ReLayer: a free, online tool for extracting retinal thickness from cross-platform OCT images

Purpose: To describe and evaluate a free, online tool for automatically segmenting optical coherence tomography (OCT) images from different devices and computing summary measures such as retinal thickness. Methods: ReLayer (https://relayer.online) is an online platform to which OCT scan images can be uploaded and analyzed. Results can be downloaded as plaintext (.csv) files. The segmentation method includes a novel, 1-dimensional active contour model, designed to locate the inner limiting membrane, inner/outer segmentand retinal pigment epithelium. The method, designed for B-scans from Heidelberg Engineering Spectralis, was adapted for Topcon 3D OCT-2000 and OptoVue AngioVue. The method was applied to scans from healthy and pathological eyes, and was validated against segmentation by the manufacturers, the 39IOWA Reference Algorithms,and manual segmentation. Results: Segmentation of a B-scan took≤ 1 second. In healthy eyes, mean difference in retinal thickness from ReLayer and the reference standard was below the resolution of the Spectralis and 3D OCT-2000, and slightly above the resolution of the AngioVue. In pathological eyes, ReLayer performed similarly to IOWA (p=0.97) and better than Spectralis (p<0.001)

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers

ReLayer: a free, online tool for extracting retinal thickness from cross-platform OCT images

Purpose: To describe and evaluate a free, online tool for automatically segmenting optical coherence tomography (OCT) images from different devices and computing summary measures such as retinal thickness. Methods: ReLayer (https://relayer.online) is an online platform to which OCT scan images can be uploaded and analyzed. Results can be downloaded as plaintext (.csv) files. The segmentation method includes a novel, one-dimensional active contour model, designed to locate the inner limiting membrane, inner/outer segment, and retinal pigment epithelium. The method, designed for B-scans from Heidelberg Engineering Spectralis, was adapted for Topcon 3D OCT-2000 and OptoVue AngioVue. The method was applied to scans from healthy and pathological eyes, and was validated against segmentation by the manufacturers, the IOWA Reference Algorithms, and manual segmentation. Results: Segmentation of a B-scan took 1 second. In healthy eyes, mean difference in retinal thickness from ReLayer and the reference standard was below the resolution of the Spectralis and 3D OCT-2000, and slightly above the resolution of the AngioVue. In pathological eyes, ReLayer performed similarly to IOWA (P ¼ 0.97) and better than Spectralis (P , 0.001). Conclusions: A free online platform (ReLayer) is capable of segmenting OCT scans with similar speed, accuracy, and reliability as the other tested algorithms, but offers greater accessibility. ReLayer could represent a valuable tool for researchers requiring the full segmentation, often not made available by commercial software. Translational Relevance: A free online platform (ReLayer) provides free, accessible segmentation of OCT images: data often not available via existing commercial software

Pheno4J: A gene to phenotype graph database

Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation. We have also developed an accompanying webserver with end-points to facilitate querying of the database