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The relationship between curvilinear structure enhancement and ridge detection approaches (2020)
Journal Article
Alhasson, H., Willcocks, C. G., Alharbi, S. S., Kasim, A., & Obara, B. (2021). The relationship between curvilinear structure enhancement and ridge detection approaches. Visual Computer, 37(8), 2263-2283. https://doi.org/10.1007/s00371-020-01985-4

Curvilinear structure detection and quantification is a large research area with many imaging applications in fields such as biology, medicine, and engineering. Curvilinear enhancement is often used as a pre-processing stage for ridge detection, but... Read More about The relationship between curvilinear structure enhancement and ridge detection approaches.

Three-dimensional data capture and analysis of intact eye lenses evidences emmetropia-associated changes and strain-dependent differences in epithelial cell organization (2020)
Journal Article
Kalligeraki, A. A., Isted, A., Pal, R., Saunter, C., Girkin, J., Jarrin, M., …Quinlan, R. A. (2020). Three-dimensional data capture and analysis of intact eye lenses evidences emmetropia-associated changes and strain-dependent differences in epithelial cell organization. Scientific Reports, 10, Article 16898. https://doi.org/10.1038/s41598-020-73625-9

Organ and tissue development are highly coordinated processes; lens growth and functional integration into the eye (emmetropia) is a robust example. An epithelial monolayer covers the anterior hemisphere of the lens, and its organization is the key t... Read More about Three-dimensional data capture and analysis of intact eye lenses evidences emmetropia-associated changes and strain-dependent differences in epithelial cell organization.

Macular hole morphology and measurement using an automated three dimensional image segmentation algorithm (2020)
Journal Article
Chen, Y., Nasrulloh, A., Wilson, I., Caspar, G., Maged, H., Obara, B., & Steel, D. (2020). Macular hole morphology and measurement using an automated three dimensional image segmentation algorithm. BMJ Open Ophthalmology, 5(1), Article e000404. https://doi.org/10.1136/bmjophth-2019-000404

Objective: Full-thickness macular holes (MH) are classified principally by size, which is one of the strongest predictors of anatomical and visual success. Using a three-dimensional (3D) automated image processing algorithm, we analysed optical coher... Read More about Macular hole morphology and measurement using an automated three dimensional image segmentation algorithm.

Convolutional networks for appearance based recommendation and visualisation of mascara products (2020)
Journal Article
Holder, C., Ricketts, S., & Obara, B. (2020). Convolutional networks for appearance based recommendation and visualisation of mascara products. Machine Vision and Applications, 31, Article 5. https://doi.org/10.1007/s00138-019-01053-5

In this work, we explore the problems of recommending and visualising makeup products based on images of customers. Focusing on mascara, we propose a two-stage approach that first recommends products to a new customer based on the preferences of othe... Read More about Convolutional networks for appearance based recommendation and visualisation of mascara products.

Exploring the semantic content of unsupervised graph embeddings: an empirical study (2019)
Journal Article
Bonner, S., Kureshi, I., Brennan, J., Theodoropoulos, G., McGough, S., & Obara, B. (2019). Exploring the semantic content of unsupervised graph embeddings: an empirical study. Data Science and Engineering, 4(3), 269-289. https://doi.org/10.1007/s41019-019-0097-5

Graph embeddings have become a key and widely used technique within the field of graph mining, proving to be successful across a broad range of domains including social, citation, transportation and biological. Unsupervised graph embedding techniques... Read More about Exploring the semantic content of unsupervised graph embeddings: an empirical study.

The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images (2019)
Journal Article
Alharbi, S. S., Sazak, C., Alhasson, H., Nelson, C. J., & Obara, B. (2020). The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images. Methods, 173, 3-15. https://doi.org/10.1016/j.ymeth.2019.05.025

Quantification and modelling of curvilinear structures in 2D and 3D images is a common challenge in a wide range of biomedical applications. Image enhancement is a crucial pre-processing step for curvilinear structure quantification. Many of the exis... Read More about The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images.

Sequential graph-based extraction of curvilinear structures (2019)
Journal Article
Alharbi, S. S., Willcocks, C., Jackson, P. T., Alhasson, H. F., & Obara, B. (2019). Sequential graph-based extraction of curvilinear structures. Signal, Image and Video Processing, 13(5), 941-949. https://doi.org/10.1007/s11760-019-01431-6

In this paper, a new approach is proposed to extract an ordered sequence of curvilinear structures in images, capturing the largest and most influential paths first and then progressively extracting smaller paths until a prespecified size is reached.... Read More about Sequential graph-based extraction of curvilinear structures.

The multiscale bowler-hat transform for blood vessel enhancement in retinal images (2018)
Journal Article
Sazak, C., Nelson, C. J., & Obara, B. (2019). The multiscale bowler-hat transform for blood vessel enhancement in retinal images. Pattern Recognition, 88, 739-750. https://doi.org/10.1016/j.patcog.2018.10.011

Enhancement, followed by segmentation, quantification and modelling of blood vessels in retinal images plays an essential role in computer-aided retinopathy diagnosis. In this paper, we introduce the bowler-hat transform method a new approach based o... Read More about The multiscale bowler-hat transform for blood vessel enhancement in retinal images.

Interactive GPU Active Contours for Segmenting Inhomogeneous Objects (2017)
Journal Article
Willcocks, C. G., Jackson, P. T., Nelson, C. J., Nasrulloh, A., & Obara, B. (2019). Interactive GPU Active Contours for Segmenting Inhomogeneous Objects. Journal of Real-Time Image Processing, 16(6), 2305-2318. https://doi.org/10.1007/s11554-017-0740-1

We present a segmentation software package primarily targeting medical and biological applications, with a high level of visual feedback and several usability enhancements over existing packages. Specifically, we provide a substantially faster GPU im... Read More about Interactive GPU Active Contours for Segmenting Inhomogeneous Objects.

Threonine 150 phosphorylation of keratin 5 is linked to EBS and regulates filament assembly, cell cycle and oxidative stress response (2017)
Journal Article
Sawant, M., Schwarz, N., Windoffer, R., Magin, T., Krieger, J., Mucke, N., …Leube, R. E. (2018). Threonine 150 phosphorylation of keratin 5 is linked to EBS and regulates filament assembly, cell cycle and oxidative stress response. Journal of Investigative Dermatology, 138(3), 627-636. https://doi.org/10.1016/j.jid.2017.10.011

A characteristic feature of the skin blistering disease epidermolysis bullosa simplex is keratin filament (KF) network collapse caused by aggregation of the basal epidermal keratin type II (KtyII) K5 and its type I partner keratin 14 (K14). Here, we... Read More about Threonine 150 phosphorylation of keratin 5 is linked to EBS and regulates filament assembly, cell cycle and oxidative stress response.

Multi-scale Segmentation and Surface Fitting for Measuring 3D Macular Holes (2017)
Journal Article
Nasrulloh, A., Willcocks, C., Jackson, P., Geenen, C., Habib, M., Steel, D., & Obara, B. (2018). Multi-scale Segmentation and Surface Fitting for Measuring 3D Macular Holes. IEEE Transactions on Medical Imaging, 37(2), 580-589. https://doi.org/10.1109/tmi.2017.2767908

Macular holes are blinding conditions where a hole develops in the central part of retina, resulting in reduced central vision. The prognosis and treatment options are related to a number of variables including the macular hole size and shape. High-r... Read More about Multi-scale Segmentation and Surface Fitting for Measuring 3D Macular Holes.

Automated analysis of Physarum network structure and dynamics (2017)
Journal Article
Fricker, M. D., Akita, D., Heaton, L. L., Jones, N., Obara, B., & Nakagaki, T. (2017). Automated analysis of Physarum network structure and dynamics. Journal of Physics D: Applied Physics, 50(25), Article 254005. https://doi.org/10.1088/1361-6463/aa72b9

We evaluate different ridge-enhancement and segmentation methods to automatically extract the network architecture from time-series of Physarum plasmodia withdrawing from an arena via a single exit. Whilst all methods gave reasonable results, judged... Read More about Automated analysis of Physarum network structure and dynamics.

Extracting 3D parametric curves from 2D images of helical objects (2016)
Journal Article
Willcocks, C., Jackson, P. T., Nelson, C. J., & Obara, B. (2016). Extracting 3D parametric curves from 2D images of helical objects. IEEE Transactions on Pattern Analysis and Machine Intelligence, 39(9), 1757-1769. https://doi.org/10.1109/tpami.2016.2613866

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosi... Read More about Extracting 3D parametric curves from 2D images of helical objects.

Evolution of Electronic Circuits using Carbon Nanotube Composites (2016)
Journal Article
Massey, M., Kotsialos, A., Volpati, D., Vissol-Gaudin, E., Pearson, C., Bowen, L., …Petty, M. (2016). Evolution of Electronic Circuits using Carbon Nanotube Composites. Scientific Reports, 6, Article 32197. https://doi.org/10.1038/srep32197

Evolution-in-materio concerns the computer controlled manipulation of material systems using external stimuli to train or evolve the material to perform a useful function. In this paper we demonstrate the evolution of a disordered composite material,... Read More about Evolution of Electronic Circuits using Carbon Nanotube Composites.

Blobs and curves: object-based colocalisation for plant cells (2014)
Journal Article
Nelson, C., Duckney, P., Hawkins, T., Deeks, M., Laissue, P., Hussey, P., & Obara, B. (2014). Blobs and curves: object-based colocalisation for plant cells. Functional Plant Biology, 42(5), 471-485. https://doi.org/10.1071/fp14047

Blobs and curves occur everywhere in plant bioimaging: from signals of fluorescence-labelled proteins, through cytoskeletal structures, nuclei staining and cell extensions such as root hairs. Here we look at the problem of colocalisation of blobs wit... Read More about Blobs and curves: object-based colocalisation for plant cells.

Bacterial cell identification in differential interference contrast microscopy images (2013)
Journal Article
Obara, B., Roberts, M. A., Armitage, J. P., & Grau, V. (2013). Bacterial cell identification in differential interference contrast microscopy images. BMC Bioinformatics, 14, Article 134. https://doi.org/10.1186/1471-2105-14-134

Background: Microscopy image segmentation lays the foundation for shape analysis, motion tracking, and classification of biological objects. Despite its importance, automated segmentation remains challenging for several widely used non-fluorescence,... Read More about Bacterial cell identification in differential interference contrast microscopy images.

Variability in the control of cell division underlies sepal epidermal patterning in Arabidopsis thaliana (2010)
Journal Article
Roeder, A. H., Chickarmane, V., Cunha, A., Obara, B., Manjunath, B., & Meyerowitz, E. M. (2010). Variability in the control of cell division underlies sepal epidermal patterning in Arabidopsis thaliana. PLoS Biology, 8(5), Article e1000367. https://doi.org/10.1371/journal.pbio.1000367

How growth and proliferation are precisely controlled in organs during development and how the regulation of cell division contributes to the formation of complex cell type patterns are important questions in developmental biology. Such a pattern of... Read More about Variability in the control of cell division underlies sepal epidermal patterning in Arabidopsis thaliana.

Bisque: a platform for bioimage analysis and management (2009)
Journal Article
Kvilekval, K., Fedorov, D., Obara, B., Singh, A. K., & Manjunath, B. (2010). Bisque: a platform for bioimage analysis and management. Bioinformatics, 26(4), 544-552. https://doi.org/10.1093/bioinformatics/btp699

Motivation: Advances in the field of microscopy have brought about the need for better image management and analysis solutions. Novel imaging techniques have created vast stores of images and metadata that are difficult to organize, search, process a... Read More about Bisque: a platform for bioimage analysis and management.