Stuart King

Jamie Burke, Justin Engelmann, Charlene Hamid et al.

Purpose: To develop an open-source, fully-automatic deep learning algorithm, DeepGPET, for choroid region segmentation in optical coherence tomography (OCT) data. Methods: We used a dataset of 715 OCT B-scans (82 subjects, 115 eyes) from 3 clinical studies related to systemic disease. Ground truth segmentations were generated using a clinically validated, semi-automatic choroid segmentation method, Gaussian Process Edge Tracing (GPET). We finetuned a UNet with MobileNetV3 backbone pre-trained on ImageNet. Standard segmentation agreement metrics, as well as derived measures of choroidal thickness and area, were used to evaluate DeepGPET, alongside qualitative evaluation from a clinical ophthalmologist. Results: DeepGPET achieves excellent agreement with GPET on data from 3 clinical studies (AUC=0.9994, Dice=0.9664; Pearson correlation of 0.8908 for choroidal thickness and 0.9082 for choroidal area), while reducing the mean processing time per image on a standard laptop CPU from 34.49s ($\pm$15.09) using GPET to 1.25s ($\pm$0.10) using DeepGPET. Both methods performed similarly according to a clinical ophthalmologist, who qualitatively judged a subset of segmentations by GPET and DeepGPET, based on smoothness and accuracy of segmentations. Conclusions: DeepGPET, a fully-automatic, open-source algorithm for choroidal segmentation, will enable researchers to efficiently extract choroidal measurements, even for large datasets. As no manual interventions are required, DeepGPET is less subjective than semi-automatic methods and could be deployed in clinical practice without necessitating a trained operator.

Jamie Burke, Justin Engelmann, Samuel Gibbon et al.

Optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO) of the eye has become essential to ophthalmology and the emerging field of oculomics, thus requiring a need for transparent, reproducible, and rapid analysis of this data for clinical research and the wider research community. Here, we introduce OCTolyzer, the first open-source toolkit for retinochoroidal analysis in OCT/SLO data. It features two analysis suites for OCT and SLO data, facilitating deep learning-based anatomical segmentation and feature extraction of the cross-sectional retinal and choroidal layers and en face retinal vessels. We describe OCTolyzer and evaluate the reproducibility of its OCT choroid analysis. At the population level, metrics for choroid region thickness were highly reproducible, with a mean absolute error (MAE)/Pearson correlation for macular volume choroid thickness (CT) of 6.7$μ$m/0.99, macular B-scan CT of 11.6$μ$m/0.99, and peripapillary CT of 5.0$μ$m/0.99. Macular choroid vascular index (CVI) also showed strong reproducibility, with MAE/Pearson for volume CVI yielding 0.0271/0.97 and B-scan CVI 0.0130/0.91. At the eye level, measurement noise for regional and vessel metrics was below 5% and 20% of the population's variability, respectively. Outliers were caused by poor-quality B-scans with thick choroids and invisible choroid-sclera boundary. Processing times on a laptop CPU were under three seconds for macular/peripapillary B-scans and 85 seconds for volume scans. OCTolyzer can convert OCT/SLO data into reproducible and clinically meaningful retinochoroidal features and will improve the standardisation of ocular measurements in OCT/SLO image analysis, requiring no specialised training or proprietary software to be used. OCTolyzer is freely available here: https://github.com/jaburke166/OCTolyzer.

Johannes N. Hansen, Edward T. A. Mitchard, Stuart King

Forests are vital for the wellbeing of our planet. Large and small scale deforestation across the globe is threatening the stability of our climate, forest biodiversity, and therefore the preservation of fragile ecosystems and our natural habitat as a whole. With increasing public interest in climate change issues and forest preservation, a large demand for carbon offsetting, carbon footprint ratings, and environmental impact assessments is emerging. Most often, deforestation maps are created from optical data such as Landsat and MODIS. These maps are not typically available at less than annual intervals due to persistent cloud cover in many parts of the world, especially the tropics where most of the world's forest biomass is concentrated. Synthetic Aperture Radar (SAR) can fill this gap as it penetrates clouds. We propose and evaluate a novel method for deforestation detection in the absence of reliable reference data which often constitutes the largest practical hurdle. This method achieves a change detection sensitivity (producer's accuracy) of 96.5% in the study area, although false positives lead to a lower user's accuracy of about 75.7%, with a total balanced accuracy of 90.4%. The change detection accuracy is maintained when adding up to 20% noise to the reference labels. While further work is required to reduce the false positive rate, improve detection delay, and validate this method in additional circumstances, the results show that Sentinel-1 data have the potential to advance the timeliness of global deforestation monitoring.

Justin Engelmann, Jamie Burke, Charlene Hamid et al.

Purpose: To develop Choroidalyzer, an open-source, end-to-end pipeline for segmenting the choroid region, vessels, and fovea, and deriving choroidal thickness, area, and vascular index. Methods: We used 5,600 OCT B-scans (233 subjects, 6 systemic disease cohorts, 3 device types, 2 manufacturers). To generate region and vessel ground-truths, we used state-of-the-art automatic methods following manual correction of inaccurate segmentations, with foveal positions manually annotated. We trained a U-Net deep-learning model to detect the region, vessels, and fovea to calculate choroid thickness, area, and vascular index in a fovea-centred region of interest. We analysed segmentation agreement (AUC, Dice) and choroid metrics agreement (Pearson, Spearman, mean absolute error (MAE)) in internal and external test sets. We compared Choroidalyzer to two manual graders on a small subset of external test images and examined cases of high error. Results: Choroidalyzer took 0.299 seconds per image on a standard laptop and achieved excellent region (Dice: internal 0.9789, external 0.9749), very good vessel segmentation performance (Dice: internal 0.8817, external 0.8703) and excellent fovea location prediction (MAE: internal 3.9 pixels, external 3.4 pixels). For thickness, area, and vascular index, Pearson correlations were 0.9754, 0.9815, and 0.8285 (internal) / 0.9831, 0.9779, 0.7948 (external), respectively (all p<0.0001). Choroidalyzer's agreement with graders was comparable to the inter-grader agreement across all metrics. Conclusions: Choroidalyzer is an open-source, end-to-end pipeline that accurately segments the choroid and reliably extracts thickness, area, and vascular index. Especially choroidal vessel segmentation is a difficult and subjective task, and fully-automatic methods like Choroidalyzer could provide objectivity and standardisation.

Jamie Burke, Samuel Gibbon, Justin Engelmann et al.

Purpose: The purpose of this study was to introduce SLOctolyzer: an open-source analysis toolkit for en face retinal vessels in infrared reflectance scanning laser ophthalmoscopy (SLO) images. Methods: SLOctolyzer includes two main modules: segmentation and measurement. The segmentation module uses deep learning methods to delineate retinal anatomy, and detects the fovea and optic disc, whereas the measurement module quantifies the complexity, density, tortuosity, and calibre of the segmented retinal vessels. We evaluated the segmentation module using unseen data and measured its reproducibility. Results: SLOctolyzer's segmentation module performed well against unseen internal test data (Dice for all-vessels = 0.91; arteries = 0.84; veins = 0.85; optic disc = 0.94; and fovea = 0.88). External validation against severe retinal pathology showed decreased performance (Dice for arteries = 0.72; veins = 0.75; and optic disc = 0.90). SLOctolyzer had good reproducibility (mean difference for fractal dimension = -0.001; density = -0.0003; calibre = -0.32 microns; and tortuosity density = 0.001). SLOctolyzer can process a 768 x 768 pixel macula-centred SLO image in under 20 seconds and a disc-centred SLO image in under 30 seconds using a laptop CPU. Conclusions: To our knowledge, SLOctolyzer is the first open-source tool to convert raw SLO images into reproducible and clinically meaningful retinal vascular parameters. SLO images are captured simultaneous to optical coherence tomography (OCT), and we believe SLOctolyzer will be useful for extracting retinal vascular measurements from large OCT image sets and linking them to ocular or systemic diseases. It requires no specialist knowledge or proprietary software, and allows manual correction of segmentations and re-computing of vascular metrics. SLOctolyzer is freely available at https://github.com/jaburke166/SLOctolyzer.

Jamie Burke, Justin Engelmann, Charlene Hamid et al.

The choroid is a key vascular layer of the eye, supplying oxygen to the retinal photoreceptors. Non-invasive enhanced depth imaging optical coherence tomography (EDI-OCT) has recently improved access and visualisation of the choroid, making it an exciting frontier for discovering novel vascular biomarkers in ophthalmology and wider systemic health. However, current methods to measure the choroid often require use of multiple, independent semi-automatic and deep learning-based algorithms which are not made open-source. Previously, Choroidalyzer -- an open-source, fully automatic deep learning method trained on 5,600 OCT B-scans from 385 eyes -- was developed to fully segment and quantify the choroid in EDI-OCT images, thus addressing these issues. Using the same dataset, we propose a Robust, Resolution-agnostic and Efficient Attention-based network for CHoroid segmentation (REACH). REACHNet leverages multi-resolution training with domain-specific data augmentation to promote generalisation, and uses a lightweight architecture with resolution-agnostic self-attention which is not only faster than Choroidalyzer's previous network (4 images/s vs. 2.75 images/s on a standard laptop CPU), but has greater performance for segmenting the choroid region, vessels and fovea (Dice coefficient for region 0.9769 vs. 0.9749, vessels 0.8612 vs. 0.8192 and fovea 0.8243 vs. 0.3783) due to its improved hyperparameter configuration and model training pipeline. REACHNet can be used with Choroidalyzer as a drop-in replacement for the original model and will be made available upon publication.

Jamie Burke, Stuart King

We introduce a novel edge tracing algorithm using Gaussian process regression. Our edge-based segmentation algorithm models an edge of interest using Gaussian process regression and iteratively searches the image for edge pixels in a recursive Bayesian scheme. This procedure combines local edge information from the image gradient and global structural information from posterior curves, sampled from the model's posterior predictive distribution, to sequentially build and refine an observation set of edge pixels. This accumulation of pixels converges the distribution to the edge of interest. Hyperparameters can be tuned by the user at initialisation and optimised given the refined observation set. This tunable approach does not require any prior training and is not restricted to any particular type of imaging domain. Due to the model's uncertainty quantification, the algorithm is robust to artefacts and occlusions which degrade the quality and continuity of edges in images. Our approach also has the ability to efficiently trace edges in image sequences by using previous-image edge traces as a priori information for consecutive images. Various applications to medical imaging and satellite imaging are used to validate the technique and comparisons are made with two commonly used edge tracing algorithms.