City Research Online

Article

Karabağ, C. ORCID: 0000-0003-4424-0471, Ortega-Ruiz, M. A. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018 (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), article number 59. doi: 10.3390/jimaging9030059

Karabağ, C. ORCID: 0000-0003-4424-0471, Jones, M. L. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018 (2021). Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells. Journal of Imaging, 7(6), article number 93. doi: 10.3390/jimaging7060093

Ananda, A., Ngan, K. H. ORCID: 0000-0001-7623-942X, Karabağ, C. ORCID: 0000-0003-4424-0471 , Ter-Sarkisov, A., Alonso, E. ORCID: 0000-0002-3306-695X & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2021). Classification and Visualisation of Normal and Abnormal Radiographs: a comparison between Eleven Convolutional Neural Network Architectures. Sensors, 21(16), article number 5381. doi: 10.3390/s21165381

Ortega-Ruiz, M. A., Karabağ, C. ORCID: 0000-0003-4424-0471, Garduño, V. G. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2020). Morphological Estimation of Cellularity on Neo-Adjuvant Treated Breast Cancer Histological Images. Journal of Imaging, 6(10), article number 101. doi: 10.3390/jimaging6100101

Karabağ, C. ORCID: 0000-0003-4424-0471, Jones, M. L., Peddie, C. J. , Weston, A. E., Collinson, L. M. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2020). Semantic segmentation of HeLa cells: An objective comparison between one traditional algorithm and four deep-learning architectures. PLOS ONE, 15(10), article number e0230605. doi: 10.1371/journal.pone.0230605

Karabağ, C. ORCID: 0000-0003-4424-0471, Verhoeven, J. ORCID: 0000-0002-0738-8517, Miller, N. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2019). Texture Segmentation: An Objective Comparison between Five Traditional Algorithms and a Deep-Learning U-Net Architecture. Applied Sciences, 9(18), article number 3900. doi: 10.3390/app9183900

Karabağ, C. ORCID: 0000-0003-4424-0471, Jones, M. L., Peddie, C. J. , Weston, A. E., Collinson, L. M. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2019). Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. Journal of Imaging, 5(9), article number 75. doi: 10.3390/jimaging5090075

Karabağ, C. ORCID: 0000-0003-4424-0471, Verhoeven, J. ORCID: 0000-0002-0738-8517, Miller, N. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2019). Texture Segmentation: An Objective Comparison between Traditional and Deep-Learning Methodologies. Preprints, doi: 10.20944/preprints201908.0001.v1

Karabağ, C. ORCID: 0000-0003-4424-0471, Jones, M. L., Peddie, C. J. , Weston, A. E., Collinson, L. M. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2019). Segmentation and modelling of hela nuclear envelope. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), pp. 1510-1513. doi: 10.1109/ISBI.2019.8759151

Karabağ, C. ORCID: 0000-0003-4424-0471, Jones, M. L., Peddie, C. J. , Weston, A. E., Collinson, L. M. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2018). Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images. Communications in Computer and Information Science, doi: 10.1007/978-3-319-95921-4_23

Conference or Workshop Item

Brito-Pacheco, D. A., Karabağ, C., Brito-Loeza, C. , Giannopoulos, P. & Reyes Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2024). Morphological Analysis of HeLa Cells and their Mitochondria under Electron Microscopy. Poster presented at the Crick BioImage Analysis Symposium 2024, 25-26 Nov 2024, London, UK.

Ananda, Karabağ, C. ORCID: 0000-0003-4424-0471, Ter-Sarkisov, A. ORCID: 0000-0002-1300-6132 , Alonso, E. ORCID: 0000-0002-3306-695X & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2020). Radiography Classification: A comparison between Eleven Convolutional Neural Networks. In: 2020 Fourth International Conference on Multimedia Computing, Networking and Applications (MCNA). 2020 Fourth International Conference on Multimedia Computing, Networking and Applications (MCNA), 19-22 Oct 2020, Online. doi: 10.1109/MCNA50957.2020.9264285

Other

Ortega-Ruiz, M. A., Karabağ, C. ORCID: 0000-0003-4424-0471, García Garduño, V. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2020). Morphological estimation of Cellularity on Neo-adjuvant treated breast cancer histological images. doi: 10.1101/2020.04.01.020719

Ortega-Ruiz, M. A., Karabağ, C. ORCID: 0000-0003-4424-0471, Garduño, V. G. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2011). Estimation of cellularity in tumours treated with Neoadjuvant therapy: A comparison of Machine Learning algorithms. doi: 10.1101/2020.04.09.034348

Thesis

Karabağ, C. ORCID: 0000-0003-4424-0471 (2020). Volumetric analysis of HeLa cancer cells imaged with serial block face scanning electron microscopy. (Unpublished Doctoral thesis, City, University of London)