Staff Profile

Boguslaw Obara is Professor of Image Informatics in the School of Computing at Newcastle University.

He obtained a first master degree in computational physics from Jagiellonian University and PhD in Image Processing from AGH University of Science and Technology.

Before joining Newcastle University as Professor; he held research assistant positions at Polish Academy of Sciences and at Computer Vision Laboratory, ETH, Fulbright Fellowship at Vision Research Laboratory, postdoctoral positions at Center for BioImage Informatics, University of California, and at Oxford e-Research Centre, University of Oxford, and assistant, associate and professor positions at Department of Computer Science at Durham University. He was also AstraZeneca Visiting Professor in Image Processing & Artificial Intelligence.

Boguslaw Obara's research focuses on the design and implementation of complex image analysis and processing, pattern recognition, computer vision and machine learning solutions applied to a wide range of domains.

Lab's website: http://boguslawobara.com/

• Singh VK, Kucukgoz B, Murphy DC, Xiong X, Steel DH, Obara B. Benchmarking Automated Detection Of The Retinal External Limiting Membrane In A 3D Spectral Domain Optical Coherence Tomography Image Dataset of Full Thickness Macular Holes. Computers in Biology and Medicine 2022, 140, 105070.
• Theodoropoulos G, Cardenas-Canto P, Obara B, Ivrissimtzis I, Kureshi I. Big data for human security: the case of COVID-19. Journal of Computational Science 2022, (ePub ahead of Print).
• Young N, Asif M, Jackson M, Fernández-Mayoralas DM, de la Peña MJ, Calleja-Pérez B, Álvarez S, Hunter-Featherstone E, Noegel AA, Höhne W, Nürnberg P, Obara B, Hussain MS, Karakesisoglou I, Fernández-Jaén A. Biallelic SYNE2 missense mutations leading to nesprin-2 giant hypo-expression are associated with intellectual disability and autism. Genes 2021, 12(9), 1294.
• Cardenas-Canto P, Obara B, Ivrissimtzis I, Kureshi I, Theodoropoulos G. Big data for national security in the era of COVID-19. In: 21st International Conference on Computational Science. 2021, Krakow, Poland.
• Jackson P, Bonner B, Jia N, Holder C, Stonehouse J, Obara B. Camera bias in fine grained classification task. In: International Joint Conference on Neural Network. 2021.
• Frawley J, Willcocks C, Maged H, Caspar G, Steel DH, Obara B. Robust 3D U-Net Segmentation of Macular Holes. In: 29th Irish Conference on Artificial Intelligence and Cognitive Science. 2021, University College, Dublin (Online).
• Frawley J, Willcocks CG, Habib M, Geenen C, Steel DH, Obara B. Robust 3D U-Net Segmentation of Macular Holes. In: The 29th Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2021). 2021, Dublin: CEUR-WS.
• Stankiewicz A, Marciniak T, Dabrowski A, Stopa M, Marciniak E, Obara B. Segmentation of Preretinal Space in Optical Coherence Tomography Images using Deep Neural Networks. Sensors 2021, 21(22), 7521.
• Rajgor A, Patel A, McCulloch D, Obara B, Bacardit J, McQueen A, Aboagye E, Ali T, O'Hara J, Hamilton D. The application of radiomics in laryngeal cancer. British Journal of Radiology 2021, 94(1128), 20210499.
• Alhasson HF, Willcocks CG, Alharbi SS, Kasim A, Obara B. The relationship between curvilinear structure enhancement and ridge detection methods. Visual Computer 2021, 37, 2263-2283.
• Cox J, Obara B. Virtual special issue: pulmonary nodules. Clinical Radiology 2021, 76(12), P916-917.
• Holder CJ, Ricketts S, Obara B. Convolutional networks for appearance-based recommendation and visualisation of mascara products. Machine Vision and Applications 2020, 31(1), 5.
• Chen Y, Nasrulloh AV, Wilson I, Geenen C, Habib M, Obara B, Steel DHW. Macular hole morphology and measurement using an automated three-dimensional image segmentation algorithm. BMJ Open Ophthalmology 2020, 5, e000404.
• Brennan J, Bonner S, Atapour-Abarghouei A, Jackson PT, Obara B, McGough AS. Not Half Bad: Exploring Half-Precision in Graph Convolutional Neural Networks. In: 2020 IEEE International Conference on Big Data. 2020, Online: IEEE.
• Murphy DC, Nasrulloh AV, Lendrem C, Graziado S, Alberti M, laCour M, Obara B, Steel DHW. Predicting Postoperative Vision for Macular Hole with Automated Image Analysis. Ophthalmology Retina 2020, 4(12), 1211-1213.
• Frawley J, Willcocks CG, Habib M, Geenen C, Steel DH, Obara B. Segmentation of Macular Edema Datasets with Small Residual 3D U-Net Architectures. In: 20th International Conference on Bioinformatics and Bioengineering (BIBE 2020). 2020, Cincinnati, OH, USA: IEEE.
• Alharbi SS, Sazak C, Nelson CJ, Alhasson HF, Obara B. The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images. Methods 2020, 173, 3-15.
• Kalligeraki AA, Isted A, Pal R, Saunter C, Girkin J, Jarrin M, Uwineza A, Obara B, Quinlan RA. Three-dimensional data capture and analysis of intact eye lenses evidences emmetropia-associated changesand strain-dependent differences in epithelial cell organization. Scientific Reports 2020, 10(1), 16898.
• Cardenas P, Obara B, Theodoropoulos G, Kureshi I. Unveiling Ideological Trends through Data Analytics to Construe National Security Instabilities. In: IEEE International Conference on Big Data (Big Data 2020). 2020, Atlanta, GA, USA: IEEE.
• Cardenas P, Obara B, Theodoropoulos G, Kureshi I. Analysing Social Media as a Hybrid Tool to Detect and Interpret likely Radical Behavioural Traits for National Security. In: IEEE International Conference on Big Data (Big Data 2019). 2019, Los Angeles, CA, USA: IEEE.
• Jia N, Holder C, Bonner S, Obara B. Coarse annotation refinement for segmentation of dot-matrix batchcodes. In: 18th IEEE International Conference on Machine Learning and Applications (ICMLA 2019). 2019, Boca Raton, FL, USA: IEEE.
• Nelson CJ, Jackson PTG, Obara B. Combining mathematical morphology and the Hilbert transform for fully automatic nuclei detection in fluorescence microscopy. In: 14th International Symposium on Mathematical Morphology and Its Applications to Signal and Image Processing (ISMM 2019). 2019, Saarbrücken, Germany: Springer Verlag.
• Alharbi SS, Sazak C, Nelson CJ, Obara B. Curvilinear Structure Enhancement by Multiscale Top-Hat Tensor in 2D/3D Images. In: International Conference on Bioinformatics and Biomedicine (BIBM 2018). 2019, Madrid, Spain: IEEE.
• Cardenas P, Obara B, Theodoropoulos G, Kureshi I. Defining an Alert Mechanism for Detecting likely threats to National Security. In: International Conference on Big Data (Big Data 2018). 2019, Seattle, WA, USA: IEEE.
• Sazak C, Nelson CJ, Obara B. Erratum to ‘The multiscale bowler-hat transform for blood vessel enhancement in retinal images’ [Pattern Recognition 88 (2019) 739-750, doi: 10.1016/j.patcog.2018.10.011]. Pattern Recognition 2019, 91, 404-404.
• Bonner S, Kureshi I, Brennan J, Theodoropoulos G, McGough AS, Obara B. Exploring the Semantic Content of Unsupervised Graph Embeddings: An Empirical Study. Data Science and Engineering 2019, 4, 269-289.
• Willcocks CG, Jackson PTG, Nelson CJ, Nasrulloh AV, Obara B. Interactive GPU active contours for segmenting inhomogeneous objects. Journal of Real-Time Image Processing 2019, 16(6), 2305-2318.
• Mohammadi M, Jaf S, McGough AS, Breckon TP, Matthews P, Theodoropoulos G, Obara B. On the Use of Neural Text Generation for the Task of Optical Character Recognition. In: 16th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA 2019). 2019, Abu Dhabi, UAE: IEEE.
• Jackson PT, Wang Y, Knight S, Chen H, Dorval T, Brown M, Bendtsen C, Obara B. Phenotypic profiling of high throughput imaging screens with generic deep convolutional features. In: 16th International Conference on Machine Vision Applications (MVA 2019). 2019, Tokyo, Japan: IEEE.
• Alharbi SS, Willcocks CG, Jackson PTG, Alhasson HF, Obara B. Sequential graph-based extraction of curvilinear structures. Signal, Image and Video Processing 2019, 13(5), 941-949.
• Jackson P, Atapour-Abarghouei A, Bonner S, Breckon TP, Obara B. Style augmentation: data augmentation via style randomization. In: CVPR Workshop 2019. 2019, Long Beach, California: CVF.
• Bonner S, Atapour Abarghouei A, Jackson P, Brennan J, Kureshi I, Theodoropoulos G, McGough S, Obara B. Temporal Neighbourhood Aggregation: Predicting Future Links in Temporal Graphs via Recurrent Variational Graph Convolutions. In: IEEE International Conference on Big Data (Big Data 2019). 2019, Los Angeles, CA, USA: IEEE.
• Sazak C, Nelson CJ, Obara B. The multiscale bowler-hat transform for blood vessel enhancement in retinal images. Pattern Recognition 2019, 88, 739-750.
• Sazak C, Nelson CJ, Obara B. The multiscale bowler-hat transform for vessel enhancement in 3D biomedical images. In: 29th British Machine Vision Conference (BMVC 2018). 2019, Northumbria University, Newcastle upon Tyne: BMVA Press.
• Holder CJ, Obara B, Ricketts S. Visual Siamese Clustering for Cosmetic Product Recommendation. In: 14th Asian Conference on Computer Vision (ACCV 2018 Workshops). 2019, Perth, Australia: Springer Verlag.
• Cardenas P, Theodoropoulos G, Obara B. Web Insights for National Security: Analysing Participative Online Activity to Interpret Crises. In: 18th International Conference on Cognitive Informatics and Cognitive Computing (ICCI*CC 2019). 2019, Milan, Italy: IEEE.
• Alhasson HF, Alharbi SS, Obara B. 2D and 3D vascular structures enhancement via multiscale fractional anisotropy tensor. In: Computer Vision – ECCV 2018 Workshops. 2018, Munich, Germany: Springer Verlag.
• Cardenas P, Theodoropoulos G, Obara B, Kureshi I. A conceptual framework for social movements analytics for national security. In: 18th International Conference on Computational Science (ICCS 2018). 2018, Wuxi, China: Springer Verlag.
• Nasrulloh AV, Willcocks CG, Jackson PTG, Geenen C, Habib MS, Steel DHW, Obara B. Multi-scale Segmentation and Surface Fitting for Measuring 3D Macular Holes. IEEE Transactions on Medical Imaging 2018, 37(2), 580-589.
• Bonner S, Brennan J, Kureshi I, Theodoropoulos G, McGough AS, Obara B. Temporal Graph Offset Reconstruction: Towards Temporally Robust Graph Representation Learning. In: IEEE International Conference on Big Data. 2018, Seattle, WA, USA: IEEE.
• Sawant M, Schwarz N, Windoffer R, Magin TM, Krieger J, Mucke N, Obara B, Jankowski V, Jankowski J, Wally V, Lettner T, Leube RE. Threonine 150 Phosphorylation of Keratin 5 Is Linked to Epidermolysis Bullosa Simplex and Regulates Filament Assembly and Cell Viability. Journal of Investigative Dermatology 2018, 138(3), 627-636.
• Medhat F, Mohammadi M, Jaf S, Willcocks CG, Breckon TP, Matthews P, McGough AS, Theodoropoulos G, Obara B. TMIXT: A process flow for Transcribing MIXed handwritten and machine-printed Text. In: IEEE International Conference on Big Data (Big Data 2018). 2018, Seattle, WA, USA: IEEE.
• Fricker MD, Akita D, Heaton LLM, Jones N, Obara B, Nakagaki T. Automated analysis of Physarum network structure and dynamics. Journal of Physics D: Applied Physics 2017, 50(25), 254005.
• Jackson PTG, Obara B. Avoiding over-detection: Towards combined object detection and counting. In: 16th International Conference on Artificial Intelligence and Soft Computing (ICAISC 2017). 2017, Zakopane, Poland: Springer Verlag.
• Sazak C, Obara B. Contrast-independent curvilinear structure enhancement in 3D biomedical images. In: 14th International Symposium on Biomedical Imaging (ISBI 2017). 2017, Melbourne, VIC, Australia: IEEE.
• Bonner S, Brennan J, Kureshi I, Theodoropoulos G, McGough AS, Obara B. Evaluating the quality of graph embeddings via topological feature reconstruction. In: 2017 IEEE International Conference on Big Data. 2017, Boston, MA, USA: IEEE.
• Willcocks CG, Jackson PTG, Nelson CJ, Obara B. Extracting 3D Parametric Curves from 2D Images of Helical Objects. IEEE Transactions on Pattern Analysis and Machine Intelligence 2017, 39(9), 1757-1769.
• Alhasson HF, Obara B. 2D Adaptive Grid-Based Image Analysis Approach for Biological Networks. In: 16th International Conference on Bioinformatics and Bioengineering (BIBE). 2016, Taichung, Taiwan: IEEE.
• Massey MK, Kotsialos A, Volpati D, Vissol-Gaudin E, Pearson C, Bowen L, Obara B, Zeze DA, Groves C, Petty MC. Evolution of Electronic Circuits using Carbon Nanotube Composites. Scientific Reports 2016, 6, 32197.
• Nelson CJ, Duckney P, Hawkins TJ, Deeks MJ, Laissue PP, Hussey PJ, Obara B. Blobs and curves: Object-based colocalisation for plant cells. Functional Plant Biology 2015, 42(5), 471-485.
• Jackson PTG, Nelson CJ, Schiefele J, Obara B. Runway detection in High Resolution remote sensing data. In: 9th International Symposium on Image and Signal Processing and Analysis (ISPA 2015). 2015, Zagreb, Croatia: IEEE.
• Lichius A, Goryachev AB, Fricker MD, Obara B, Castro-Longoria E, Read ND. CDC-42 and RAC-1 regulate opposite chemotropisms in Neurospora crassa. Journal of Cell Science 2014, 127(9), 1953-1965.
• Scales TME, Jayo A, Obara B, Holt MR, Hotchin NA, Berditchevski F, Parsons M. 3β1 integrins regulate CD151 complex assembly and membrane dynamics in carcinoma cells within 3D environments. Oncogene 2013, 32(34), 3965-3979.
• Obara B, Jabeen A, Fernandez N, Laissue PP. A novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles. Histochemistry and Cell Biology 2013, 139(3), 391-402.
• Obara B, Roberts MA, Armitage JP, Grau V. Bacterial cell identification in differential interference contrast microscopy images. BMC Bioinformatics 2013, 14, 134.
• Jabeen A, Miranda-Sayago JM, Obara B, Spencer PS, Dealtry GB, Hayrabedyan S, Shaikly V, Laissue PP, Fernandez N. Quantified colocalization reveals heterotypic histocompatibility class I antigen associations on trophoblast cell membranes: Relevance for human pregnancy. Biology of Reproduction 2013, 89(4), 94.
• Obara B, Grau V, Fricker MD. A bioimage informatics approach to automatically extract complex fungal networks. Bioinformatics 2012, 28(18), 2374-2381.
• Heaton L, Obara B, Grau V, Jones N, Nakagaki T, Boddy L, Fricker MD. Analysis of fungal networks. Fungal Biology Reviews 2012, 26(1), 12-29.
• Obara B, Fricker M, Grau V. Coherence enhancing diffusion filtering based on the Phase Congruency Tensor. In: 9th IEEE International Symposium on Biomedical Imaging (ISBI 2012). 2012, Barcelona, Spain: IEEE.
• Obara B, Fricker M, Grau V. Contrast independent detection of branching points in network-like structures. In: Medical Imaging 2012: Image Processing. 2012, San Diego, California, United States: SPIE.
• Obara B, Fricker M, Gavaghan D, Grau V. Contrast-independent curvilinear structure detection in biomedical images. IEEE Transactions on Image Processing 2012, 21(5), 2572-2581.
• Brown MT, Steel BC, Silvestrin C, Wilkinson DA, Delalez NJ, Lumb CN, Obara B, Armitage JP, Berry RM. Flagellar hook flexibility is essential for bundle formation in swimming Escherichia coli cells. Journal of Bacteriology 2012, 194(13), 3495-3501.
• Obara B, Fricker M, Grau V. Local phase approaches to extract biomedical networks. In: 9th IEEE International Symposium on Biomedical Imaging (ISBI 2012). 2012, Barcelona, Spain: IEEE.
• Kowalik-Urbaniak I, Vrscay ER, Wang Z, Cavaro-Menard TC, Koff D, Wallace B, Obara B. The impact of skull bone intensity on the quality of compressed CT neuro images. In: Medical Imaging 2012: Image Processing. 2012, San Diego, California, United States: SPIE.
• Obara B, Kozusnikova A, Scucka J. Automatic identification of microcracks observed on microscopic images of coarse-grained sandstone. International Journal of Rock Mechanics and Mining Sciences 2011, 48(4), 681-686.
• Obara B, Veeman M, Choi JH, Smith W, Manjunath BS. Segmentation of ascidian notochord cells in DIC timelapse images. Microscopy Research and Technique 2011, 74(8), 727-734.
• Piedrahita D, Hernandez I, Lopez-Tobon A, Fedorov D, Obara B, Manjunath BS, Boudreau RL, Davidson B, LaFerla F, Gallego-Gomez JC, Kosik KS, Cardona-Gomez GP. Silencing of CDK5 reduces neurofibrillary tangles in transgenic Alzheimer's mice. Journal of Neuroscience 2010, 30(42), 13966-13976.
• Roeder AHK, Chickarmane V, Cunha A, Obara B, Manjunath BS, Meyerowitz EM. Variability in the control of cell division underlies sepal epidermal patterning in Arabidopsis thaliana. PLoS Biology 2010, 8(5), e1000367.
• Drelie Gelasca E, Obara B, Fedorov D, Kvilekval K, Manjunath BS. A biosegmentation benchmark for evaluation of bioimage analysis methods. BMC Bioinformatics 2009, 10, 368.
• Chworos A, Obara B. Automatic analysis of conjugated polyelectrolyte-DNA interactions based on sequential analysis of AFM imaging. IEEE Transactions on Nanotechnology 2009, 8(4), 457-462.
• Kvilekval K, Fedorov D, Obara B, Singh A, Manjunath BS. Bisque: A platform for bioimage analysis and management. Bioinformatics 2009, 26(4), 544-552.
• Gelasca ED, Byun J, Obara B, Manjunath BS. Evaluation and benchmark for biological image segmentation. In: 15th IEEE International Conference on Image Processing (ICIP 2008). 2008, San Diego, CA, USA: IEEE.
• Stepien T, Obara B. The cycloid and skeletonization methods for morphometric analysis of fetal brain vessels. Folia Neuropathologica 2008, 46(4), 278-285.
• Obara B. A new algorithm using image colour system transformation for rock grain segmentation. Mineralogy and Petrology 2007, 91(3-4), 271-285.
• Obara B. An image processing algorithm for the reversed transformation of rotated microscope images. Computers and Geosciences 2007, 33(7), 853-859.
• Obara B. Identification of transcrystalline microcracks observed in microscope images of a dolomite structure using image analysis methods based on linear structuring element processing. Computers and Geosciences 2007, 33(2), 151-158.
• Obara B, Kozusnikova A. Utilisation of the image analysis method for the detection of the morphological anisotropy of calcite grains in marble. Computational Geosciences 2007, 11(4), 275-281.
• Obara B, Nizankowski RT. Application of image analysis methods for vascular blood flow assessment with angiographic imaging. Przeglad Elektrotechniczny 2005, 81(3), 76-78.
• Obara B. Developing of the image segmentation methods to rock microcracks analysis. In: Impact of Human Activity on the Geological Environment - Proceedings of the International Symposium of the International Society for Rock Mechanics (EUROCK 2005). 2005, Brno, Czech Republic: CRC Press.