Biomedical Signal and Image Computing Laboratory

Highlights

2014-04

We are looking for two excellent Post Doctoral Fellows and two MASc students to join our team. The ideal candidate will have excellent software development skills, is a team player and is interested in collaborative research focused on ultrasound image processing spanning both theory and clinical applications.

Links: More information and application instructions

2013-09

We are pleased to announce TurtleSeg 1.3, the latest release of our new interactive 3D image segmentation software.

Links: TurtleSeg website

2014-09

Our BiSICL paper on Auto Localization and Segmentation of Occluded Vessels in Robot-Assisted Partial Nephrectomy has been awarded Best Paper Award at the 2014 International Conference on Medical Image Computing and Computer Assisted Interventions in Boston, USA. Congratulations to member Alborz Amir-Khalili for his Young Scientist Award.

Video: YouTube, Paper: Auto Localization of Vessels from Endoscope

2013-06

Our TurtleSeg software was showcased in the Brain Research Centre newsletter.

Links: Article

2012-12

Our work on TurtleSeg has won the WAGS Innovation in Technology Award. TurtleSeg is an uncertainty-guided 3D medical image segmentation software that features a unique "Active Learning" capability. Our Spoltlight feature intelligently alerts the software user to regions within the 3D image that require interactive input resulting in huge savings in segmentation times at excellent accuracy and robustness levels.

Links: TurtleSeg website

News

2017-04

BiSICL members Prashant Pandey and Olivia Paserin will be presenting their work at CAOS 2017 in Aachen, Germany.

2017-03

Niamul Quader's work on "Automatic Evaluation of Scan Adequacy and Dysplasia Metrics in 2-D Ultrasound Images of the Neonatal Hip" has been accepted to the journal of Ultrasound in Medicine and Biology.

2016-09

BiSICL welcomes three new students Colleen Ogilvie, Prashant Pandey, and Olivia Paserin to the lab.

2016-07

BiSICL members Mohammad Arafat Hussain, Niamul Quader and Chendi Wang will be presenting their work at MICCAI 2016 in Athens, Greece.

Papers: Segmentation-Free Kidney Volume Estimation, Automatic DDH Characterization, Brain Subnetwork Extraction

2016-04

Congratulations to BiSICL member, Negar Mohagheh-Harandi, who has successfully defended her PhD thesis titled " 3D Subject-Specific Biomechanical Modeling and Simulation of the Oropharynx with Application to Speech Production".

2016-02

Congratulations to BiSICL member, Ahmet Burak Yoldemir, who has successfully defended his PhD thesis titled "Multimodal Fusion for Assessing Functional Segregation and Integration in the Human Brain".

2015-12

Congratulations to BiSICL member, Md Moshiur Rahman Farazi, who has successfully defended his MASc thesis titled "3D Biomechanical Oropharyngeal Model for Training and Diagnosis of Dysphagia".

2015-09

BiSICL member, Burak Yoldemir's work on "Stable Overlapping Replicator Dynamics for Brain Community Detection" has been accepted to appear in IEEE Transactions on Medical Imaging.

Papers: Stable Overlapping Replicator Dynamics for Brain Community Detection

2015-08

Our paper on Auto Localization and Segmentation of Occluded Vessels in Robot-Assisted Partial Nephrectomy has been selected as a Best Paper in the 2015 International Medical Informatics Association Yearbook of Medical Informatics.

Papers: Link

2015-06

BiSICL members Alborz Amir-Khalili and Chendi Wang will be presenting their work at MICCAI 2015 in Munich, Germany.

Papers: Multimodal Cortical Parcellation, Automatic Vessel Segmentation from Pulsatile Radial Distension

2015-05

BiSICL members Arafat Hussain and Niamul Quader will be presenting their work at CAOS 2015 in Vancouver, Canada.

2015-02

BiSICL members Mohammad Bajammal, Moshiur Farazi, Negar Harandi, Niamul Quader, Chendi Wang, and Burak Yoldemir will be presenting their work at ISBI 2015 in Brooklyn, USA.

Papers: Assesment of Dysplasia, Cortical Parcellation, Swallowing Simulation, Comparison of Brain Connectivity, Speech Modelling

2014-12

BiSICL member, Burak Yoldemir's work on "Stable Overlapping Replicator Dynamics for Subnetwork Identification" has been presented at the 2014 NIPS workshop on Networks: From Graphs to Rich Data.

2014-07

BiSICL members and collaborators Alborz Amir-Khalili, Arafat Hussain, Jeremy Kawahara, and Masoud Nosrati will be presenting their work at the 2014 International Conference on Medical Image Computing and Computer Assisted Interventions in Boston, USA.

Papers: Auto Localization of Vessels from Endoscope, Robust Bone Detection in Ultrasound, Detecting Kidney Cancer in Ultrasound,
Multi-Organ Segmentation from Endoscope

2014-07

BiSICL members Mohammad Bajammal, Niamul Quader, and Burak Yoldemir will be presenting their work at the 2014 International Conference on Medical Image Computing and Computer Assisted Interventions workshops in Boston, USA.

Papers: CDMRI 2014, CLIP 2014

2013-12

BiSICL member, Ivan Figueroa's work on "Biomedical Kidney Model for Predicting Tumor Displacement in the Presence of External Pressure" has been accepted to appear in IEEE International Symposium on Biomedical Imaging in April 2014.

Paper: Biomedical Kidney Model for Predicting Tumor Displacement in the Presence of External Pressure

2013-11

BiSICL member, Burak Yoldemir's work on "Effects of Tractography Approach on Consistency Between Anatomical and Functional Connectivity Estimates" has been accepted to appear in IEEE International Symposium on Biomedical Imaging in April 2014.

Paper: Effects of Tractography Approach on Consistency Between Anatomical and Functional Connectivity Estimates

2013-09

We are pleased to announce TurtleSeg 1.3, the latest release of our new interactive 3D image segmentation software.

Links: TurtleSeg website

2013-09

Our TurtleSeg software was featured in the Spring 2013/Summer 2013 issuer of UBC Ingenuity newsletter.

Links: Spring 2013/Summer 2013 Ingenuity

2013-09

BiSICL member Negar Mohaghegh received the best paper award for her work on "Minimally Interactive MRI Segmentation for Subject-Specific Modelling of the Human Tongue" at the 2013 MICCAI workshop on Bio-Imaging and Visualization for Patient-Customized Simulations.

Paper: Minimally Interactive MRI Segmentation for Subject-Specific Modelling of the Human Tongue

2013-09

BiSICL members Al Amir-Khalili, Negar Mohaghegh, and Burak Yoldemir will be presenting their work at the 2013 International Conference on Medical Image Computing and Computer Assisted Interventions in Nagoya, Japan.

Paper: MICCAI 2013, BIVPCS 2013, ABDI 2013, MIAR 2013

2013-06

BiSICL welcomes four new students Mohammad Bajammal, Niamul Quader, Arafat Hussain, and Ivan Figueroa to the lab.

2013-06

BiSICL member, Al Amir-Khalili's work on "Using Graphics Processing Units to Achieve Real-Time Bone Surface Extraction From Volumetric Medical Ultrasound Image Data Using Local Phase Features" has been presented at the Computer Assisted Orthopedic Surgery International Conference in June 2013.

Paper: Real-Time Extraction of Local Phase Features From Volumetric Medical Image Data

2013-05

BiSICL member, Burak Yoldemir's work on "Overlapping Replicator Dynamics for Functional Subnetwork Identification" has been accepted to appear in MICCAI in September 2013.

Paper: Overlapping Replicator Dynamics for Functional Subnetwork Identification

2013-03

BiSICL member, Burak Yoldemir's work on "Fiber Connectivity Integrated Brain Activation Detection" has been accepted to appear in the International Conference on Information Processing in Medical Imaging on July 2013.

Paper: Fiber Connectivity Integrated Brain Activation Detection

2013-03

BiSICL member, Al Amir-Khalili's work on "Real-Time Extraction of Local Phase Features From Volumetric Medical Image Data" has been accepted to appear in IEEE International Symposium on Biomedical Imaging: From Nano to Micro on April 2013.

Paper: Real-Time Extraction of Local Phase Features From Volumetric Medical Image Data

2012-10

BiSICL member, Anna Brounstein's work on "3D Ultrasound-CT Registration in Orthopaedic Trauma Using GMM Registration with Optimized Particle Simulation-Based Data Reduction" was presented at the 2012 International Conference on Medical Image Computing and Computer Assisted Intervention in Nice, France.

Paper: 3D Ultrasound-CT Registration in Orthopaedic Trauma Using GMM Registration

2012-10

BiSICL member, Sylvain Bernhardt's work on "Robust Dense Endoscopic Stereo Reconstruction for Minimally Invasive Surgery" was presented at the 2012 International Conference on Medical Image Computing and Computer Assisted Intervention in Nice, France.

Paper: Robust Dense Endoscopic Stereo Reconstruction for Minimally Invasive Surgery

2012-10

BiSICL member, Burak Yoldemir's work on "Deconfounding the Effects of Resting State Activity on Task Activation Detection in fMRI" was presented at the 2012 International Conference on Medical Image Computing and Computer Assisted Intervention in Nice, France.

Paper: Deconfounding the Effects of Resting State Activity on Task Activation Detection in fMRI

2012-08

BiSICL member, Al Amir-Khalili presented his poster at the 3rd North American Summer School on Image Guided Interventions, Surgical Robotics and Simulation in London, Ontario.

Poster: Stereo Reconstruction for Robotic Assisted Partial Nephrectomy

2012-05

BiSICL member, Krishna Nand Keshava Murthy's work on "Diffusion Tensor Image Processing Using Biquaternions" was presented at the 2012 International Symposium on Biomedical Imaging in Barcelona, Spain.

Paper: DTI Processing Using Biquaternions

2012-04

Congratulations to BiSICL member, Krishna Nand Keshava Murthy, who has successfully defended his M.A.Sc. thesis titled "Novel Representation and Low level Computer Vision Techniques for Manifold Valued Diffusion Tensor MRI".

2012-02

Congratulations to BiSICL member, Anna Brounstein, who has successfully defended her M.A.Sc. thesis titled "Towards real-time registration of ultrasound and CT in computer aided orthopaedic surgery applications".

2011-09

Congratulations to BiSICL member, Bernard Ng, who has successfully defended his Ph.D. thesis titled "Prior-informed Multivariate Models for Functional Magnetic Resonance Imaging".

2011-09

BiSICL members, Bernard Ng, Krishna Nand K and Anna Brounstein presented their research at the 2011 International Conference on Medical Image Computing and Computer Assisted Intervention in Toronto, Canada.

Papers: Connectivity Informed fMRI, Structures in DTI, US to CT Bone Registration

2011-07

BiSICL member, Bernard Ng, presented his research at the 2011 Information Processing in Medical Imaging conference in Irsee, Germany.

Paper: fMRI Generalized Sparse Regulation

2011-06

Dr. Rafeef Abugharbieh was awarded a research grant from the Qatar National Research Fund (QNRF). In collaboration with a team of collaborators from Canada, the US and Qatar, the grant will fund a major new project on real-time computer-assisted navigation in minimally-invasive robotic surgery.

2011-06

BiSICL member, Bernard Ng, presented his research at the 17th annual meeting of the organization on Human Brain Mapping (HBM 2011), Quebec, Canada.

Paper: fMRI Activation Spatial Modulation

2011-06

BiSICL member, Bernard Ng presented his research at the 24th IEEE conference on Computer vision and Pattern recognition (CVPR2011) Colorado Springs, USA.

Paper: fMRI Generalized Group Sparse Classifier

2011-06

BiSICL member, Ilker Hacihaliloglu's application to MITACS for a strategic project under the NCE-MITACS postdoctoral research projects program was selected for funding for 2 years.

2011-06

BiSICL member, Ilker Hacihaliloglu presented his research at the 11th annual meeting of the International Society for Computer Assisted Orthopaedic surgery (CAOS 2011), London, UK.

Paper: 2D optimized phase features

2011-05

BiSICL member, Bernard Ng presented his research at the 2011 IEEE International workshop on pattern recognition in NeuroImaging, Seoul, Korea.

Paper: fMRI Generalized Sparse Classifier

2011-03

Dr. Rafeef Abugharbieh was awarded an Early Career Scholar Award by the Peter Wall Institute for Advanced Studies.

2010-09

BiSICL member, Bernard Ng presented his research at the 2010 International Conference on Medical Image Computing and Computer Assisted Intervention in Beijing, China.

Papers: fMRI Group Random Walker, fMRI Sparse Classifier

2010-07

BiSICL member, Bernard Ng presented his research at the 23rd IEEE conference on Computer vision and Pattern recognition (CVPR2010) San Francisco, USA.

Paper: Group MRF for fMRI

2010-07

BiSICL member, Ilker Hacihaliloglu presented his research at the 10th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery (CAOS 2010) Paris, France.

Paper: Ultrasound Volume Stitching

2010-04

Congratulations to BiSICL member, Ilker Hacihaliloglu, who has successfully defended his Ph.D. thesis titled "Towards a novel minimally invasive 3D ultrasound imaging based computer assisted orthopaedic surgery system for bone fracture reduction".

2010-04

Congratulations to BiSICL member, Albert Huang, who has successfully defended his Ph.D. thesis titled "Novel statistical and geometric models for automated brain tissue labeling in magnetic resonance images".

2010-04

Dr. Rafeef Abugharbieh is awarded a grant from the Martha Piper Research Fund, titled "Unveiling the Mysteries of Brain Networks".

2010-03

Congratulations to BiSICL member, Victor Sanchez, who has successfully defended his Ph.D. thesis titled "Advances in medical image compression: Novel schemes for highly efficient storage, transmission and on demand scalable access for 3D and 4D medical imaging data".

2010-02

BiSICL member, Rupin Dalvi presented his research at the 2010 SPIE Medical Imaging conference held in San Diego, California.

Paper: Ultrasound Volume Stitching

2010-02

Dr. Rafeef Abugharbieh is awarded a Killam Faculty Research Fellowship.

2009-12

Newly released code for vessel segmentation: Live-Vessel; Interactive Vascular Image Segmentation with Simultaneous Extraction of Optimal Medial and Boundary Paths.

Links: Code

2009-12

BiSICL members, Josna Rao and Ilker Hacihaliloglu presented their research at the 2009 International symposium on Visual Computing in Las Vegas, US.

Papers: Adaptive Energy Parameterization, Automatic Phase bone Localization

2009-12

BiSICL member, Victor Sanchez presented his research at the 2009 IEEE International Conference on Image Processing in Cairo, Egypt.

Paper: 3D Scalable Lossless Compression

2009-09

Congratulations to BiSICL member, Rupin Dalvi, who has received his M.A.Sc. degree. His Thesis was titled: "Novel Approaches for Multi-Modal Imaging and Fusion in Orthopaedic Research for Analysis of Bone and Joint Anatomy and Motion".

2009-09

BiSICL member, Albert Huang and Bernard Ng, presented his research at the 2009 International Conference on Medical Image Computing and Computer Assisted Intervention in London, UK.

Papers: frbHMM, Segment fMRI ANSPCA, Random Walker fMRI

2009-09

BiSICL welcomes 2 new members to our lab for the upcoming fall 2009 semester - Anna Brounstein (Master) and Krishna Nand Keshava Murthy (Master).

2009-07

BiSICL member, Ilker Hacihaliloglu, presented his research at the 2009 International Society for Computer Assisted Orthopaedic Surgery conference in Boston, Massachusetts.

Paper: Surface Localization Accuracy in 3DUS using CT

2009-07

BiSICL member, Bernard Ng, presented his research at the 2009 Information Processing in Medical Imaging conference in Williamsburg, Virginia.

Paper: Discovering Sparse Functional Brain Networks

2009-07

BiSICL member, Bernard Ng, presented his research at the 2009 Information Processing in Medical Imaging conference in Williamsburg, Virginia.

Paper: Discovering Sparse Functional Brain Networks

2009-02

BiSICL member, Bernard Ng, presented his research at the 2009 SPIE Medical Imaging conference in Orlando, Florida.

Paper: Effects of Warping on Spatial fMRI Anaysis

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