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Spatial statistical modelling of capillary non-perfusion in the retina

Ian J. C. MacCormick, Yalin Zheng, Silvester Czanner, Yitian Zhao, Peter J. Diggle, Simon P. Harding, Gabriela Czanner
2017 Scientific Reports  
Manual grading of lesions in retinal images is relevant to clinical management and clinical trials, but it is time-consuming and expensive. Furthermore, it collects only limited information -such as lesion size or frequency. The spatial distribution of lesions is ignored, even though it may contribute to the overall clinical assessment of disease severity, and correspond to microvascular and physiological topography. Capillary non-perfusion (CNP) lesions are central to the pathogenesis of major
more » ... causes of vision loss. Here we propose a novel method to analyse CNP using spatial statistical modelling. This quantifies the percentage of CNP-pixels in each of 48 sectors and then characterises the spatial distribution with goniometric functions. We applied our spatial approach to a set of images from patients with malarial retinopathy, and found it compares favourably with the raw percentage of CNP-pixels and also with manual grading. Furthermore, we were able to quantify a biological characteristic of macular CNP in malaria that had previously only been described subjectively: clustering at the temporal raphe. Microvascular location is likely to be biologically relevant to many diseases, and so our spatial approach may be applicable to a diverse range of pathological features in the retina and other organs. The retinal microcirculation is exquisitely accessible to clinical observation, and unlike other organs, the retinal vasculature is arranged perpendicular to an optical axis. Consequently alterations to small vessel flow can be easily mapped using techniques such as fluorescein angiography (FA) and optical coherence tomography angiography (OCT-A). Capillary non-perfusion (CNP) appears as distinctive dark areas with geographic boundaries, and develops when blood fails to reach areas of the capillary bed (Fig. 1a-c) . It is a feature of several major causes of blindness including diabetic maculopathy, retinal vein occlusion, and retinal artery occlusion 1 . CNP also occurs in malarial retinopathy, and can be graded manually according to a validated scheme 2 . Malarial retinopathy is seen in children and adults with cerebral malaria, which has a high mortality rate. The retina and brain sustain similar damage in cerebral malaria, and several retinal signs are associated with death (reviewed in 3 ). As with grading schemes for retinal vein occlusion 4,5 the malarial retinopathy grading scheme assesses the overall area of CNP in various large retinal regions. Manual grading is necessarily semi-quantitative, time consuming and costly. These and other constraints mean that manual grading is impractical for large image datasets, and at best captures only a tiny fraction of the biological information contained in a retinal image. Beyond lesion type, frequency, and area, spatial characteristics may be a particularly relevant aspect of a retinal image. This is because the retinal microvasculature is not homogenous but rather composed of regions with different vascular topology, geometry, and corresponding haemorheology and physiology. For example, the foveal avascular zone is a unique region where the retina is supplied solely from the underlying choriocapillaris. The perifoveal region has one capillary layer, which forms an oxygen diffusion watershed with the choriocapillaris. The temporal macula and horizontal raphe contain a further watershed between superior and inferior temporal arcades 3 . Therefore, the biological meaning of CNP in one sub-region of the macula may be different from that of a lesion of similar size in an adjacent region. Current grading techniques are too coarse to allow such distinctions.
doi:10.1038/s41598-017-16620-x pmid:29196702 pmcid:PMC5711887 fatcat:hfvvgjx5hvfhfescn5xiwmk4li

Automatic detection of glaucoma via fundus imaging and artificial intelligence: A review [article]

Lauren Coan, Bryan Williams, Krishna Adithya Venkatesh, Swati Upadhyaya, Silvester Czanner, Rengaraj Venkatesh, Colin E. Willoughby, Srinivasan Kavitha, Gabriela Czanner
2022 arXiv   pre-print
Gabriela Czanner, Dr. Silvester Czanner, Professor Colin E. Willoughby and Dr. Srinivasan Kavitha.  ... 
arXiv:2204.05591v1 fatcat:4vuterhtpvhgrka42euetn7hii

EffUnet-SpaGen: An Efficient and Spatial Generative Approach to Glaucoma Detection

Venkatesh Krishna Adithya, Bryan M. Williams, Silvester Czanner, Srinivasan Kavitha, David S. Friedman, Colin E. Willoughby, Rengaraj Venkatesh, Gabriela Czanner
2021 Journal of Imaging  
Current research in automated disease detection focuses on making algorithms "slimmer" reducing the need for large training datasets and accelerating recalibration for new data while achieving high accuracy. The development of slimmer models has become a hot research topic in medical imaging. In this work, we develop a two-phase model for glaucoma detection, identifying and exploiting a redundancy in fundus image data relating particularly to the geometry. We propose a novel algorithm for the
more » ... p and disc segmentation "EffUnet" with an efficient convolution block and combine this with an extended spatial generative approach for geometry modelling and classification, termed "SpaGen" We demonstrate the high accuracy achievable by EffUnet in detecting the optic disc and cup boundaries and show how our algorithm can be quickly trained with new data by recalibrating the EffUnet layer only. Our resulting glaucoma detection algorithm, "EffUnet-SpaGen", is optimized to significantly reduce the computational burden while at the same time surpassing the current state-of-art in glaucoma detection algorithms with AUROC 0.997 and 0.969 in the benchmark online datasets ORIGA and DRISHTI, respectively. Our algorithm also allows deformed areas of the optic rim to be displayed and investigated, providing explainability, which is crucial to successful adoption and implementation in clinical settings.
doi:10.3390/jimaging7060092 fatcat:dtggkwewxnfyrert3zinwmuum4

Learning Capacity in Simulated Virtual Neurological Procedures

Mattia Samuel Mancosu, Silvester Czanner, Martin Punter
2020 Journal of WSCG  
doi:10.24132/csrn.2020.3001.13 fatcat:uytlm7nytrhmnk553ellfhl54a

Growth animation of human organs

Roman ?urikovi?, Silvester Czanner, Hirofumi Inoue
2001 Journal of Visualization and Computer Animation  
The growth of the organs of human embryo is changing significantly over a short period of time in the mother body. The shape of the human organs is organic and has many folds that are difficult to model or animate with conventional techniques. Convolution surface and function representation are a good choice in modelling such organs as human embryo stomach and brain. Two approaches are proposed for animating the organ growth: First, uses a simple line segment skeleton demonstrated on a stomach
more » ... odel and the other method uses a tubular skeleton calculated automatically from a 2D object outline. The growth speed varies with the position within the organ and thus the model is divided into multiple geometric primitives that are later glued by a blending operation. Animation of both the embryo stomach and brain organs is shown.
doi:10.1002/vis.271 fatcat:5qqknudpfrgsnml7g7xhgpk6by

Applet Competition as an Educational Tool in Creating Novel e-Textbook [article]

Silvester Czanner, Andrej Ferko, Juraj Stugel, Pavla Nunukova
2009 Eurographics State of the Art Reports  
Czanner [DCPC99] . The aim of this project was to create video and shipping documents. Material on the videotape illustrated some graphics algorithms "in action".  ... 
doi:10.2312/eged.20091016 fatcat:w3sijaarfvhl5ovvcgn4lvykfi

Correction: Accurate, fast, data efficient and interpretable glaucoma diagnosis with automated spatial analysis of the whole cup to disc profile

Ian J. C. MacCormick, Bryan M. Williams, Yalin Zheng, Kun Li, Baidaa Al-Bander, Silvester Czanner, Rob Cheeseman, Colin E. Willoughby, Emery N. Brown, George L. Spaeth, Gabriela Czanner
2019 PLoS ONE  
Reference 1 . 1 MacCormick IJC, Williams BM, Zheng Y, Li K, Al-Bander B, Czanner S, et al. (2019) Accurate, fast, data efficient and interpretable glaucoma diagnosis with automated spatial analysis of  ...  10.1371/journal.pone.0215056 April 3, 2019 1 / 1 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: MacCormick IJC, Williams BM, Zheng Y, Li K, Al-Bander B, Czanner  ... 
doi:10.1371/journal.pone.0215056 fatcat:dv4oxwfqqvfmzf4v7balagfhmm

High Dynamic Range Video for Cultural Heritage Documentation and Experimental Archaeology [article]

Jassim Happa, Alessandro Artusi, Silvester Czanner, Alan Chalmers
2010 VAST: International Symposium on Virtual Reality  
Video recording and photography are frequently used to document Cultural Heritage (CH) objects and sites. High Dynamic Range (HDR) imaging is increasingly being used as it allows a wider range of light to be considered that most current technologies are unable to natively acquire and reproduce. HDR video content however has only recently become possible at desirable, high definition resolution and dynamic range. In this paper we explore the potential use of a 20 f-stop HDR video camera for CH
more » ... cumentation and experimental archaeology purposes. We discuss data acquisition of moving caustics, flames, distant light and in participating media. Comparisons of Low Dynamic Range (LDR) and HDR content are made to illustrate the additional data that this new technology is able to capture, and the benefits this is likely to bring to CH documentation and experimental archaeology.
doi:10.2312/vast/vast10/017-024 fatcat:okrnm6lavjfdrii5uvwstwtmea

Accurate, fast, data efficient and interpretable glaucoma diagnosis with automated spatial analysis of the whole cup to disc profile

Ian J. C. MacCormick, Bryan M. Williams, Yalin Zheng, Kun Li, Baidaa Al-Bander, Silvester Czanner, Rob Cheeseman, Colin E. Willoughby, Emery N. Brown, George L. Spaeth, Gabriela Czanner, Sanjoy Bhattacharya
2019 PLoS ONE  
Glaucoma is the leading cause of irreversible blindness worldwide. It is a heterogeneous group of conditions with a common optic neuropathy and associated loss of peripheral vision. Both over and under-diagnosis carry high costs in terms of healthcare spending and preventable blindness. The characteristic clinical feature of glaucoma is asymmetrical optic nerve rim narrowing, which is difficult for humans to quantify reliably. Strategies to improve and automate optic disc assessment are therefore needed to prevent sight loss.
doi:10.1371/journal.pone.0209409 pmid:30629635 pmcid:PMC6328156 fatcat:el4vtxvi4nggpm7hbrt3wloqy4

A High-Fidelity Virtual Environment for the Study of Paranoia

Matthew R. Broome, Eva Zányi, Thomas Hamborg, Elmedin Selmanovic, Silvester Czanner, Max Birchwood, Alan Chalmers, Swaran P. Singh
2013 Schizophrenia Research and Treatment  
Psychotic disorders carry social and economic costs for sufferers and society. Recent evidence highlights the risk posed by urban upbringing and social deprivation in the genesis of paranoia and psychosis. Evidence based psychological interventions are often not offered because of a lack of therapists. Virtual reality (VR) environments have been used to treat mental health problems. VR may be a way of understanding the aetiological processes in psychosis and increasing psychotherapeutic
more » ... s for its treatment. We developed a high-fidelity virtual reality scenario of an urban street scene to test the hypothesis that virtual urban exposure is able to generate paranoia to a comparable or greater extent than scenarios using indoor scenes. Participants (n=32) entered the VR scenario for four minutes, after which time their degree of paranoid ideation was assessed. We demonstrated that the virtual reality scenario was able to elicit paranoia in a nonclinical, healthy group and that an urban scene was more likely to lead to higher levels of paranoia than a virtual indoor environment. We suggest that this study offers evidence to support the role of exposure to factors in the urban environment in the genesis and maintenance of psychotic experiences and symptoms. The realistic high-fidelity street scene scenario may offer a useful tool for therapists.
doi:10.1155/2013/538185 pmid:24455255 pmcid:PMC3877649 fatcat:feor326denazfpo255ijtcgemq

Supervised classification of etoposide-treated in vitro adherent cells based on noninvasive imaging morphology

Anna Leida Mölder, Johan Persson, Zahra El-Schich, Silvester Czanner, Anette Gjörloff-Wingren
2017 Journal of Medical Imaging  
Acknowledgments The authors would like to thank Gabriela Czanner for invaluable comments on the statistics.  ... 
doi:10.1117/1.jmi.4.2.021106 pmid:28382315 pmcid:PMC5366068 fatcat:w7e375orfvg5bltassag4binvy

Adult bacterial conjunctivitis: resistance patterns over 12 years in patients attending a large primary eye care centre in the UK

Alexander Silvester, Timothy Neal, Gabriela Czanner, Michael Briggs, Simon Harding, Stephen Kaye
2016 BMJ Open Ophthalmology  
Staphylococcus aureus Streptococcus pneumoniae Silvester A, et al.  ...  Figure 1 1 Percentage of Staphylococcus aureus isolated resistant to methicillin Silvester A, et al.  ... 
doi:10.1136/bmjophth-2016-000006 pmid:29354693 pmcid:PMC5763641 fatcat:6fhks3b4vffedoq4lzhgjyrlla

Reliability in multi-site structural MRI studies: Effects of gradient non-linearity correction on phantom and human data

Jorge Jovicich, Silvester Czanner, Douglas Greve, Elizabeth Haley, Andre van der Kouwe, Randy Gollub, David Kennedy, Franz Schmitt, Gregory Brown, James MacFall, Bruce Fischl, Anders Dale
2006 NeuroImage  
Acknowledgments The authors thank: (a) our human phantoms, (b) Steve Pieper and Charles Guttmann (Brigham Women's Hospital) for coordinating the phantom scans at BWH, (c) Gabriela Czanner (Massachusetts  ... 
doi:10.1016/j.neuroimage.2005.09.046 pmid:16300968 fatcat:7ib6iwpi5ndohf7lbmgcmvpq5y

Reliability of MRI-derived measurements of human cerebral cortical thickness: The effects of field strength, scanner upgrade and manufacturer

Xiao Han, Jorge Jovicich, David Salat, Andre van der Kouwe, Brian Quinn, Silvester Czanner, Evelina Busa, Jenni Pacheco, Marilyn Albert, Ronald Killiany, Paul Maguire, Diana Rosas (+4 others)
2006 NeuroImage  
In vivo MRI-derived measurements of human cerebral cortex thickness are providing novel insights into normal and abnormal neuroanatomy, but little is known about their reliability. We investigated how the reliability of cortical thickness measurements is affected by MRI instrument-related factors, including scanner field strength, manufacturer, upgrade and pulse sequence. Several data processing factors were also studied. Two test -retest data sets were analyzed: 1) 15 healthy older subjects
more » ... nned four times at 2-week intervals on three scanners; 2) 5 subjects scanned before and after a major scanner upgrade. Within-scanner variability of global cortical thickness measurements was <0.03 mm, and the point-wise standard deviation of measurement error was approximately 0.12 mm. Variability was 0.15 mm and 0.17 mm in average, respectively, for cross-scanner (Siemens/GE) and cross-field strength (1.5 T/3 T) comparisons. Scanner upgrade did not increase variability nor introduce bias. Measurements across field strength, however, were slightly biased (thicker at 3 T). The number of (single vs. multiple averaged) acquisitions had a negligible effect on reliability, but the use of a different pulse sequence had a larger impact, as did different parameters employed in data processing. Sample size estimates indicate that regional cortical thickness difference of 0.2 mm between two different groups could be identified with as few as 7 subjects per group, and a difference of 0.1 mm could be detected with 26 subjects per group. These results demonstrate that MRI-derived cortical thickness measures are highly reliable when MRI instrument and data processing factors are controlled but that it is important to consider these factors in the design of multi-site or longitudinal studies, such as clinical drug trials. D
doi:10.1016/j.neuroimage.2006.02.051 pmid:16651008 fatcat:3ziatpskqnfx7mqtvrevf2cdym

MRI-derived measurements of human subcortical, ventricular and intracranial brain volumes: Reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths

Jorge Jovicich, Silvester Czanner, Xiao Han, David Salat, Andre van der Kouwe, Brian Quinn, Jenni Pacheco, Marilyn Albert, Ronald Killiany, Deborah Blacker
2009 NeuroImage  
We thank Gabriela Czanner, Mark Vangel and David Raunig for useful discussions on the statistical analyses of the data.  ...  ., 2005; Czanner et al., 2006) . Measurement of these reliability effects is especially important for longitudinal studies.  ... 
doi:10.1016/j.neuroimage.2009.02.010 pmid:19233293 pmcid:PMC2866077 fatcat:5jmoe77aubanrhzp2mv7wtr7ja
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