VAVlabPUBLICATIONS & PATENTS
- Semantics, Ontologies, Similarity
Assessment,
Search & Retrieval
- Image Processing and Analysis for CT Colonography
- Multi-Dimensional Image Processing & Simulation
- Brain Research: dMRI, fMRI Processing and Analysis
- ECG Processing and Analysis
- Software Development and Human-Computer Interaction
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Semantics, Ontologies,
Similarity
Assessment, Search & Retrieval
Journals:
Computer-Aided Medical Image Annotation: Preliminary Results with Liver Lesions in CT
Marvasti, N.B., Yörük, E., Acar B.
IEEE Journal of Biomedical & Health Informatics, Vol. 22/5, pp. 1561-1570 (2018)
Towards an Ontology-Driven Clinical Experience Sharing Ecosystem: Demonstration with Liver Cases
Roldán-García M. del Mar, Uskudarli A., Marvasti N.B. Acar B., Aldana-Montes J.F.
Expert Systems with Applications, Vol. 101, pp. 176-195 (2018)
A Fully Automatic End-to-End Method for Content-Based Image Retrieval of CT Scans with Similar Liver Lesion Annotations
Spanier A.B., Caplan N., Sosna J., Acar B., Joskowicz L.
Int. J. Computer Assisted Radiology and Surgery, Vol. 13/1, pp. 165–174 (2018)
Semantic
Description of Liver CT Images: An Ontological Approach
Kokciyan N., Turkay R., Uskudarli S., Yolum P., Bakır B., Acar B.
IEEE Journal of Biomedical & Health Informatics, July
2014, Vol.18/4, pp 1363-1369
Future PACS for
decision support: content-based case retrieval
Akgul C.B. , Acar B.
International Hospital, Vol 38, March/April 2012
Content Based Image Retrieval in Radiology:Current Status and Future
Directions
Akgul C.B., Rubin D.L., Napel S., Beaulieu C.F., Greenspan H.,
Acar B.
Journal of Digital Imaging, 2011, Vol. 24/2, pp 208-222.
Conferences:
General Overview
of ImageCLEF at the CLEF 2015 Labs
Villegas M., Muller H., ..., Acar B, Uskudarli S,
Marvasti NB, Aldana JF, Garcia M
In Experimental IR Meets Multilinguality, Multimodality and Interaction,
Lecture Notes in Computer Science, Volume 9283, pp. 444-461 URL
ImageCLEF Liver
CT Image Annotation Task 2014
Marvasti N.B., Kokciyan N., Turkay R., Yazici A., Yolum P., Uskudarli
S., Acar B.
In CLEF 2104 Working Notes, CEUR Workshop Proceedings, vol. 1180, pp.
329-340
URL
Clinical
Experience Sharing by Similar Case Retrieval
Marvasti N.B., Akgul C.B., Acar B., Kokciyan N., Uskudarli S., Yolum
P., Turkey R., Bakir B.
In Proceedings of 1st ACM MM Workshop on Multimedia Indexing and
Information Retrieval
for Healthcare (ACM MM'13)
pdf
ONLIRA - A
Semantic Knowledge Representation of Liver CT Images
Kokciyan N., Turkay R., MD, Uskudarli S., Yolum P., Acar B., PhD;
Bakir B., MD
In Proceedings of RSNA 2013, Chicago, IL, USA (Supplement of Radiology)
CARERA –
Karaciğer Vakalarında Klinik Deneyim Paylaşım Platformu
Kokciyan N.,Turkay R., Uskudarli S., Yolum P., Bakir B., Acar B.
In Proceedings of Turkiye Radyoloji Kongresi (TURKRAD) 2013, Antalya,
Turkey
pdf
Theses:
Content Based Medical Image Retrieval
Neda B. Marvasti
Bogazici University, Electrical and Electronics Engineering, Turkey
November 2017. Ask
for a reprint
Image Processing and Analysis for
CT Colonography
Journals:
Polyp Enhancing
Level Set Evolution of Colon Wall: Method and Pilot
Study
Konukoglu E., Acar B., Paik D.S.,Beaulieu CF,Rosenberg J., Napel S.
IEEE Transactions on Medical Imaging, December 2007, Vol. 26-12,
pp.1649-1656.
HDF: Heat Diffusion Fields for Polyp Detection in CT Colonography
Konukoglu E., Acar B.
Signal Processing (Elsevier), October 2007, Vol. 87, Issue: 10, pp.
2407-2416.
Registration of Central Paths and Colonic Polyps between Supine and
Prone Scans in CT Colonography
Li P., Napel S., Acar B., Paik D.S., Jeffrey, Jr. R.B., Beaulieu C.F.
Medical Physics, October 2004, Vol. 31, Issue: 10, pp. 2912-2923
Surface Normal
Overlap: A Computer-Aided Detection Algorithm With
Application to Colonic Polyps and Lung Nodules in Helical CT
Paik D.S., Beaulieu C.F., Rubin G.D., Acar B., Jeffrey Jr R.B., Yee J.,
Dey J., Napel S.
IEEE Transactions on Medical Imaging, June 2004, Vol. 23-6, pp. 661-675
Edge Displacement Field Based-Classification for Improved Detection of
Polyps in CT Colonography
Acar B., Beaulieu C.F., Gokturk S.B., Tomasi C., Paik D.S., Jeffrey,
Jr. R,B,, Yee J., Napel S.
IEEE Transactions on Medical Imaging, December 2002, Vol. 21-12, pp.
1461-1467
A statistical 3D pattern processing method for computer aided detection
of polyps in CT colonography
Gokturk S.B., Tomasi C., Acar B., Beaulieu C.F., Paik D.S., Jeffrey
R.B., Jr., Yee J., Napel S.
IEEE Transactions on Medical Imaging, December 2001, Vol. 20-12, pp.
1251-1260
Conferences:
Assessment of MRF
Based Joint Scale Selection and Segmentation for 3D Liver Vessel
Segmentation
N.B. Marvasti, B. Acar
Proc. Sinyal Isleme ve Uygulamaları Kurultayı (SIU), Kıbrıs, 2013
pdf
Detecting Tubular
Structures Via Direct Vector Field Singularity Characterization
A.D. Cabuk, E. Alpay, E., B. Acar
Proc. 32nd Annual International Conference of the IEEE Engineering in
Medicine and Biology Society (EMBC2010), Buenos Aires, Argentina, IEEE,
2010. pdf
Polyp Enhancement Scheme for Improved Detection of Colonic Polyps in CT
Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology)
pdf
Registration of Supine and Prone CT Colonography Data Using Dynamic
Time Warping: Method and Evaluation
Balci S.K., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology)
pdf
Registration of Supine and Prone CT Colonography Data: Method and
Evaluation
Acar B., Napel S., Paik D.S., Li P., Yee J., Beaulieu C.F., Jeffrey Jr.
R.B.
Radiology, November 2001, Vol. 221(P), pp. 332 (87th Annual Meeting of
Radiological Society of North America (RSNA 2001), Chicago, USA, 25-30
November 2001). pdf
Medial axis registration of supine and prone CT colonography data
Acar B., Napel S., Paik D.S., Li P., Yee J., Jeffrey Jr. R.B., Beaulieu
C.F.
In Proceedings of EMBC 2001, Istanbul, Turkey, 25-28 October 2001. pdf
Polyp Enhancement
Scheme for Improved Detection of Colonic Polyps in CT
Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology)
pdf
Heat Diffusion Based Detection Of Colonic Polyps In CT Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of EUSIPCO 2005, European Signal Processing Conference,
Antalya, Turkey (3rd place in
EUSIPCO2005 student paper contest)pdf
Computer Aided Detection Of Polyps In Virtual Colonoscopy Using 3D Heat
Diffusion Fields
Konukoglu E., Acar B., Paik D., Beaulieu C.F., Napel S.
In Proceedings of.The 5th Int. Symposium on Virtual
Colonoscopy, Boston, MA, USA, 2004 pdf
3D Differential Descriptors for Computer Aided Diagnosis of Colonic
Polyps in CTC
Acar B., Beaulieu C.F., Paik D.S., Yee J., Jeffrey, Jr. R.B., Napel S.
Radiology, December 2002, Vol. 225(P), pp. 405 (88th Annual Meeting of
Radiological Society of North America (RSNA 2002), Chicago, USA, 1-6
December 2002). pdf
Using Optical Flow Fields For Polyp Detection In Virtual Colonoscopy
Acar B., Napel S., Paik D., Gokturk S.B., Tomasi C., Beaulieu C.F.
In Medical Image Computing and Computer-Assisted Intervention – MICCAI
2001 Utrecht, The Netherlands, 14-17 October 2001, W.J. Niessen and
M.A. Viergever ed., LNCS 2208, Springer-Verlag, pp. 637-644. pdf
A Learning Method For Automated Polyp Detection
Gokturk S.B., Tomasi C., Acar B., Paik D., Beaulieu C.F., Napel S.
In Medical Image Computing and Computer-Assisted Intervention – MICCAI
2001 Utrecht, The Netherlands, 14-17 October 2001, W.J. Niessen and
M.A. Viergever ed., LNCS 2208, Springer-Verlag, pp. 85-93. pdf
Assessment of an optical flow field-based polyp detector for CT
colonography
Acar B., Beaulieu C.F., Paik D.S., Gokturk S.B., Tomasi C., Yee J.,
Napel S.
In Proceedings of 23rd Annual International Conference of the IEEE
Engineering in Medicine and Biology Society (EMBC 2001), Istanbul,
Turkey, 25-28 October 2001. pdf
Theses:
Liver Segmentation in 3D CT Data
Serkan Cimen
Bogazici University, Electrical and Electronics Engineering, Turkey
September 2011. Ask
for a reprint
PELS: Polyp
Enhancing Level-Sets for CT Colonography
Ender Konukoglu
Bogazici University, Dept. of Electrical & Electronics Engineering,
Turkey
June 2005 Ask
for a reprint
Patents:
Method for matching and registering medical image data.
Acar B., Beaulieu C.F., Paik D.S., Napel S.A., Jeffrey R.B.Jr.
US Patent Office: US7224827 29/05/2007
Method for detecting and classifying a structure of interest in medical
images.
Acar B., Beaulieu C.F., Gokturk S.B., Tomasi C., Paik D.S., Jeffrey
R.B.Jr., Napel S.A.
US Patent Office: US7272251 18/09/2007
Three-dimensional pattern recognition method to detect shapes in
medical images.
Gokturk S.B., Tomasi C., Acar B., Beaulieu C.F., Napel S.A., Paik D.S.
US Patent Office: US7346209 18/03/2008
Heat diffusion based detection of structures of interest in medical
images.
Acar B., Konukoglu E., Beaulieu C.F., Napel S.A., Paik D.S.
US Patent Office: US7729739 10/06/2010
Multi-Dimensional Image
Processing & Simulation
Journals:
Multi-ray Medical Ultrasound Simulation Without Explicit Speckle Modeling
Tuzer M., Yazici A., Turkay R., Boyman M., Acar B.
Int. Journal of Computer Assisted Radiology and Surgery, 2018, vol. 13(7), pp. 1009-1017
Magnetic
resonance and diffusion tensor imaging analyses indicate heterogeneous
strains along human medial gastrocnemius fascicles caused by submaximal
plantar-flexion activity
Karakuzu A., Pamuk U., Ozturk C., Acar B.and Yucesoy C.A.
Journal of Biomechanics, May 2017, vol. 57, pp. 69-78
Combined Magnetic
Resonance And Diffusion Tensor Imaging Analyses
Provide A Powerful Tool For In Vivo Assessment Of Deformation Along
Human Muscle Fibers
Pamuk U., Karakuzu A., Ozturk C., Acar B.and Yucesoy C.A., ,
Journal of the Mechanical Behavior of Biomedical
Materials, October 2016, vol. 63, pp. 207-219
Conferences:
Combined
Diffusion Tensor and Magnetic Resonance Imaging for in vivo Assessment
of Human Muscle Function
Karakuzu A., Pamuk U., Ozturk C., Acar B., Yucesoy C.A.
In Congress of the European College of Sport Science, 2016
Using
Advanced
MRI Techniques for Estimating Strain Distributions Along Muscle Fibers
During Isometric Plantar-Flexion Activity of Human Medial
Gastrocnemius, In Vivo
Karakuzu A., Pamuk U., Acar B., Ozturk C., Yucesoy C.A.
Int. Society of Biomechanics Congress, ISB 2015, Glasgow, UK
MRI and DTI
Analyses Combined Provide A Powerful Tool for Quantifying
Deformation Along Human Muscle Fibers In Vivo
Pamuk U., Karakuzu A., Acar B., Ozturk C., Yucesoy C.A.
Int. Society of Biomechanics Congress, ISB 2015, Glasgow, UK
A Multiray Approach To Phased Array US Simulation From CT Images
M. Tuzer, A. Yazici, B. Acar, M. Boyman
Proc. of Computer
Assisted Radiology and Surgery (CARS 2015), Barcelona, Spain, 2015
MRI analyses
Indicate Non-uniform Human Muscle Tissue Deformations and
Confirm
Theoretically Anticipated Sarcomere Length Heterogeneity, In Vivo
U Pamuk, A Karakuzu, P Akyazi, B Acar, C Ozturk, CA Yucesoy
18th National Biomedical Engineering Meeting (BIYOMUT), 2014, Istanbul
Theses:
Ultrasound Simulations Using Computed Tomography Images as Priors
Mert Tuzer
Bogazici University, Department of Physics, Turkey
July 2015. Ask
for a reprint
Skeletal Muscle
Deformation Analysis Using Diffusion Tensor Magnetic Resonance Imaging
Pinar Akyazi
Bogazici University, Electrical & Electronics Eng. Dept., Turkey
August 2013 Ask
for a reprint
Brain Research: dMRI, fMRI
Processing and Analysis
Journals:
SMT: A Reliability Based Interactive DTI Tractography Algorithm
Yoldemir B., Acar B., Firat Z., Kilickesmez O.
IEEE Transactions on Medical Imaging, October 2012, Vol. 31-10, pp.
1929-1940.
Characterizing Non-Gaussian Diffusion by Using Generalized Diffusion
Tensors
Liu C., Bammer R., Acar B., Moseley M.E.
Magnetic Resonance in Medicine, May 2004, Vol. 51, pp. 924-937.
Analysis and generalized correction of the effect of spatial gradient
field distortions in diffusion-weighted imaging
Bammer R., Markl M., Barnett A., Acar B., Alley M.T., Pelc N.J., Glover
G.H., Moseley M.E.
Magnetic Resonance in Medicine, September 2003, Vol. 50-3, pp. 560-569.
In vivo MR Tractography Using Diffusion Imaging
Bammer R., Acar B., Moseley M.E.
European J. of Radiology, 2003, Vol. 45-3, pp.223-234
Conferences:
fMRI Guided Personalization of Cortical Parcellation Maps
Onay M.S., Kucukaslan U., Acar B.
RSNA 2018, Chicago, USA pdf
Multi-modal Brain Tensor Factorization: Preliminary Results with AD Patients
Durusoy G., Karaaslanlı A., Yüksel Dal D., Yıldırım Z., Acar B.
In: Wu G., Rekik I., Schirmer M., Chung A., Munsell B. (eds)
Connectomics in NeuroImaging. CNI 2018. Lecture Notes in Computer
Science, vol 11083. Springer, Cham link / pdf
Differential
Resting State Connectivity and Its Relationship with Cognitive
Performance among Participants with Subjective Cognitive Impairment
(SCI), Mild Cognitive Impairment (MCI), and Early Stage Alzheimer’s
Disease (AD)
Yildirim
E., Buyukiscan E.S., Kurt E., Yildiz C.U., Tatlidede A.D., Bilgiç B.,
Hanagasi H., Bayram A., Acar B., Demiralp T, Gurvit H.I.
AAIC 2017, London, England
bootSMT:Bootstrap
Split/Merge Fiber Tractography for DT-MRI Data
Yoldemir A.B., Acar B.
RSNA 2011, Chicago, USA
A Pointwise Correspondence Based DT-MRI Fiber Similarity Measure
Berkiten S., Acar B.
Proc. 32nd Annual International Conference of the IEEE Engineering in
Medicine and Biology Society (EMBC2010), Buenos Aires, Argentina, IEEE,
2010. pdf
SMT: Split & Merge Fiber Tractography for DT-MRI
Bozkaya U., Acar B.
Lecture Notes in Computer Science, Vol. 4792, pp.153-160 ; Springer,
2007 (MICCAI 2007, Brisbane, Australia) pdf
DT-MRI Connectivity And/Or Tractography?: Two New Algorithms
Acar B.
EU FP7 SIMILAR NoE, WP10, Workshop on Tensor Toolboxes, 15-17 November,
2006, Las Palmas, Gran Canaria, Spain.
pdf
A Physical Model for MR-DTI Based Connectivity Map Computation
Yoruk E., Acar B., Bammer R.
Lecture Notes in Computer Science, Vol. 3749 / Part 1, pp.
213-220, Springer, 2005 (MICCAI 2005, Palm Springs, CA) pdf
Structure Preserving Regularization Of DT-MRI Vector Fields by
Nonlinear Anisotropic Diffusion Filtering
Yoruk E., Acar B.
Proceedings of EUSIPCO 2005, European Signal Processing Conference,
Antalya, Turkey pdf
SNR Dependence of DTI Fiber Tracking Protocols
Aksoy M., Acar B., Bammer R.
ISMRM Workshop on Methods for Quantitative Diffusion MRI of Human
Brain, 13-16 March 2005, Lake Louise, Alberta, Canada pdf
Comparative Assessment Of DT-MRI Fiber Tractography Algorithms
Acar B., Bammer R., Moseley M.E.
Proceedings of ISMRM 2003, pp. 2164, July 2003, Toronto, Canada pdf
Generalized Diffusion Tensor Imaging (GDTI) Using Higher Order Tensor
(HOT) Statistics
Liu C., Bammer R., Acar B., Moseley M.E.
Proceedings of ISMRM 2003, pp. 242,July 2003, Toronto, Canada pdf
Book Chapters/Sections:
DT-MRI Connectivity and/or Tractography?: Two New Algorithms
Acar, B., Yoruk, E.
Tensors in Image Processing and Computer Vision, Aja-Fernández, S.; de
Luis GarcÃa, R.; Tao, D.; Li, X. (Eds.), Series: Advances in Pattern
Recognition, ISBN: 978-1-84882-298-6, Springer, 2009 Ask
for a reprint
Similar Tensor Arrays: A Framework for Storage of Tensor Array Data
Brun, A., Martin-Fernandez, M., Acar, B., Munoz-Moreno, E., Cammoun,
L., Sigfridsson, A., Sosa-Cabrera, D., Svensson, B., Herberthson, M.,
Knutsson, H.
Tensors in Image Processing and Computer Vision, Aja-Fernández, S.; de
Luis GarcÃa, R.; Tao, D.; Li, X. (Eds.), Series: Advances in Pattern
Recognition, ISBN: 978-1-84882-298-6, Springer, 2009 Ask
for a reprint
Theses:
Seed-based and Data-driven Analyses of Default Mode Network Connectivity Measures in Dementia
Basak Kilic
Bogazici University, Systems and Control Eng. Program, Turkey
January 2017 Ask
for a reprint
Assessing DT-MRI
Tractography Results via Sampling The Fiber Tract Space
A. Burak Yoldemir
Bogazici University, Electrical & Electronics Eng. Dept., Turkey
June 2011 Ask
for a reprint
Diffusion Tensor Field Visualization
Sila Girgin
Bogazici University, Computer Engineering, Turkey
January 2008. Ask
for a reprint
SMT: Split/Merge Fiber Tractography
Ugur Bozkaya
Bogazici University, Institute of Biomedical Engineering, Turkey
May 2006 Ask
for a reprint
Patents:
Characterization and Correction of Spatial Gradient Field
Nonuniformities.
Bammer R., Markl M., Acar B., Pelc N., Moseley M.E.
US Patent Office: US6969991 17/06/2004 (Licensed by GE)
Journals:
QT dispersion does not represent electrocardiographic interlead
heterogeneity of ventricular repolarization
Malik, M., Acar, B., Gang, Y., Yap, Y.G., Hnatkova, K., Camm, A.J.
Journal Of Cardiovascular Electrophysiology, 11(8), 835-843 (2000)
Analysis of 12-lead T-wave morphology for risk stratification after
myocardial infarction
Zabel, M., Acar, B., Klingenheben, T., Franz, M.R., Hohnloser, S.H.,
Malik, M.
Circulation, 102(11), 1252-1257 (2000)
Automatic Ectopic Beat Elimination In Short-term Heart Rate Variability
Measurement
Acar, B., Savelieva, I., Hemingway H., Malik, M.
Computer Methods And Programs In Biomedicine, 63(2), 123-131 (2000)
SVD Based Online Exercise ECG Signal Orthogonalization
Acar, B., Köymen, H.
IEEE Transactions On Biomedical Engineering, 46(3), 311-321 (1999)
Spatial, Temporal And Wavefront Direction Characteristics Of 12-Lead T
Wave Morphology
Acar, B., Yi, G., Hnatkova K., Malik, M.
Medical & Biological Engineering & Computing, 37(5), 574-584
(1999)
New approaches to T-wave analysis from surface ECG
Acar, B.
Cardiac ElectroPhysiology Review (CEPR), 3(4), 319-323 (1999), CEPR has
been merged into Journal of Interventional Cardiac
Electrophysiology
Patents:
Methods of characterizing ventricular operations and applications
thereof
Malik, M., Acar B., Batchvarov V.N.. US Patent Office: US6438409
20/08/2002
Methods of characterizing ventricular operations and applications
thereof
Acar B., Batchvarov V.N., Malik, M.,. European Patent Office: EP1038498
27/09/2000
Software Development and Human-Computer Interaction
Journals:
Masterpiece: Physical Interaction and 3D Content-Based Search in VR
Applications
Moustakas K., Tzovaras D., Strintzis M. G., Carbini S., Bernier O.,
Viallet J.E., Raidt S., Mancas M., Dimiccoli M., Yagci E., Balci S.,
Leon E.I.
IEEE Multimedia Magazine, Vol 13/3, pp. 92-100, June 2006
Conferences:
DTI Application with Haptic Interfaces
M. Aksoy, N. Avcu, S. Merino-Caviedes, D. Diktas, M.A.
Martin-Fernandez, S. Girgin, I. Marras, E. Munoz-Moreno, E. Tekeli, B.
Acar, R. Bammer, M. Martin-Fernandez, A.V. Sahiner, S. Uskudarli
Proceedings of Enterface 2007 Workshop, EU 6th Framework Programme
SIMILAR NoE, Istanbul, Turkey, July-August 2007 pdf
A Stereo Tracking System For Arbitrary Slicing Of Volumetric
Radiological Data
Yagci E., Acar B.
Sinyal Isleme ve Uygulamalari Kurultayi, SIU 2007, Eskisehir, Turkey,
June 2007 pdf
VAVframe: A New Concept in Platform Design
Durusut E., Bozkaya U., Yagci E., Acar B.
EUROCON 2005, Serbia & Montenegro, Belgrade, November 22-24, 2005 pdf
Theses:
3D Stylus: A Human Computer Interface For 3D Environment
Enver Yagci
Bogazici University, System & Control Engineering, Turkey
June 2007. Ask
for a reprint
VAVframe: Volumetric Analysis and Visualization Framework
Erhan Durusut
Bogazici University, Dept. of Computer Engineering, Turkey
April 2005. Ask
for a reprint