City Research Online

Article

Ortega-Ruíz, M. A., Karabağ, C., Roman-Rangel, E. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2024). DRD-UNet, a UNet-like architecture for multi-class breast cancer semantic segmentation. IEEE Access, 12, pp. 40412-40424. doi: 10.1109/access.2024.3377428

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.

Brito-Pacheco, D., Karabağ, C., Brito-Loeza, C. , Giannopoulos, P. ORCID: 0000-0002-6261-1961 & Reyes Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2024). Relationship between irregularities of the nuclear envelope and mitochondria in hela cells observed with electron microscopy. Paper presented at the IEEE International Symposium on Biomedical Imaging, 27-30 May 2024, Athens, Greece. doi: 10.1109/ISBI56570.2024.10635639

Rada, L., Azzawi, I., Kumar, P. , Brito-Loeza, C. F., Karabağ, C. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2024). Image Processing and Machine Learning Techniques for Chagas Disease Detection and Identification. In: Medical Image Understanding and Analysis Proceedings Part I. 28th Annual Conference Medical Image Understanding and Analysis, 24-26 Jul 2024, Manchester, UK. doi: 10.1007/978-3-031-66955-2_14

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

Brito-Pacheco, D., Karabağ, C., Brito-Loeza, C. , Giannopoulos, P. ORCID: 0000-0002-6261-1961 & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2023). Relationship Between Irregularities of the Nuclear Envelope and Mitochondria in HeLa cells Observed with Electron Microscopy. doi: 10.1101/2023.11.14.567016

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)

Working Paper

Karabağ, C., Jones, M. L., Peddie, C. J. , Weston, A. E., Collinson, L. M. & Reyes-Aldasoro, C. C. ORCID: 0000-0002-9466-2018view all authors (2020). Geometric differences between nuclear envelopes of Wild-type and Chlamydia trachomatis-infected HeLa cells (10.1101/2020.04.02.021733). .