A design for an automated Optical Coherence Tomography analysis system

Karthik Gopinath


Age related macula degeneration (AMD), Cystoid Macular Edema (CME) and glaucoma are retinal diseases that affects vision and often lead to irreversible blindness. Many imaging modalities have been used for screening of retinal diseases. Optical coherence tomography (OCT) is one such imaging modality that provides structural information of retina. Optical coherence tomography angiography (OCTA) also provides vascular information of retina in addition to structural information. With advancement in OCT and OCTA technology, the number of patients being scanned using these modalities is increasing exponentially. Manual analysis of vast data often makes human experts feel fatigue. Also, this extends the time to treat any patient and creates a demand to develop a fast and accurate automated OCT image analysis system. The system proposed in this thesis aims at analysing retinal anatomy and its diseases. We approach the problem of automatically analysing the retinal anatomy by segmenting its layers using a deep learning framework. In literature these algorithms usually requires preprocessing steps, such as denoising, image flatenning and edge detection, all of which involve separate parameter tunings. We propose a deep learning technique to automate all these steps and handle the presence/absence of pathologies. This model consists of a combination of Convolutional Neural Network (CNN) and Long Short Term Memory (LSTM). The CNN is used to extract layers of interest image and extract the edges, while the LSTM is used to trace the layer boundary. This model is trained on a mixture of normal and AMD cases using minimal data. Validation results on three public datasets show that the pixel-wise mean absolute error obtained with our system is 1.30 ± 0.48 which is lower than inter-marker error of 1.79 ± 0.76. The performance of the proposed module is also on par with the existing methods. We next propose three modules for disease analysis, first for diagnosing them at volume level, second at slice level and finally at pixel level by segmenting the abnormality. Firstly, we propose a novel method for glaucoma assessment at volume level using data from OCTA modality. The goal of this module is to gain insights about glaucoma indicators from both structural information (OCT volume) and vascular information (angioflow images). The proposed method achieves a mean sensitivity of 94% specificity of 91% and accuracy of 92% on 49 normal and 18 glaucomatous volumes. Secondly, for slice level disease(AMD and CME) classification from OCT volumes, we learn a decision boundary using a CNN in the new extremal representation space ofan image. Evaluating on four publically available datasets with training set consisting of 3500 OCT slices and test set having 1995 OCT slices, this module achieves a mean sensitivity of 96%. specificity of 97% and accuracy of 96%. Finally, we propose an automated cyst segmentation algorithm from OCT volumes. We propose a biologically inspired method based on selective enhancement of the cysts, by inducing motion to a given OCT slice. A CNN is designed to learn a mapping function that combines the result of multiple such motions to produce a probability map for cyst locations in a given slice. The final segmentation of cysts is obtained via a simple clustering of the detected cyst locations. The proposed method is trained on OPTIMA Cyst segmentation challenge (OCSC) train test and achieves a mean Dice Coefficient (DC) of 0.71, 0.69 and 0.79 on the OCSC test set, DME dataset and AEI dataset respectively. Thus, the complete system can be employed in screening scenarios to aid retinal experts in accurate and faster analysis of retinal anatomy and disease.


Year of completion:  July 2017
 Advisor : Jayanthi Sivaswamy

Related Publications

  • Karthik G and Jayanthi Sivaswamy - Segmentation of retinal cysts from Optical Coherence Tomography volumes via selective enhancement IEEE Journal of Biomedical Health Informatics 2018 [PDF]

  • Karthik G, Rangrej S and Jayanthi Sivaswamy - A deep learning framework for segmentation of retinal layers from OCT images ACPR, Nanjing [PDF]

  • Karthik Gopinath, Jayanthi Sivaswamy and Tarannum Mansoori - Automatic Glaucoma Assessment from Angio-OCT Images Proc. of IEEE International Symposium on Bio-Medical Imaging(ISBI), 2016, 13 - 16 April, 2016, Prague. [PDF]