact:
Dr B.Lelieveldt[AT]lumc.nl
Phone: +31 71 526 1130
or
Dr J.Dijkstra[AT]lumc.nl
Phone: +31 71 526 2270
Please email your application letter to:
Prof. dr ir J.H.C. Reiber, PhD (J.H.C.Reiber[AT]lumc.nl)
Phone:+31 71 526 3935
Fax: +31 71 526 6801

The Computer Aided Diagnosis Group Nijmegen is offering two senior research positions.

Organization
The Computer Aided Diagnosis Group Nijmegen is a research division of the department of Radiology of the Radboud University Nijmegen Medical Center. The focus of the group is development and validation of novel computer aided diagnosis methods in a broad range of medical imaging applications. Research topics include image analysis, image segmentation, machine learning, and the design of decision support systems. Key to the success of the group is close cooperation with clinical partners and a disease oriented approach. Currently the group consists of 16 researchers, including 10 PhD students.

Job profile
Computer Aided Diagnosis (CAD) is a rapidly expanding field in medical imaging, and is aimed at developing applications to help radiologists to detect and diagnose disease. Two positions are available for researchers who will investigate new methods and applications in CAD. Initially, research will be focused on projects in breast and/or lung imaging. It is expected, however, that research is expanded to other domains, such as neuro-imaging. Initiation of new research projects in collaboration with clinical partners, other academic institutions, and industry will be an important task. The research will be embedded in the newly established Fraunhofer Mevis Nijmegen Project Group.

Requirements
The candidates should have a strong background in medical image analysis and have affinity or experience with pattern recognition. The candidates should have obtained a PhD in the field of medical imaging and be capable of initiating and supervising research projects and of building a strong international network. Experience in the field should be evidenced by peer reviewed publications on topics that are relevant for this position. Further requirements are excellent communication skills and expertise in software development.

Terms of employment
The appointments will initially be for a period of 2 years, but will lead to long term positions if the research is successful. In the initial period, employment will be arranged within the German Fraunhofer Institute (information about Fraunhofer Mevis can be found at http://www.mevis.fraunhofer.de). The salary will be competitive with comparable positions at Dutch universities.

Information
For more information contact Dr.ir. N. Karssemeijer (n.karssemeijer@rad.umcn.nl) or Dr. B. van Ginneken (bramvanginneken@gmail.com).

Application
Send applications as a single pdf file to n.karssemeijer@rad.umcn.nl and bramvanginneken@gmail.com. In this pdf file the following should be included: CV, motivation and preprints of at most four peer reviewed papers relevant for the position.

Venue: Senaatzaal of the Aula of the Delft University of Technology, Mekelweg 5, Delft.