Dr Spyridon Bakas
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Educational Qualifications
- Ph.D. in Medical Image Computing & Analysis - Kingston University (London, UK)
- M.Sc. in Vision, Imaging & Virtual Environments - University College London (UK)
- B.Sc. (Hons) in Computer Science - Kingston University (London, UK)
Research Summary
My research interest focusses on the development and application of computational algorithms in oncological imaging, with the intention of improving the assessment, quantification and diagnosis of cancer in the current clinical practice. Eagerly embracing the concept of personalized/precision medicine, I am also involved in radiogenomic research where correlations between quantitative imaging features and genomic information lead to highly accurate imaging biomarkers, which can enable treatment selection models customized on an individual patient basis.Publications
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Jared M. Pisapia,
Martin Rozycki,
Hamed Akbari,
Spyridon Bakas,
Jayesh P. Thawani,
Julie S. Moldenhauer,
Phillip B. Storm,
Deborah M. Zarnow,
Christos Davatzikos,
Gregory G. Heuer
"Correlations of Atrial Diameter and Fronto-Occipital Horn Ratio with Ventricle Size in Fetal Ventriculomegaly",
Journal of Neurosurgery: Pediatrics,
1-7, 2016. DOI: 10.3171/2016.9.PEDS16210
(View Preprint) (Publisher's version) -
Spyridon Bakas,
Katerina Chatzimichail,
Gordon Hunter,
Bastien Labbe,
Paul S. Sidhu,
Dimitrios Makris,
"Fast Semi-Automatic Segmentation of Focal Liver Lesions in Contrast-Enhanced Ultrasound, Based on a Probabilistic Model",
TCIV Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization,
2015. DOI: 10.1080/21681163.2015.1029642
(View Preprint) (Publisher's Version) -
Spyridon Bakas,
Katerina Chatzimichail,
Andreas Hoppe,
Vasileios Galariotis,
Gordon Hunter,
Dimitrios Makris,
"Histogram-based Motion Segmentation and Characterisation of Focal Liver Lesions in CEUS",
Annals of the BMVA (Special Issue),
2012.
(View)
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Ke Zeng,
Spyridon Bakas,
Aristeidis Sotiras,
Hamed Akbari,
Martin Rozycki,
Saima Rathore,
Sarthak Pati,
Christos Davatzikos,
"Segmentation of Gliomas in Pre-Operative and Post-Operative Multimodal Magnetic Resonance Imaging Volumes Based on a Hybrid Generative-Discriminative Framework",
In Proceedings of the Multimodal Brain Tumor Image Segmentation Challenge held in conjunction with MICCAI 2016 (MICCAI-BRATS 2016),
(Athens, Greece, 17-21 Oct 2016) -
Spyridon Bakas,
Ke Zeng,
Aristeidis Sotiras,
Saima Rathore,
Hamed Akbari,
Bilwaj Gaonkar,
Martin Rozycki,
Sarthak Pati,
Christos Davatzikos,
"GLISTRboost: Combining Multimodal MRI Segmentation, Registration, and Biophysical Tumor Growth Modeling with Gradient Boosting Machines for Glioma Segmentation",
Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries, Springer, LNCS,
9556:144-155, 2016. DOI: 10.1007/978-3-319-30858-6_13
(Technische Universität München (T.U.M.), Munich, Germany, 5-9 Oct 2015)
(Publisher's Version) -
Spyridon Bakas,
Ke Zeng,
Aristeidis Sotiras,
Saima Rathore,
Hamed Akbari,
Bilwaj Gaonkar,
Martin Rozycki,
Sarthak Pati,
Christos Davatzikos,
"Segmentation of Gliomas in Multimodal Magnetic Resonance Imaging Volumes Based on a Hybrid Generative-Discriminative Framework",
In Proceedings of the Multimodal Brain Tumor Image Segmentation Challenge held in conjunction with MICCAI 2015 (MICCAI-BRATS 2015),
(Technische Universität München (T.U.M.), Munich, Germany, 5-9 Oct 2015) -
Spyridon Bakas,
Katerina Chatzimichail,
Paul Sidhu,
Dimitrios Makris,
"Automatic Identification and Localisation of Potential Malignancies in Contrast-Enhanced Ultrasound Liver Scans Using Spatio-Temporal Features",
6th MICCAI Workshop on Abdominal Imaging - Computational and Clinical Applications, Springer, LNCS,
8676:13-22, 2014. DOI: 10.1007/978-3-319-13692-9_2
(Massachusetts Institute of Technology (M.I.T.), Boston, U.S.A., 14-18 Sep 2014)
(View) (Publisher's Version) -
Spyridon Bakas,
Bastien Labbe,
Gordon J.A. Hunter,
Paul Sidhu,
Katerina Chatzimichail,
Dimitrios Makris,
"Fast Segmentation of Focal Liver Lesions in Contrast-Enhanced Ultrasound Data",
In Proceedings of the 18th Annual Conference on Medical Image Understanding and Analysis (MIUA),
73-78, 2014. DOI: 10.13140/2.1.1769.0400
(London, U.K., 9-11 Jul 2014)
(View) (Publisher's Version) -
Spyridon Bakas,
Bastien Labbe,
Gordon J.A. Hunter,
"Making the Best Use of Fifty (or more) Shades of Gray: Intelligent Contrast Optimisation for Image Segmentation in False-Colour Video",
10th International Conference on Intelligent Environments - IE'14, IEEE,
218-221, 2014. DOI: 10.1109/IE.2014.41
(Shanghai, China, 30 Jun-4 Jul 2014)
(View) (Publisher's Version) -
Spyridon Bakas,
Paul Sidhu,
Maria Sellars,
Gordon J.A. Hunter,
Dimitrios Makris,
Katerina Chatzimichail,
"Non-Invasive Offline Characterisation of Contrast-Enhanced Ultrasound Evaluations of Focal Liver Lesions: Dynamic Assessment Using a New Tracking Method",
20th European Congress of Radiology, European Society of Radiology,
2014. DOI: 10.1594/ecr2014/C-1378
(Vienna, Austria, 6-10 Mar 2014)
(View) (Publisher's Version) -
Spyridon Bakas,
Gordon J.A. Hunter,
Celia Thiebaud,
Dimitrios Makris,
"Spot the Best Frame: Towards Intelligent Automated Selection of the Optimal Frame for Initialisation of Focal Liver Lesion Candidates in Contrast Enhanced Ultrasound Video Sequences",
9th International Conference on Intelligent Environments - IE'13, IEEE,
196-203, 2013. DOI: 10.1109/IE.2013.20
(Athens, Greece, 18-19 Jul 2013)
(View) (Publisher's version) -
Spyridon Bakas,
Katerina Chatzimichail,
Andreas Hoppe,
Vasileios Galariotis,
Gordon Hunter,
Dimitrios Makris,
"Focal Liver Lesion Tracking in CEUS for Characterisation based on Dynamic Behaviour",
Springer, Advances in Visual Computing, 8th International Symposium on Visual Computing (ISVC), LNCS,
7431:32-41, 2012. DOI: 10.1007/978-3-642-33179-4_4
(Crete, Greece, 16-18 July 2012)
(View) (Publisher's version) -
Spyridon Bakas,
Katerina Chatzimichail,
Awen Autret,
Andreas Hoppe,
Vasileios Galariotis,
Dimitrios Makris,
"Localisation and characterisation of focal liver lesions using contrast-enhanced ultrasonographic visual cues",
In Proceedings of the 15th Annual Conference on Medical Image Understanding and Analysis (MIUA),
2011. DOI: 10.13140/2.1.1474.1280
(London, U.K., 14 - 15 July 2011)
(View) (Publisher's version)
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Zev A. Binder,
Spyridon Bakas,
E. Paul Wileyto,
Hamed Akbari,
Saima Rathore,
Martin Rozycki,
Jennifer J.D. Morrissette,
Maria Martinez-Lage,
Nadia Dahmane,
Christos Davatzikos,
Donald M. O'Rourke,
"Extracellular EGFR289 activating mutations confer poorer survival and exhibit radiographic signature of enhanced motility in primary glioblastoma",
Neuro-Oncology, Vol.18, Suppl.6, VI105-VI106, 2016, DOI: 10.1093/neuonc/now212.441
(Presented in the 21st Annual Scientific Meeting of the Society for Neuro-Oncology (SNO), Scottsdale, Arizona, U.S.A., 17-20 November 2016) -
Saima Rathore,
Hamed Akbari,
Martin Rozycki,
Spyridon Bakas,
Christos Davatzikos,
"Imaging pattern analysis reveals three distinct phenotypic subtypes of GBM with different survival rates",
Neuro-Oncology, Vol.18, Suppl.6, VI128, 2016, DOI: 10.1093/neuonc/now212.532
(Presented in the 21st Annual Scientific Meeting of the Society for Neuro-Oncology (SNO), Scottsdale, Arizona, U.S.A., 17-20 November 2016) -
Jared M. Pisapia,
Martin Rozycki,
Hamed Akbari,
Hannah E. Goldstein,
Spyridon Bakas,
Julie S. Moldenhauer,
Phillip B. Storm,
Deborah M. Zarnow,
Richard C. E. Anderson,
Gregory G. Heuer,
Christos Davatzikos,
"Fetal Ventriculomegaly: External validity of a fetal MRI-based model to predict the need for post-natal CSF diversion", 2016.
(Oral Presentation in the 44th Annual Meeting of the International Society for Pediatric Neurosurgery, Kobe, Japan) -
Jared M. Pisapia,
Hamed Akbari,
Spyridon Bakas,
Martin Rozycki,
Julie S. Moldenhauer,
Phillip B. Storm,
Deborah M. Zarnow,
Gregory G. Heuer
Christos Davatzikos,
"Fetal Ventriculomegaly: Predicting Need for Post-Natal Shunt using Machine Learning and Fetal MRI", 2015.
(Oral Presentation in the 44th Annual Meeting of the AANS/CNS Section on Pediatric Neurological Surgery, Seattle, Washington, U.S.A., 8-11 December 2015) -
Jared M. Pisapia,
Hamed Akbari,
Spyridon Bakas,
Martin Rozycki,
Julie S. Moldenhauer,
Jayesh P. Thawani,
Phillip B. Storm,
Deborah M. Zarnow,
Christos Davatzikos,
Gregory G. Heuer
"Fetal Ventriculomegaly: Ventricle Size Correlates Better with Atrial Diameter than with Fronto-Occipital Horn Ratio", 2015.
(Presented in the 44th Annual Meeting of the AANS/CNS Section on Pediatric Neurological Surgery, Seattle, Washington, U.S.A., 8-11 December 2015) -
Hamed Akbari,
Spyridon Bakas,
Martin Rozycki,
Xiao Da,
Jared Pisapia,
Michel Bilello,
Donald M. O'Rourke,
Christos Davatzikos,
"Non-Invasive Determination of Epidermal Growth Factor Receptor Variant III Expression in Glioblastoma through Analysis of Multi-Parametric Magnetic Resonance Imaging", 2015
(Oral Presentation in 101st Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA), Chicago, Illinois, U.S.A., 29 November – 4 December 2015) -
Spyridon Bakas,
Hamed Akbari,
Jared Pisapia,
Martin Rozycki,
Donald M. O'Rourke,
Christos Davatzikos,
"Identification of Imaging Signatures of the Epidermal Growth Factor Receptor Variant III (EGFRvIII) in Glioblastoma",
Neuro-Oncology, Vol.17, Suppl.5, V154-V154, 2015, DOI: 10.1093/neuonc/nov225.05
(Oral Presentation in the 20th Annual Scientific Meeting of the Society for Neuro-Oncology (SNO), San Antonio, Texas, U.S.A., 19-22 November 2015) -
Spyridon Bakas,
Christos Davatzikos,
"Predictive Modeling in Brain Cancer Using Machine Learning, Imaging and Genomics: Using Informatics to Obtain Rich Characterizations of Aggressive Brain Tumors, in Support of Precision Medicine",
Invited talk in MICCAI NIH Workshop on Computational Precision Medicine II,
2015.
(Technische Universität München (T.U.M.), Munich, Germany, 5-9 Oct 2015) -
Spyridon Bakas,
Bilwaj Gaonkar,
Christos Davatzikos,
"Improved Prediction of Post-surgical Survival in Glioblastoma Through Integrative Genomic and Epigenomic Analysis",
The Cancer Genome Atlas' 4th Annual Scientific Symposium,
2015. DOI: 10.13140/RG.2.1.1156.1841
(National Institutes of Health (NIH) Campus, Bethesda, MD, U.S.A., 11-12 May 2015)
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Spyridon Bakas,
Gordon Hunter,
Paul Sidhu,
Dimitrios Makris,
"Computer-Aided Solutions for the Assessment of Focal Liver Lesions in Contrast-Enhanced Ultrasound",
Oncology News, 10(2):58-61, 2015.
(View) (Publisher's Version)
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"Computer-Aided Localisation, Segmentation and Quantification of Focal Liver Lesions in Contrast-Enhanced Ultrasound",
Kingston University - Faculty of Science, Engineering & Computing (SEC) - Digital Imaging Research Centre (DIRC) - BioImaging Group (BIG)
(Ph.D. Thesis - 2014) -
"Discriminative vs. Generative Methods for Face Detection",
University College London (UCL) - Department of Computer Science (CS) - Vision, Imaging & Virtual Environments
(M.Sc. Thesis - 2007) -
"Three-Dimensional Reconstruction from Two-Dimensional Representations",
Kingston University - Faculty of Technology - School of Computing and Information Systems
(B.Sc. Dissertation - 2005)
Software
- Cancer and Phenomics Toolkit: (+)
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[ - Project Page - ]
The Cancer And Phenomics Toolkit (CapTk) showcases some of the highlight applications from the Center for Biomedical Image Computing and Analytics (CBICA) along with advanced visualization and interactive capabilities to make it a complete radiological tool.
It provides the initialization front-end for:
- GLioma Image SegmenTation and Registration (GLISTR)
- GLISTRboost (The best performing method during BRATS 2015 challenge)
- Pre-Operative and post-Recurrence brain Tumor Registration (PORTR)
- Evaluating the status of the EGFRvIII mutant in pre-operative scans of patients with brain tumors
- Producing infiltration/recurrence maps
- Performing a segmentation of brain tumors using a geodesic segmentation
- Peritumoral Heterogeneity Index (PHI) Estimator: (+)
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[ - Project Page - ]
Peritumoral Heterogeneity Index (PHI) Estimator is a lightweight tool built towards the following goals:
- Perform quantitative pattern analysis of the spatial heterogeneity of peritumoral perfusion imaging dynamics, retrieved from Dynamic Susceptibility Contrast Magnetic Resonance Imaging (DSC-MRI) data.
- Evaluate the imaging biomarker of the Epidermal Growth Factor Receptor variant III (EGFRvIII) mutation status, in individual patients diagnosed with Glioblastoma.
- Brain Tumor Viewer: (+)
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[ - Project Page - ]
Brain Tumor Viewer (BTV) is a lightweight viewer, built for fast and simple interaction with MRI image volumes. BTV is primarily designed for visualizing multi-modal MRI brain volumes and initializing seed-points for the following software packages:
- GLioma Image SegmenTation and Registration (GLISTR)
- Pre-Operative and post-Recurrence brain Tumor Registration (PORTR)