Livelayer

Livelayer: a semi-automatic software program for segmentation of layers and diabetic macular edema in optical coherence tomography images

Given the capacity of Optical Coherence Tomography (OCT) imaging to display structural changes in a wide variety of eye diseases and neurological disorders, the need for OCT image segmentation and the corresponding data interpretation is latterly felt more than ever before. In this paper, we wish to address this need by designing a semi-automatic software program for applying reliable segmentation of 8 different macular layers as well as outlining retinal pathologies such as diabetic macular edema. The software accommodates a novel graph-based semi-automatic method, called “Livelayer” which is designed for straightforward segmentation of retinal layers and fluids. This method is chiefly based on Dijkstra’s Shortest Path First (SPF) algorithm and the Live-wire function together with some preprocessing operations on the to-be-segmented images. The software is indeed suitable for obtaining detailed segmentation of layers, exact localization of clear or unclear fluid objects and the ground truth, demanding far less endeavor in comparison to a common manual segmentation method. It is also valuable as a tool for calculating the irregularity index in deformed OCT images. The amount of time (seconds) that Livelayer required for segmentation of Inner Limiting Membrane, Inner Plexiform Layer–Inner Nuclear Layer, Outer Plexiform Layer–Outer Nuclear Layer was much less than that for the manual segmentation, 5 s for the ILM (minimum) and 15.57 s for the OPL–ONL (maximum). The unsigned errors (pixels) between the semi-automatically labeled and gold standard data was on average 2.7, 1.9, 2.1 for ILM, IPL–INL, OPL–ONL, respectively. The Bland–Altman plots indicated perfect concordance between the Livelayer and the manual algorithm and that they could be used interchangeably. The repeatability error was around one pixel for the OPL–ONL and < 1 for the other two. The unsigned errors between the Livelayer and the manual algorithm was 1.33 for ILM and 1.53 for Nerve Fiber Layer–Ganglion Cell Layer in peripapillary B-Scans. The Dice scores for comparing the two algorithms and for obtaining the repeatability on segmentation of fluid objects were at acceptable levels.

Supplementary Video

For further details of the performance of the software, please watch the video created as part of the supplementary material for the paper.

paper: https://www.nature.com/articles/s41598-021-92713-y#Abs1

code: github