- 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.
- 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.
Dr Cefa Karabağ
Contact details
Address
Dr Cefa Karabağ
City, University of London
Northampton Square
London EC1V 0HB
United Kingdom
Northampton Square
London EC1V 0HB
United Kingdom
About
Overview
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 Istanbul, Turkey. Cefa worked as a Lecturer in Mathematics at Centre for Applied Sciences, City and Islington College, London. He also worked as a Research Fellow before he became a Lecturer at the Department of Computer Science, City, University of London. In his research, in collaboration with The Francis Crick Institute, Cefa worked on automated segmentation and volumetric analysis of HeLa cancer cells from Electron Microscopy Images. Together with Dr Constantino Carlos Reyes-Aldasoro, Cefa developed a segmentation algorithm in MATLAB to analyse cervical cancer cells.
Qualifications
- PhD, City, University of London, United Kingdom
Postgraduate training
- PGCE in Mathematics, London Metropolitan University, London, United Kingdom
Employment
- Lecturer in Computer Science, City, University of London, Aug 2021 – present
- Lecturer in Mathematics, City and Islington College, Feb 2013 – Sep 2021
Languages
English (can read, write, speak, understand spoken and peer review), German (can read and write), Spanish; Castilian (can read and write) and Turkish (can read, write, speak, understand spoken and peer review).
Publications
Publications by category
Conference papers and proceedings (5)
- 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.
- Karabag, 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.
- 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.