School of Computing and Digital Media staff profiles content store_hidden Cefa Karabag Our staff

Cefa received his PhD in Electrical and Electronic Engineering at City, University of London. He obtained his MSc (German Diplom) degree in Physics from Leibniz University of Hannover, Germany with his thesis titled “Circular photo galvanic effects in Quantum Wells” after his BSc degree in Physics in İstanbul, Türkiye. Cefa worked as a lecturer in Mathematics at the Centre for Applied Sciences, City and Islington College, London (Electrical and Electronic Engineering Foundation Year at City, University of London).

He also worked as a Research Fellow and a Lecturer at the Department of Computer Science, City, University of London before he became a senior lecturer in Computer Science and Applied Computing at London Metropolitan University. In his research, in collaboration with The Francis Crick Institute, Cefa works on automated segmentation and volumetric analysis of HeLa cancer cells from Electron Microscopy Images. He is a Senior Fellow of the Higher Education Academy and is a member of The British Machine Vision Association (BMVA), The British Association for Cancer Research (BACR), and the European Association for Cancer Research (EACR). He is also a reviewer of PLOS One and IEEE Access.

Research interests:

• Image Processing
• Image Analysis
• Medical Image Analysis and Computing
• Data Visualisation

M. A. Ortega-Ruíz, C. Karabağ, E. Roman-Rangel and C. C. Reyes-Aldasoro, "DRD-UNet, a UNet-Like Architecture for Multi-Class Breast Cancer Semantic Segmentation," in IEEE Access, vol. 12, pp. 40412-40424, 2024, doi: 10.1109/ACCESS.2024.3377428.

D. Brito-Pacheco, C. Karabağ, C. Brito-Loeza, P. Giannopoulos, C.C. Reyes-Aldasoro, "Relationship Between Irregularities of the Nuclear Envelope and Mitochondria in HeLa cells Observed with Electron Microscopy," 2024 IEEE 21st International Symposium on Biomedical Imaging (ISBI 2024), Athens, Greece, 2024.

Karabağ, C., Ortega-Ruíz, M.A. and Reyes-Aldasoro, C.C. (2023). Impact of Training Data, Ground Truth and Shape Variability in the Deep Learning-Based Semantic Segmentation of HeLa Cells Observed with Electron Microscopy. Journal of Imaging, 9(3), pp. 59–59. doi:10.3390/jimaging9030059.

Ananda, A., Ngan, K.H., Karabağ, C., Ter-Sarkisov, A., Alonso, E. and Reyes-Aldasoro, C.C. (2021). Classification and Visualisation of Normal and Abnormal Radiographs; A Comparison between Eleven Convolutional Neural Network Architectures. Sensors, 21(16), pp. 5381–5381. doi:10.3390/s21165381.

Karabağ, C., Jones, M.L. and Reyes-Aldasoro, C.C. (2021). Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells. Journal of Imaging, 7(6), pp. 93–93. doi:10.3390/jimaging7060093. This paper was selected as an Issue Cover.

Karabağ, C., Jones, M.L., Peddie, C.J., Weston, A.E., Collinson, L.M. and Reyes-Aldasoro, C.C. (2020). Semantic segmentation of HeLa cells: An objective comparison between one traditional algorithm and four deep-learning architectures. PLOS ONE, 15(10). doi:10.1371/journal.pone.0230605.

Ortega-Ruiz, M.A., Karabağ, C., Garduño, V.G. and Reyes-Aldasoro, C.C. (2020). Morphological Estimation of Cellularity on Neo-Adjuvant Treated Breast Cancer Histological Images. Journal of Imaging, 6(10), pp. 101–101. doi:10.3390/jimaging6100101.

Karabağ, C., Verhoeven, J., Miller, N.R. and Reyes-Aldasoro, C.C. (2019). Texture Segmentation: An Objective Comparison between Five Traditional Algorithms and a Deep-Learning U-Net Architecture. Applied Sciences, 9(18), pp. 3900–3900. doi:10.3390/app9183900.

Karabağ, C., Jones, M.L., Peddie, C.J., Weston, A.E., Collinson, L.M. and Reyes-Aldasoro, C.C. (2019). Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. Journal of Imaging, 5(9), pp. 75–75. doi:10.3390/jimaging5090075.

Dese, K., Karabağ, C., Giannopoulos, P. and Reyes-Aldasoro, C.C. (2023). Investigation of topological features of the 3D cellular nuclear envelope as observed with Electron Microscopy. 27th Conference on Medical Image Understanding and Analysis 2023.

Karabağ, C. and Reyes-Aldasoro, C.C. (2022).
Evaluation of Training Data, Ground Truth and Shape Variability in the Semantic Segmentation of HeLa cells Observed with Electron Microscopy. Crick BioImage Analysis Symposium (CBIAS) 2022 21-22 November, London, UK.

Karabağ, C., Jones, M.L. and Reyes-Aldasoro, C.C. (2021). Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells. BioImage Informatics 2021 29 Nov 2021 – 1 Dec 2021, Paris, France.

Karabağ, C., Jones, M.L. and Reyes-Aldasoro, C.C. (2021). Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells. Crick BioImage Analysis Symposium (CBIAS) 2021 22-23 November, London, UK.

Karabağ, C., Jones, M.L., Peddie, C.J., Westor, A.E., Collinson, L.M. and Reyes-Aldasoro, C.C. (2019). Segmentation And Modelling of Helanuclear Envelope. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI) 8-11 April. doi:10.1109/isbi.2019.8759151

Karabağ, C., Jones, M.L., Peddie, C.J., Weston, A.E., Collinson, L.M. and Reyes-Aldasoro, C.C. (2018). Segmentation and Modelling of HeLa Nuclear Envelope. BACR Student Conference 26 November, London, UK.

Karabağ, C., Jones, M.L., Peddie, C.J., Weston, A.E., Collinson, L.M. and Reyes-Aldasoro, C.C. (2018). Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images. 22nd Conference on Medical Image Understanding and Analysis 2018. doi:10.1007/978-3-319-95921-4_23

• EurekAlert – Academics develop algorithm to analyse HeLa cancer cells
• Ecancer – Academics develop algorithm to analyse HeLa cancer cells
• Researchers reflect on the remarkable life of Henrietta Lacks for UK Black History Month
• Science Codex – Academics develop algorithm to analyse HeLa cancer cells

• International Science Partnerships Fund (ISPF) from British Council with Full Economic Cost (FEC) £99,853 - Awaiting Outcome
• Networking Grant from The Academy of Medical Sciences - £24,396
• Full Tuition Fee Waiver for PhD in Electrical and Electronic Engineering from City, University of London - £6,750
• The British Machine Vision Association (BMVA) Travel Bursary for International Conference - £372
• Grant for Teaching Physics and Mathematics from The Peabody Trust - £7,000

Dr Cefa Karabağ
Senior Lecturer in Computer Science and Applied Computing
c.karabag@londonmet.ac.uk