Automated detection of hyperreflective foci in the outer nuclear layer of the retina.

PURPOSE: Hyperreflective foci are poorly understood transient elements seen on optical coherence tomography (OCT) of the retina in both healthy and diseased eyes. Systematic studies may benefit from the development of automated tools that can map and track such foci. The outer nuclear layer (ONL) of the retina is an attractive layer in which to study hyperreflective foci as it has no fixed hyperreflective elements in healthy eyes. In this study, we intended to evaluate whether automated image analysis can identify, quantify and visualize hyperreflective foci in the ONL of the retina. METHODS: This longitudinal exploratory study investigated 14 eyes of seven patients including six patients with optic neuropathy and one with mild non-proliferative diabetic retinopathy. In total, 2596 OCT B-scan were obtained. An image analysis blob detector algorithm was used to detect candidate foci, and a convolutional neural network (CNN) trained on a manually labelled subset of data was then used to select those candidate foci in the ONL that fitted the characteristics of the reference foci best. RESULTS: In the manually labelled data set, the blob detector found 2548 candidate foci, correctly detecting 350 (89%) out of 391 manually labelled reference foci. The accuracy of CNN classifier was assessed by manually splitting the 2548 candidate foci into a training and validation set. On the validation set, the classifier obtained an accuracy of 96.3%, a sensitivity of 88.4% and a specificity of 97.5% (AUC 0.989). CONCLUSION: This study demonstrated that automated image analysis and machine learning methods can be used to successfully identify, quantify and visualize hyperreflective foci in the ONL of the retina on OCT scans.

Range-wide variation in grey seal (Halichoerus grypus) skull morphology.

The large interspecific variation in marine mammal skull and dental morphology reflects ecological specialisations to foraging and communication. At the intraspecific level, the drivers of skull shape variation are less well understood, having implications for identifying putative local foraging adaptations and delineating populations and subspecies for taxonomy, systematics, management and conservation. Here, we assess the range-wide intraspecific variation in 71 grey seal skulls by 3D surface scanning, collection of cranial landmarks and geometric morphometric analysis. We find that skull shape differs slightly between populations in the Northwest Atlantic, Northeast Atlantic and Baltic Sea. However, there was a large shape overlap between populations and variation was substantially larger among animals within populations than between. We hypothesize that this pattern of intraspecific variation in grey seal skull shape results from balancing selection or phenotypic plasticity allowing for a remarkably generalist foraging behaviour. Moreover, the large overlap in skull shape between populations implies that the separate subspecies status of Atlantic and Baltic Sea grey seals is questionable from a morphological point of view.

InSegtCone: interactive segmentation of crystalline cones in compound eyes.

BACKGROUND: Understanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography (micro-CT) is a promising high-throughput imaging technique that enables to reconstruct the 3D anatomy of eyes, but powerful tools are needed to perform fast conversions of anatomical reconstructions into functional eye models. RESULTS: We developed a computing method named InSegtCone to automatically segment the crystalline cones in the apposition compound eyes of arthropods. Here, we describe the full auto-segmentation process, showcase its application to three different insect compound eyes and evaluate its performance. The auto-segmentation could successfully label the full individual shapes of 60-80% of the crystalline cones and is about as accurate and 250 times faster than manual labelling of the individual cones. CONCLUSIONS: We believe that InSegtCone can be an important tool for peer scientists to measure the orientation, size and dynamics of crystalline cones, leading to the accurate optical modelling of the diversity of arthropod eyes with micro-CT.

Evaluation of 2D super-resolution ultrasound imaging of the rat renal vasculature using ex vivo micro-computed tomography.

Super-resolution ultrasound imaging (SRUS) enables in vivo microvascular imaging of deeper-lying tissues and organs, such as the kidneys or liver. The technique allows new insights into microvascular anatomy and physiology and the development of disease-related microvascular abnormalities. However, the microvascular anatomy is intricate and challenging to depict with the currently available imaging techniques, and validation of the microvascular structures of deeper-lying organs obtained with SRUS remains difficult. Our study aimed to directly compare the vascular anatomy in two in vivo 2D SRUS images of a Sprague-Dawley rat kidney with ex vivo µCT of the same kidney. Co-registering the SRUS images to the µCT volume revealed visually very similar vascular features of vessels ranging from ~ 100 to 1300 µm in diameter and illustrated a high level of vessel branching complexity captured in the 2D SRUS images. Additionally, it was shown that it is difficult to use µCT data of a whole rat kidney specimen to validate the super-resolution capability of our ultrasound scans, i.e., validating the actual microvasculature of the rat kidney. Lastly, by comparing the two imaging modalities, fundamental challenges for 2D SRUS were demonstrated, including the complexity of projecting a 3D vessel network into 2D. These challenges should be considered when interpreting clinical or preclinical SRUS data in future studies.

Determination of peripapillary vessel density in optic disc drusen using EDI-OCT and OCT angiography.

Optical coherence tomography angiography (OCTA) is a rapidly developing technique which generates angiographic images non-invasively. This study proposes a method to determine the vessel density in OCTA scans in general and especially the local peripapillary vessel density. The method produces vessel density heatmaps that contain information about the local vessel density. We apply the method in a small study to demonstrate its applicability and its potential to investigate the influence of local conditions on the vessel density. In the study, we combine information from enhanced depth imaging optical coherence tomography (EDI-OCT) about the location of optic disc drusen (ODD) with information from OCTA about the vessel density. We see a reduction in local peripapillary vessel density in peripapillary sections with a large volume of ODD.

Quantitatively Measured Anatomic Location and Volume of Optic Disc Drusen: An Enhanced Depth Imaging Optical Coherence Tomography Study.

Purpose: Optic disc drusen (ODD) are found in up to 2.4% of the population and are known to cause visual field defects. The purpose of the current study was to investigate how quantitatively estimated volume and anatomic location of ODD influence optic nerve function. Methods: Anatomic location, volume of ODD, and peripapillary retinal nerve fiber layer and macular ganglion cell layer thickness were assessed in 37 ODD patients using enhanced depth imaging optical coherence tomography. Volume of ODD was calculated by manual segmentation of ODD in 97 B-scans per eye. Anatomic characteristics were compared with optic nerve function using automated perimetric mean deviation (MD) and multifocal visual evoked potentials. Results: Increased age (P = 0.015); larger ODD volume (P = 0.002); and more superficial anatomic ODD location (P = 0.007) were found in patients with ODD visible by ophthalmoscopy compared to patients with buried ODD. In a multivariate analysis, a worsening of MD was significantly associated with larger ODD volume (P < 0.0001). No association was found between MD and weighted anatomic location, age, and visibility by ophthalmoscopy. Decreased ganglion cell layer thickness was significantly associated with worse MD (P = 0.025) and had a higher effect on MD when compared to retinal nerve fiber layer thickness. Conclusions: Large ODD volume is associated with optic nerve dysfunction. The worse visual field defects associated with visible ODD should only be ascribed to larger ODD volume and not to a more superficial anatomic ODD location.