ShadiAlbarqouni

Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

Shadi Albarqouni

Dr. Shadi Albarqouni

  • Postdoctoral Research Associate

  • Email: shadi.albarqouni [@] tum.de

  • Address:

Chair for Computer Aided Medical Procedures & Augmented Reality
Fakultät für Informatik
Technische Universität München
Boltzmannstr. 3
85748 Garching b. München

Short Curriculum Vitae

2017- Postdoctoral Research Associate, CAMP - Technische Universität München (TUM), Munich, Germany
2013-2016 Visiting Scholar, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
2010-2012 Lecturer in Electrical and Computer Engineering Departments, The Islamic University of Gaza, Palestine
2007-2012 Lecturer in Information Technology Department, University College of Applied Science, Palestine
2005-2007 Teaching Assistant in Electrical Engineering Department, The Islamic University of Gaza, Palestine

Background

2013-2017 Ph.D. Informatics,Chair for Computer Aided Medical Procedures (CAMP), Technical University Munich, Germany
under the supervision of Prof. Dr. Nassir Navab
2005-2007 M.Sc. Electrical Engineering, The Islamic University of Gaza, Palestine
Thesis: Re-evaluation and re-design of stand alone PV solar lighting projects: Gaza Strip, Palestine
under the supervision of Prof. Dr. Mohammed T. Hussein
2001-2005 B.Sc. Electrical Engineering, The Islamic University of Gaza, Palestine
Finished within 4 years instead of the regular period of 5 years.

Scholarship & Awards

  • Reviewer Commendation at MICCAI 2018, Granada, Spain
  • Best Paper Award at MIAR Conference 2016, Bern, Switzerland
  • 3rd rank in MICCAI-AMIDA13 challenge for Automatic Models for Mitosis Detection in Breast Cancer Histology Images
  • Ph.D. Fellowship
  • Best Master Thesis Award in Faculty of Engineering, Jun. 2010, The Islamic University of Gaza, Palestine.
  • Arab Bank Scholarship, Sept. 2001-Sept. 2002, Gaza, Palestine.

Professional Activities

Reviewer

Organizer

Member

Student Projects

Feel free to contact me to any of the following projects. open: drop by and ask!.

Available

Running
Master ThesisUncertainty in Deep Learning for Medical Application
(Dr. Shadi Albarqouni, Prof. Dr. Nassir Navab)
Master ThesisUncertainty-Driven Active Learning in Deep Hybrid Models
(Dr. Shadi Albarqouni, Prof. Dr. Nassir Navab)
IDPGuided Attention Segmentation Networks
(Dr. Shadi Albarqouni, Hasan Sarhan, Prof. Dr. Nassir Navab)
IDPFew-Shot Learning
(Dr. Shadi Albarqouni, Prof. Dr. Nassir Navab)

Finished
ProjectExplainability of Artificial Intelligence (XAI): Taxonomy
(Dr. Shadi Albarqouni, Prof. Dr. Nassir Navab)
Master ThesisStainGAN: Stain style transfer for digital histological images
(Shadi Albarqouni, Christoph Baur, Prof. Dr. Nassir Navab)
Master ThesisLeft Atrium Segmentation in 3D Ultrasound Using Volumetric Convolutional Neural Networks
(Shadi Albarqouni, Prof. Dr. Nassir Navab)
Master ThesisSiemens AG: Detection of Complex Stents in Live Fluoroscopic Images for Endovascular Aneurysm Repair
(Shadi Albarqouni, Stefanie Demirci, Prof. Dr. Nassir Navab)
Master ThesisWeakly-Supervised Anomaly Detection assisted by Attention Models
(Shadi Albarqouni, Diana Mateus, Prof. Nassir Navab)
Master ThesisWeakly-Supervised Liver Lesion Localisation and Classification with Spectral CT Data
(Shadi Albarqouni, Peter Noel, Prof. Dr. Nassir Navab)
IDPMS Lesion Segmentation in multi-channel subtraction images
(Christoph Baur, Shadi Albarqouni, Prof. Dr. Nassir Navab)
Master ThesisRohde & Schwarz: Deep feature representation with auxiliary embedding
(Shadi Albarqouni, Athanasios Karamalis, Prof. Nassir Navab)
Bachelor ThesisMeta-Learning of Regularization Parameters in X-ray Computed Tomography
(Shadi Albarqouni, Tobias Lasser)
DA/MA/BAA comparative study on unsupervised deep learning methods
(Shadi Albarqouni, Christoph Baur, Prof. Nassir Navab)
Master ThesisSiemens AG: X-ray PoseNet - Recovering the Poses of Portable X-Ray Device with Deep Learning
(Shadi Albarqouni, Slobodan Ilic, Prof. Nassir Navab)
Master ThesisA Deep Learning Approach to Synthesize Virtual CT based on Transmission Scan in hybrid PET/MR
(Sailesh Conjeti, Kuangyu Shi, Shadi Albarqouni, Prof. Dr. Nassir Navab)
ProjectCreating Diagnostic Model for Assessing the Success of Treatment for Eye Melanoma
(Shadi Albarqouni, Prof. Nassir Navab)
Bachelor ThesisComparative Study on CNN Initialization
(Shadi Albarqouni, Prof. Nassir Navab)
IDPCancer Matestasis detection in Lymph nodes
(Shadi Albarqouni, Stefanie Demirci, Prof. Nassir Navab)
ProjectDepth Estimation for Catheters from Single-View Interventional X-ray Imaging
(Shadi Albarqouni, Stefanie Demirci, Pascal Fallavollita, Prof. Nassir Navab)
Bachelor ThesisGamification in the Medical Context
(Shadi Albarqouni,Stefanie Demirci, Maximilian Baust, Prof. Nassir Navab)
IDPCrowdsourcing in the Medical Context
(Shadi Albarqouni,Stefanie Demirci, Prof. Nassir Navab)
Master ThesisDepth Recovery from Single-View Interventional X-ray Imaging
(Shadi Albarqouni, Stefanie Demirci, Lichao Wang, Prof. Nassir Navab)

Hot Stuff

Internship Offers

Teaching

List of Publications

2018
M. Degel, N. Navab, S. Albarqouni
Domain and Geometry Agnostic CNNs for Left Atrium Segmentation in 3D Ultrasound
Proceedings of 21st International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Granada, Spain, September 2018
A pre-print version is available online at arXiv.
(bib)
A. Sanchez, S. Albarqouni, D. Mateus
Capsule Networks against Medical Imaging Data Challenges
Proceedings of MICCAI Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis, Granada, Spain, September 2018
A pre-print version is available online at arXiv.
(bib)
M. Bui, S. Albarqouni, S. Ilic, N. Navab
Scene Coordinate and Correspondence Learning for Image-Based Localization
Proceedings of the British Machine Vision Conference, 3-6 September, 2018, Newcastle (Oral presentation) (bib)
C. Baur, B. Wiestler, S. Albarqouni, N. Navab
Deep Autoencoding Models for Unsupervised Anomaly Segmentation in Brain MR Images
Accepted to the Proceedings of the Brain Lesion Workshop at the 21th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Granada, Spain, September 2018
A pre-print version is available online at arXiv.
(bib)
C. Baur, S. Albarqouni, N. Navab
Generating Highly Realistic Images of Skin Lesions with GANs
Accepted to the Proceedings of the ISIC Skin Image Analysis Workshop at the 21th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Granada, Spain, September 2018
A longer pre-print version is available at arXiv.
(bib)
M. Molina-Romero, PA. Gómez, S. Albarqouni, JI. Sperl, MI. Menzel, B. Menze
Deep learning with synthetic data for free water elimination in diffusion MRI
Proceedings of the International Society of Magnetic Resonance in Medicine (ISMRM), Paris, France, June 2018 (bib)
M. Bui, S. Zakharov, S. Albarqouni, S. Ilic, N. Navab
When Regression meets Manifold Learning for Object Recognition and Pose Estimation
Proceedings of IEEE International Conference on Robotics and Automation (ICRA), 21-25 May, 2018, Brisbane, Australia (bib)
K. Breininger, S. Albarqouni, T. Kurzendorfer, M. Pfister, M. Kowarschik, A. Maier
Intraoperative Stent Segmentation in X-ray Fluoroscopy for Endovascular Aortic Repair
International Journal of Computer Assisted Radiology and Surgery (IJCARS) (bib)
C. Baur, S. Albarqouni, N. Navab
MelanoGANs: High Resolution Skin Lesion Synthesis with GANs
Submitted to the 1st International conference on Medical Imaging with Deep Learning (MIDL), Amsterdam, Netherlands, July 2018
A pre-print version is available online at arXiv.
(bib)
S. Hariharan, N. Strobel, C. Kaethner, M. Kowarschik, S. Demirci, S. Albarqouni, R. Fahrig, N. Navab
A photon recycling approach to denoising of ultra-low dose X-ray sequences
International Journal of Computer Assisted Radiology and Surgery / 9th International Conference on Information Processing in Computer-Assisted Interventions (IPCAI), Berlin, Germany, June 2018. (bib)
M. T. Shaban, C. Baur, N. Navab, S. Albarqouni
StainGAN: Stain Style Transfer for Digital Histological Images
Submitted to the 21st International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Granada, Spain, September 2018
A pre-print version is available online at arXiv.
(bib)
2017
B. Wiestler, C. Baur, P. Eichinger, , T. Zhang, V. Biberacher, C. Zimmer, , J. Kirschke, S. Albarqouni
Fully Automated Multiple Sclerosis lesion detection on multi-channel subtraction images through an integrated Computer Vision- Machine Learning pipeline
Clinical Neuroradiolgy (2017) 27:S1-S118 (bib)
A. Kazi, S. Albarqouni, A. Sanchez, C. Kirchhoff, P. Biberthaler, N. Navab, D. Mateus
Automatic Classification of Proximal Femur Fractures based on Attention Models
Proceedings of MICCAI Workshop on Machine Learning in Medical Imaging (MLMI), Quebec, Canada, September 2017 (bib)
J. Cardoso, T. Arbel, J. Lee, V. Cheplygina, S. Balocco, D. Mateus, G. Zahnd, L. Maier-Hein, S. Demirci, E. Granger, L. Duong, M. A. Carbonneau, S. Albarqouni, G. Carneiro
Intravascular imaging and computer assisted stenting, and large-scale annotation of biomedical data and expert label synthesis
MICCAI 2017 Workshops (bib)
S. Albarqouni, J. Fotouhi, N. Navab
X-ray In-Depth Decomposition: Revealing The Latent Structures
Accepted to Proceedings of the 20th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Quebec, Canada, September 2017
A pre-print version is available online at arXiv.
(bib)
M. Bui, S. Albarqouni, M. Schrapp, N. Navab, S. Ilic
X-ray PoseNet: 6 DoF Pose Estimation for Mobile X-ray Devices
Proceedings of IEEE Winter Conference on Applications of Computer Vision (WACV), Mar 24, 2017 - Mar 31, 2017, Santa Rosa, USA
The first two authors contribute equally to this paper.
(bib)
C. Baur, S. Albarqouni, N. Navab
Semi-Supervised Learning for Fully Convolutional Networks
Accepted to Proceedings of the 20th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Quebec, Canada, September 2017
A pre-print version is available online at arXiv.
The first two authors contribute equally to this paper.
(bib)
2016
S. Albarqouni, S. Matl, M. Baust, N. Navab, S. Demirci
Playsourcing: A Novel Concept for Knowledge Creation in Biomedical Research
Proceedings of MICCAI Workshop on Large-scale Annotation of Biomedical data and Expert Label Synthesis, Athens, Greece, October 2016
The first two authors contribute equally to this paper.
(bib)
C. Baur, S. Albarqouni, S. Demirci, N. Navab, P. Fallavollita
CathNets: Detection and Single-View Depth Prediction of Catheter Electrodes
7th International Conference on Medical Imaging and Augmented Reality (MIAR), 24-26 August, 2016, Bern, Switzerland. (Best Paper Award) (bib)
S. Albarqouni, U. Konrad, L. Wang, N. Navab, S. Demirci
Single-View X-Ray Depth Recovery: Towards a Novel Concept for Image-Guided Interventions
International Journal of Computer Assisted Radiology and Surgery (IJCARS), 2016, June 2016, Volume 11, Issue 6, pp 873-880. (bib)
S. Albarqouni, C. Baur, F. Achilles, V. Belagiannis, S. Demirci, N. Navab
AggNet: Deep Learning from Crowds for Mitosis Detection in Breast Cancer Histology Images
IEEE Transactions on Medical Imaging (TMI), Special Issue on Deep Learning, vol. 35, no. 5, pp. 1313 - 1321, 2016.
The first two authors contribute equally to this paper.
(bib)
A. Vahadane, T. Peng, A. Sethi, S. Albarqouni, L. Wang, M. Baust, K. Steiger, A. M. Schlitter, I. Esposito, N. Navab
Structure-Preserving Color Normalization and Sparse Stain Separation for Histological Images
IEEE Transactions on Medical Imaging (TMI), vol. 35, no. 8, pp. 1962 - 1971, 2016. (bib)
2015
S. Albarqouni, M. Baust, S. Conjeti, A. Al-Amoudi, N. Navab
Multi-scale Graph-based Guided Filter for De-noising Cryo-Electron Tomographic Data
Proceedings of the British Machine Vision Conference (BMVC), pages 17.1-17.10. BMVA Press, September 2015 (bib)
A. Vahadane, T. Peng, S. Albarqouni, M. Baust, K. Steiger, A. M. Schlitter, A. Sethi, I. Esposito, N. Navab
Structure-Preserved Color Normalization for Histological Images
International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, New York, USA, April 2015 (bib)
2014
S. Albarqouni, T. Lasser, W. Alkhaldi, A. Al-Amoudi, N. Navab
Gradient Projection for Regularized Cryo-Electron Tomographic Reconstruction
Proceedings of MICCAI Workshop on Computational Methods for Molecular Imaging, Boston, USA, September 2014. (bib)

Collaboration

  • Rohde & Schwarz GmbH? & Co. KG.
  • Siemens AG, Corporate Technology Research & Technology Center
  • Augenklinik der Universität München
  • Siemens Healthineers

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UsersForm
Title: Dr.
Circumference of your head (in cm):  
Firstname: Shadi
Middlename:  
Lastname: Albarqouni
Picture: 0d6e8f1.jpg
Birthday: 07.08.1984
Nationality: Palestine
Languages: English, German, Arab
Groups: Medical Imaging, Machine Learning for Medical Applications, Microscopic Image Analysis, Crowdsourcing
Expertise: Medical Imaging
Position: Scientific Staff
Status: Active
Emailbefore: Shadi.Albarqouni
Emailafter: tum.de
Room: MI 03.13.056
Telephone: +49 89 289 19405
Alumniactivity:  
Defensedate: 22 November 2017
Thesistitle: Machine Learning for Biomedical Applications: From Crowdsourcing to Deep Learning
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