A publicly available vessel segmentation algorithm for SLO images

Background and Objective: Infra-red scanning laser ophthalmoscope (IRSLO) images are akin to colour fundus photographs in displaying the posterior pole and retinal vasculature fine detail. While there are many trained networks readily available for retinal vessel segmentation in colour fundus photographs, none cater to IRSLO images. Accordingly, we aimed to develop (and release as open source) a vessel segmentation algorithm tailored specifically to IRSLO images. Materials and Methods: We used 23 expertly annotated IRSLO images from the RAVIR dataset, combined with 7 additional images annotated in-house. We trained a U-Net (convolutional neural network) to label pixels as 'vessel' or 'background'. Results: On an unseen test set (4 images), our model achieved an AUC of 0.981, and an AUPRC of 0.815. Upon thresholding, it achieved a sensitivity of 0.844, a specificity of 0.983, and an F1 score of 0.857. Conclusion: We have made our automatic segmentation algorithm publicly available and easy to use. Researchers can use the generated vessel maps to compute metrics such as fractal dimension and vessel density.

A method for quantifying sectoral optic disc pallor in fundus photographs and its association with peripapillary RNFL thickness

Purpose: To develop an automatic method of quantifying optic disc pallor in fundus photographs and determine associations with peripapillary retinal nerve fibre layer (pRNFL) thickness. Methods: We used deep learning to segment the optic disc, fovea, and vessels in fundus photographs, and measured pallor. We assessed the relationship between pallor and pRNFL thickness derived from optical coherence tomography scans in 118 participants. Separately, we used images diagnosed by clinical inspection as pale (N=45) and assessed how measurements compared to healthy controls (N=46). We also developed automatic rejection thresholds, and tested the software for robustness to camera type, image format, and resolution. Results: We developed software that automatically quantified disc pallor across several zones in fundus photographs. Pallor was associated with pRNFL thickness globally (\b{eta} = -9.81 (SE = 3.16), p < 0.05), in the temporal inferior zone (\b{eta} = -29.78 (SE = 8.32), p < 0.01), with the nasal/temporal ratio (\b{eta} = 0.88 (SE = 0.34), p < 0.05), and in the whole disc (\b{eta} = -8.22 (SE = 2.92), p < 0.05). Furthermore, pallor was significantly higher in the patient group. Lastly, we demonstrate the analysis to be robust to camera type, image format, and resolution. Conclusions: We developed software that automatically locates and quantifies disc pallor in fundus photographs and found associations between pallor measurements and pRNFL thickness. Translational relevance: We think our method will be useful for the identification, monitoring and progression of diseases characterized by disc pallor/optic atrophy, including glaucoma, compression, and potentially in neurodegenerative disorders.

Cross-linguistically Consistent Semantic and Syntactic Annotation of Child-directed Speech

While corpora of child speech and child-directed speech (CDS) have enabled major contributions to the study of child language acquisition, semantic annotation for such corpora is still scarce and lacks a uniform standard. We compile two CDS corpora with sentential logical forms, one in English and the other in Hebrew. In compiling the corpora we employ a methodology that enforces a cross-linguistically consistent representation, building on recent advances in dependency representation and semantic parsing. The corpora are based on a sizable portion of Brown's Adam corpus from CHILDES (about 80% of its child-directed utterances), and to all child-directed utterances from Berman's Hebrew CHILDES corpus Hagar. We begin by annotating the corpora with the Universal Dependencies (UD) scheme for syntactic annotation, motivated by its applicability to a wide variety of domains and languages. We then proceed by applying an automatic method for transducing sentential logical forms (LFs) from UD structures. The two representations have complementary strengths: UD structures are language-neutral and support direct annotation, whereas LFs are neutral as to the interface between syntax and semantics, and transparently encode semantic distinctions. We verify the quality of the annotated UD annotation using an inter-annotator agreement study. We then demonstrate the utility of the compiled corpora through a longitudinal corpus study of the prevalence of different syntactic and semantic phenomena.