Retinal layer segmentation in rodent OCT images: Local intensity profiles & fully convolutional neural networks
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Retinal layer segmentation in rodent OCT images : Local intensity profiles & fully convolutional neural networks. / Morales, Sandra; Colomer, Adrián; Mossi, José M.; del Amor, Rocío; Woldbye, David; Klemp, Kristian; Larsen, Michael; Naranjo, Valery.
In: Computer Methods and Programs in Biomedicine, Vol. 198, 105788, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Retinal layer segmentation in rodent OCT images
T2 - Local intensity profiles & fully convolutional neural networks
AU - Morales, Sandra
AU - Colomer, Adrián
AU - Mossi, José M.
AU - del Amor, Rocío
AU - Woldbye, David
AU - Klemp, Kristian
AU - Larsen, Michael
AU - Naranjo, Valery
PY - 2021
Y1 - 2021
N2 - Background and Objective: Optical coherence tomography (OCT) is a useful technique to monitor retinal layer state both in humans and animal models. Automated OCT analysis in rats is of great relevance to study possible toxic effect of drugs and other treatments before human trials. In this paper, two different approaches to detect the most significant retinal layers in a rat OCT image are presented. Methods: One approach is based on a combination of local horizontal intensity profiles along with a new proposed variant of watershed transformation and the other is built upon an encoder-decoder convolutional network architecture. Results: After a wide validation, an averaged absolute distance error of 3.77 ± 2.59 and 1.90 ± 0.91 µm is achieved by both approaches, respectively, on a batch of the rat OCT database. After a second test of the deep-learning-based method using an unseen batch of the database, an averaged absolute distance error of 2.67 ± 1.25 µm is obtained. The rat OCT database used in this paper is made publicly available to facilitate further comparisons. Conclusions: Based on the obtained results, it was demonstrated the competitiveness of the first approach since outperforms the commercial Insight image segmentation software (Phoenix Research Labs) as well as its utility to generate labelled images for validation purposes speeding significantly up the ground truth generation process. Regarding the second approach, the deep-learning-based method improves the results achieved by the more conventional method and also by other state-of-the-art techniques. In addition, it was verified that the results of the proposed network can be generalized to new rat OCT images.
AB - Background and Objective: Optical coherence tomography (OCT) is a useful technique to monitor retinal layer state both in humans and animal models. Automated OCT analysis in rats is of great relevance to study possible toxic effect of drugs and other treatments before human trials. In this paper, two different approaches to detect the most significant retinal layers in a rat OCT image are presented. Methods: One approach is based on a combination of local horizontal intensity profiles along with a new proposed variant of watershed transformation and the other is built upon an encoder-decoder convolutional network architecture. Results: After a wide validation, an averaged absolute distance error of 3.77 ± 2.59 and 1.90 ± 0.91 µm is achieved by both approaches, respectively, on a batch of the rat OCT database. After a second test of the deep-learning-based method using an unseen batch of the database, an averaged absolute distance error of 2.67 ± 1.25 µm is obtained. The rat OCT database used in this paper is made publicly available to facilitate further comparisons. Conclusions: Based on the obtained results, it was demonstrated the competitiveness of the first approach since outperforms the commercial Insight image segmentation software (Phoenix Research Labs) as well as its utility to generate labelled images for validation purposes speeding significantly up the ground truth generation process. Regarding the second approach, the deep-learning-based method improves the results achieved by the more conventional method and also by other state-of-the-art techniques. In addition, it was verified that the results of the proposed network can be generalized to new rat OCT images.
KW - Convolutional neural networks
KW - Intensity profile
KW - Layer segmentation
KW - Optical coherence tomography
KW - Rat OCT
KW - Rodent OCT
U2 - 10.1016/j.cmpb.2020.105788
DO - 10.1016/j.cmpb.2020.105788
M3 - Journal article
C2 - 33130492
AN - SCOPUS:85093674753
VL - 198
JO - Computer Methods and Programs in Biomedicine
JF - Computer Methods and Programs in Biomedicine
SN - 0169-2607
M1 - 105788
ER -
ID: 255098733