Spyridon Bakas, PhD

Assistant Professor of Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania

Contact InformationUniversity of Pennsylvania
Richards Medical Research Laboratories
3700 Hamilton Walk
Floor 7

Philadelphia, PA, 19104
Office: 267-752-5209


Specialty Division

Immunobiology and Experimental Pathology

Research Expertise

Biomedical Image Analysis
Machine Learning
Cancer Imaging
Computational Pathology
Pattern Analysis

Itmat Expertise

Computational Pathology;
Machine learning;
Pattern analysis;
Image segmentation


BS (Hons) (Computer Science), Kingston University, 2006
MS (Vision, Imaging & Virtual Environments), University College London, 2007
PhD (Medical Image Computing & Analysis), Kingston University, 2014

Specialty Certification

Postgraduate Training

Postdoctoral Researcher Fellow, University of Pennsylvania, 2014-2018

Awards and Honors

Second Prize Award for Best Poster Presentation:
British Machine Vision Association / Engineering and Physical Sciences Research Council Summer School on Computer Vision, 2009
Fully Funded Ph.D. Studentship: Kingston University, Faculty of Science, Engineering and Computing, 2011
First Prize Award for Best Poster Presentation: Kingston University PhD Poster Competition, 2013
Best Clinical Research Presentation: Pan-Philadelphia Neurosurgery Conference, 2015
First Prize Award for the Best Performing Segmentation Method: International Multimodal Brain Tumor Segmentation (BRATS) Challenge 2015, in conjunction with MICCAI 2015, 2015
Top-ranked abstract and featured at the Highlight Plenary Lecture: World Molecular Imaging Conference, 2017
Featured paper in journal’s frontpage: Nature Scientific Data journal, 2017
Featured paper in Newsletter of (NIH/NCI): National Institutes of Health/National Cancer Institute’s "Division of Cancer Treatment and Diagnosis", 2017
Magna Cum Laude for Scientific Abstract at the 44th Pendergrass Day Symposium of the UPenn: Prognostic Stratification of GBM Patients via Computational Analysis of Preoperative Structural MRI, 2018
Top-ranked & featured as 1/5 Highlights (23rd Annual SNO Meeting): “Non-invasive in vivo signature of IDH1 mutational status in high grade glioma, from clinically-acquired multi-parametric magnetic resonance imaging, using multivariate machine learning”, 2018
Highlighted Conference Session at the IEEE International Symposium on Biomedical Imaging (ISBI) 2018: Half-Day Tutorial on CaPTk featured in the Best-of-ISBI events by Computer Vision News, 2018
First Prize Award for Best Poster Presentation on the NIH Annual Scientific Meeting of the Informatics Technology for Cancer Research program: “The Federated Tumor Segmentation (FeTS) platform”, 2020

Memberships and Professional Organizations

Member - European Association for Cancer Research, 2012 - Present
Member - British Machine Vision Association (BMVA), 2012 - 2015
Member - British Association for Cancer Research, 2012 - Present
Member, Medical Image Computing & Computer-Assisted Interventions (MICCAI), 2014 - Present
Member - Society for Neuro-Oncology (SNO), 2015 - Present
Member - IEEE Engineering in Medicine and Biology Society (IEEE-EMBS), 2018 - Present
Member - Institute of Electrical and Electronics Engineers (IEEE), 2018 - Present

Web Links

Selected Publications

“Brain Extraction on MRI Scans in Presence of Diffuse Glioma: Multi-institutional Performance Evaluation of Deep Learning Methods and Robust Modality-Agnostic Training”

S.Thakur, J.Doshi, S.Pati, S.Rathore, C.Sako, M.Bilello, S.M.Ha, G.Shukla, A.Flanders, A.Kotrotsou, M.Milchenko, S.Liem, G.Alexander, J.Lombardo, J.D.Palmer, P.LaMontagne, A.Nazeri, S.Talbar, U.Kulkarni, D.Marcus, R.Colen, C.Davatzikos, G.Erus, S.Bakas, NeuroImage 220(): 117081, 2020

“Imaging signatures of glioblastoma molecular characteristics: A radiogenomics review”

A.F.Kazerooni, S.Bakas, H.S.Rad, C.Davatzikos, Journal of Magnetic Resonance Imaging 52(): 54-69, 2020

“Novel Population-based Histologic Stain Normalization Reference Standard”

J.L.Agraz, C.M.Grenko, A.N.Viaene, M.P.Nasrallah, M.D.Feldman, H.Akbari, S.Bakas, Pendergrass Symposium, 2020

“iGLASS: Imaging integration into the Glioma Longitudinal AnalySiS Consortium”

S.Bakas, D.R.Ormond, K.D.Alfaro, M.Smits, L.A.D.Cooper, R.Verhaak, L.M.Poisson, for iGLASS and the GLASS consortium, NeuroOncology 20(10): 1545-1546, 2020, PMID:32644158

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“Multi-institutional non-invasive in vivo characterization of IDH, 1p/19q, and EGFRvIII in glioma using Neuro-Cancer Imaging Phenomics Toolkit (neuro-CaPTk)”

S.Rathore, S.Mohan, S.Bakas, C.Sako, C.Badve, S.Pati, A.Singh, D.Bounias, P.Ngo, H.Akbari, A.Gastounioti, M.Bergman, M.Bilello, R.T.Shinohara, P.Yushkevich, D.M.O’Rourke, A.E.Sloan, D.Kontos, M.P.Nasrallah, J.S.Barnholtz-Sloan, C.Davatzikos, Neuro-Oncology Advances, 2020

“Histopathology-validated machine learning radiographic biomarker for non-invasive discrimination between true progression and pseudo-progression in glioblastoma”

H.Akbari, S.Rathore, S.Bakas, M.P.Nasrallah, G.Shukla, E.Mamourian, M.Rozycki, S.J.Bagley, J.D.Rudie, A.E.Flanders, A.P.Dicker, A.S.Desai, D.M.O’Rourke, S.Brem, R.Lustig, S.Mohan, R.L.Wolf, M.Bilello, M.Martinez-Lage, C.Davatzikos, Cancer 126(11): 2625-2636, 2020

“Integrated Biophysical Modeling and Image Analysis: Application to Neuro-Oncology”

A.Mang*, S.Bakas*, S.Subramanian, C.Davatzikos, G.Biros, Annual Review of Biomedical Engineering 22(): 309-341, 2020

“Longitudinal Brain Tumor Segmentation Prediction in MRI Using Feature and Label Fusion”

L.Pei, S.Bakas, A.Vossough, S.M.S.Reza, C.Davatzikos, K.M.Iftekharuddin, Biomedical Signal Processing and Control 55(): 101648, 2020

“O-Net: An Overall Convolutional Network for Segmentation Tasks”

O.H.Maghsoudi, A.Gastounioti, S.Bakas, L.Pantalone, C.Davatzikos, D.Kontos, Machine Learning in Medical Imaging 12436(): 199-209, 2020

“The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview”

S.Pati, A.Singh, S.Rathore, A.Gastounioti, M.Bergman, P.Ngo, S.M.Ha, D.Bounias, J.Minock, G.Murphy, H.Li, A.Bhattarai, A.Wolf, P.Sridaran, R.Kalarot, H.Akbari, A.Sotiras, S.P.Thakur, R.Verma, R.T.Shinohara, P.Yushkevich, Y.Fan, D.Kontos, C.Davatzikos, S.Bakas, Brainlesion 11993(): 380-394, 2020, PMID:32754723

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