nnUNet RASPP for Retinal OCT Fluid Detection, Segmentation and Generalisation over Variations of Data Sources

Abstract: Retinal Optical Coherence Tomography (OCT), a noninvasive cross-sectional scan of the eye with qualitative 3D visualization of the retinal anatomy is use to study the retinal structure and the presence of pathogens. The advent of the retinal OCT has transformed ophthalmology and it is currently paramount for the diagnosis, monitoring and treatment of many eye pathogens including Macular Edema which impairs vision severely or Glaucoma that can cause irreversible blindness. However the quality of retinal OCT images varies among device manufacturers. Deep Learning methods have had their success in the medical image segmentation community but it is still not clear if the level of success can be generalised across OCT images collected from different device vendors. In this work we propose two variants of the nnUNet [8]. The standard nnUNet and an enhanced vision call nnUnet_RASPP (nnU-Net with residual and Atrous Spatial Pyramid Pooling) both of which are robust and generalise with consistent high performance across images from multiple device vendors. The algorithm was validated on the MICCAI 2017 RETOUCH challenge dataset [1] acquired from 3 device vendors across 3 medical centers from patients suffering from 2 retinal disease types. Experimental results show that our algorithms outperform the current state-of-the-arts algorithms by a clear margin for segmentation obtaining a mean Dice Score (DS) of 82.3% for the 3 retinal fluids scoring 84.0%, 80.0%, 83.0% for Intraretinal Fluid (IRF), Subretinal Fluid (SRF), and Pigment Epithelium Detachments (PED) respectively on the testing dataset. Also we obtained a perfect Area Under the Curve (AUC) score of 100% for the detection of the presence of fluid for all 3 fluid classes on the testing dataset.