segPLEX

PLEX Elite 9000 retinal B-scan segmentation and ETDRS grid

All previously preprocessed folders containing all files (e.g. ‘SamplePatient_01’, ‘SamplePatient_02’, etc.) should be inserted into a 'preprocessed' folder, which should be located inside the current directory (sample input dataset: https://www.kaggle.com/cnzakimuena/retinal-oct-and-octa-data-4).

The segmentation of PLEX Elite 9000 retinal B-scan (size 3mm x 3mm) retinal-vitreous interface (RVI), top and bottom retinal pigment epithelium (RPE), and Bruch’s membrane (BM) is provided. Two image segmentation algorithms are featured. The first consists of a cross-sectional pre-segmentation using A-scan gradients and an implementation of Dijkstra's shortest path algorithm [1]. The second approach is a refinement of the pre-segmentation and involves a graph-cuts algorithm [2]. The segmentation algorithms were previously described and implemented on OCT images generated using a different device [3].

An algorithm for structuring data into an Early Treatment Diabetic Retinopathy Study (ETDRS) grid [4] is also provided.

[1] G. Gallo and S. Pallottino, "Shortest path algorithms," Annals of operations research, vol. 13, no. 1, pp. 1-79, 1988.

[2] K. Li, X. Wu, D. Z. Chen, and M. Sonka, "Optimal surface segmentation in volumetric images-a graph-theoretic approach," IEEE transactions on pattern analysis and machine intelligence, vol. 28, no. 1, pp. 119-134, 2006.

[3] J. Mazzaferri, L. Beaton, G. Hounye, D. N. Sayah, and S. Costantino, "Open-source algorithm for automatic choroid segmentation of OCT volume reconstructions," Scientific reports, vol. 7, p. 42112, 2017.

[4] E. R. Group, "Classification of diabetic retinopathy from fluorescein angiograms," ETDRS report 1991.