Quantifying the smoothness of different layers of the retina can potentially be an important and ... more Quantifying the smoothness of different layers of the retina can potentially be an important and practical biomarker in various pathologic conditions like diabetic retinopathy. The purpose of this study is to develop an automated machine learning algorithm which uses support vector regression method with wavelet kernel and automatically segments two hyperreflective retinal layers (inner plexiform layer (IPL) and outer plexiform layer (OPL)) in 50 optical coherence tomography (OCT) slabs and calculates the smoothness index (SI). The Bland–Altman plots, mean absolute error, root mean square error and signed error calculations revealed a modest discrepancy between the manual approach, used as the ground truth, and the corresponding automated segmentation of IPL/ OPL, as well as SI measurements in OCT slabs. It was concluded that the constructed algorithm may be employed as a reliable, rapid and convenient approach for segmenting IPL/OPL and calculating SI in the appropriate layers.
The purpose of current study was to introduce a new marker for discriminating different grades of... more The purpose of current study was to introduce a new marker for discriminating different grades of ptosis called Sector Area Index (SAI) and a semi-automated technique to calculate it. In this cross-sectional comparative case series, after choosing two points as the medial and lateral canthus and manually selecting the palpebral fissure region, a circle enclosing the intercanthal distance was automatically drawn. Finally, 15-degree-apart sectors are applied to the enclosed circle. SAI was measured automatically by dividing the area of each 15-degree sector marked with the upper eyelid contour by the total area of the sector marked with the edge of the surrounding circle. SAI values and inter-eye SAI differences were compared between patients with different grades of ptosis as well as normal patients. One hundred six eyes were recruited (30, 25, 27, and 24 eyes in the control, mild, moderate, and severe ptosis groups, respectively). Mean values of SAI in all sectors showed a decreasin...
Wireless capsule endoscopy (WCE) has provided us with the ability to non-invasively visualize the... more Wireless capsule endoscopy (WCE) has provided us with the ability to non-invasively visualize the gastrointestinal (GI) tract with high quality. This work presents an assistant diagnostic system to accelerate the costly and time-consuming process of manually evaluating captured videos. Due to the fact that the major portion of WCE frames is Normal, a diagnostic model with a high negative predictive value (NPV) is desired and is highly demanded by gastroenterologists. In this study, we have proposed six deep convolutional neural networks (DCNNs) to satisfy the need for high classification accuracy and high NPV. The proposed architectures consist of a convolutional part coming from some well-known trained networks and a specifically designed classifier part. VG_BFCG exhibited the best classification performance (test_acc:0.967, NPV: 0.989). As a contribution, we realized that the proposed architectures could avoid mislabeling new pathologies not included in the training dataset, which...
Choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence tomogr... more Choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence tomography (OCT) images for measuring and evaluating the choroidal vascular structure. CVI is the ratio of the choroidal luminal area (LA) to the total choroidal area (TCA). The automatic calculation of this index is important for ophthalmologists but has not yet been explored. In this study, we proposed a fully automated method based on deep learning for calculating CVI in three main steps: 1- segmentation of the choroidal boundary, 2- detection of the choroidal luminal vessels, and 3- computation of the CVI. The proposed method is evaluated in complex situations like the presence of diabetic retinopathy and pachychoroid spectrum. In pachychoroid spectrum, the choroid is thickened, and the boundary between choroid and sclera (sclerochoroidal junction) is blurred, which makes the segmentation more challenging. The proposed method is designed based on the U-Net model, and a new loss function is...
Fully automated and volumetric segmentation of critical tumors may play a crucial role in diagnos... more Fully automated and volumetric segmentation of critical tumors may play a crucial role in diagnosis and surgical planning. One of the most challenging tumor segmentation tasks is localization of Pancreatic Ductal Adenocarcinoma (PDAC). Exclusive application of conventional methods does not appear promising. Deep learning approaches has achieved great success in the computer aided diagnosis, especially in biomedical image segmentation. This paper introduces a framework based on convolutional neural network (CNN) for segmentation of PDAC mass and surrounding vessels in CT images by incorporating powerful classic features, as well. First, a 3D-CNN architecture is used to localize the pancreas region from the whole CT volume using 3D Local Binary Pattern (LBP) map of the original image. Segmentation of PDAC mass is subsequently performed using 2D attention U-Net and Texture Attention U-Net (TAU-Net). TAU-Net is introduced by fusion of dense Scale-Invariant Feature Transform (SIFT) and L...
The choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence to... more The choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence tomography (OCT) images for measuring and evaluating the choroidal vascular structure. The CVI is the ratio of the choroidal luminal area (LA) to the total choroidal area (TCA). The automatic calculation of this index is important for ophthalmologists but has not yet been explored. In this study, we proposed a fully automated method based on deep learning for calculating the CVI in three main steps: 1—segmentation of the choroidal boundary, 2—detection of the choroidal luminal vessels, and 3—computation of the CVI. The proposed method was evaluated in complex situations such as the presence of diabetic retinopathy and pachychoroid spectrum. In pachychoroid spectrum, the choroid is thickened, and the boundary between the choroid and sclera (sclerochoroidal junction) is blurred, which makes the segmentation more challenging. The proposed method was designed based on the U-Net model, and a ne...
Background: Despite the benefits of radioactive iodine (RAI) therapy as an adjunctive treatment f... more Background: Despite the benefits of radioactive iodine (RAI) therapy as an adjunctive treatment for thyroid cancer, it can be associated with several side effects. The main purpose of this study was to determine the changes in serum alkaline phosphatase (ALP), calcium (Ca), and parathyroid hormone (PTH) at different doses of RAI therapy among patients who were referred to the nuclear medicine department of Namazi Hospital, Shiraz. Materials and Methods: This cross-sectional study was conducted on 60 patients with papillary thyroid cancer who underwent RAI therapy at different doses of 100, 150, and 200 mCi. The ALP, Ca, and PTH levels of patients were measured before and 60 days after RAI therapy. Results: Our study revealed that RAI therapy at all doses significantly increased ALP level in comparison with baseline amounts (P≤0.05). However, changes in PTH and Ca levels were not significant among patients who received different doses of RAI (P˃0.05). Conclusion: RAI therapy could af...
Given the capacity of Optical Coherence Tomography (OCT) imaging to display symptoms of a wide va... more Given the capacity of Optical Coherence Tomography (OCT) imaging to display symptoms of 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 (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, deman...
Background To assess the impact of brachytherapy on macular microvasculature utilizing optical co... more Background To assess the impact of brachytherapy on macular microvasculature utilizing optical coherence tomography angiography (OCTA) in treated choroidal melanoma. Methods In this retrospective observational case series, we reviewed the recorded data of the patients with unilateral extramacular choroidal melanoma treated with ruthenium − 106 (106Ru) plaque radiotherapy with a follow-up period of more than 6 months. Automatically measured OCTA retinal parameters were analysed after image processing. Results Thirty-one eyes of 31 patients with the mean age of 51.1 years were recruited. Six eyes had no radiation maculopathy (RM). From 25 eyes with RM, nine eyes (36%) revealed a burnout macular microvasculature with imperceptible vascular details. Twenty-one non-irradiated fellow eyes from the enrolled patients were considered as the control group. Foveal and optic disc radiation dose had the highest value to predict the burnout pattern (ROC, AUC: 0.763, 0.727). Superficial and deep f...
Fuchs uveitis (FU) is a chronic and often unilateral ocular inflammation and characteristic iris ... more Fuchs uveitis (FU) is a chronic and often unilateral ocular inflammation and characteristic iris atrophic changes, other than heterochromia, are common in FU and are key to the correct diagnosis in many cases. With the advent of anterior segment optical coherence tomography (AS-OCT), some investigators attempted to quantitatively study these atrophic changes; mostly by introducing various methods to measure iris thickness in AS-OCT images. We aimed to present an automated method in an observational case series to measure the smoothness index (SI) of the iris surface in AS-OCT images. The ratio of the length of the straight line connecting the most peripheral and central points of the anterior iris border (in nasal and temporal sides) to the actual length of this border on AS-OCT images, was defined as SI. In a uveitis referral center, twenty-two eyes of 11 patients with unilateral Fuchs uveitis (FU) (7 female) and 22 eyes of 11 healthy control subjects underwent AS-OCT imaging. Imag...
Quantifying the smoothness of different layers of the retina can potentially be an important and ... more Quantifying the smoothness of different layers of the retina can potentially be an important and practical biomarker in various pathologic conditions like diabetic retinopathy. The purpose of this study is to develop an automated machine learning algorithm which uses support vector regression method with wavelet kernel and automatically segments two hyperreflective retinal layers (inner plexiform layer (IPL) and outer plexiform layer (OPL)) in 50 optical coherence tomography (OCT) slabs and calculates the smoothness index (SI). The Bland–Altman plots, mean absolute error, root mean square error and signed error calculations revealed a modest discrepancy between the manual approach, used as the ground truth, and the corresponding automated segmentation of IPL/ OPL, as well as SI measurements in OCT slabs. It was concluded that the constructed algorithm may be employed as a reliable, rapid and convenient approach for segmenting IPL/OPL and calculating SI in the appropriate layers.
The purpose of current study was to introduce a new marker for discriminating different grades of... more The purpose of current study was to introduce a new marker for discriminating different grades of ptosis called Sector Area Index (SAI) and a semi-automated technique to calculate it. In this cross-sectional comparative case series, after choosing two points as the medial and lateral canthus and manually selecting the palpebral fissure region, a circle enclosing the intercanthal distance was automatically drawn. Finally, 15-degree-apart sectors are applied to the enclosed circle. SAI was measured automatically by dividing the area of each 15-degree sector marked with the upper eyelid contour by the total area of the sector marked with the edge of the surrounding circle. SAI values and inter-eye SAI differences were compared between patients with different grades of ptosis as well as normal patients. One hundred six eyes were recruited (30, 25, 27, and 24 eyes in the control, mild, moderate, and severe ptosis groups, respectively). Mean values of SAI in all sectors showed a decreasin...
Wireless capsule endoscopy (WCE) has provided us with the ability to non-invasively visualize the... more Wireless capsule endoscopy (WCE) has provided us with the ability to non-invasively visualize the gastrointestinal (GI) tract with high quality. This work presents an assistant diagnostic system to accelerate the costly and time-consuming process of manually evaluating captured videos. Due to the fact that the major portion of WCE frames is Normal, a diagnostic model with a high negative predictive value (NPV) is desired and is highly demanded by gastroenterologists. In this study, we have proposed six deep convolutional neural networks (DCNNs) to satisfy the need for high classification accuracy and high NPV. The proposed architectures consist of a convolutional part coming from some well-known trained networks and a specifically designed classifier part. VG_BFCG exhibited the best classification performance (test_acc:0.967, NPV: 0.989). As a contribution, we realized that the proposed architectures could avoid mislabeling new pathologies not included in the training dataset, which...
Choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence tomogr... more Choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence tomography (OCT) images for measuring and evaluating the choroidal vascular structure. CVI is the ratio of the choroidal luminal area (LA) to the total choroidal area (TCA). The automatic calculation of this index is important for ophthalmologists but has not yet been explored. In this study, we proposed a fully automated method based on deep learning for calculating CVI in three main steps: 1- segmentation of the choroidal boundary, 2- detection of the choroidal luminal vessels, and 3- computation of the CVI. The proposed method is evaluated in complex situations like the presence of diabetic retinopathy and pachychoroid spectrum. In pachychoroid spectrum, the choroid is thickened, and the boundary between choroid and sclera (sclerochoroidal junction) is blurred, which makes the segmentation more challenging. The proposed method is designed based on the U-Net model, and a new loss function is...
Fully automated and volumetric segmentation of critical tumors may play a crucial role in diagnos... more Fully automated and volumetric segmentation of critical tumors may play a crucial role in diagnosis and surgical planning. One of the most challenging tumor segmentation tasks is localization of Pancreatic Ductal Adenocarcinoma (PDAC). Exclusive application of conventional methods does not appear promising. Deep learning approaches has achieved great success in the computer aided diagnosis, especially in biomedical image segmentation. This paper introduces a framework based on convolutional neural network (CNN) for segmentation of PDAC mass and surrounding vessels in CT images by incorporating powerful classic features, as well. First, a 3D-CNN architecture is used to localize the pancreas region from the whole CT volume using 3D Local Binary Pattern (LBP) map of the original image. Segmentation of PDAC mass is subsequently performed using 2D attention U-Net and Texture Attention U-Net (TAU-Net). TAU-Net is introduced by fusion of dense Scale-Invariant Feature Transform (SIFT) and L...
The choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence to... more The choroidal vascularity index (CVI) is a new biomarker defined for retinal optical coherence tomography (OCT) images for measuring and evaluating the choroidal vascular structure. The CVI is the ratio of the choroidal luminal area (LA) to the total choroidal area (TCA). The automatic calculation of this index is important for ophthalmologists but has not yet been explored. In this study, we proposed a fully automated method based on deep learning for calculating the CVI in three main steps: 1—segmentation of the choroidal boundary, 2—detection of the choroidal luminal vessels, and 3—computation of the CVI. The proposed method was evaluated in complex situations such as the presence of diabetic retinopathy and pachychoroid spectrum. In pachychoroid spectrum, the choroid is thickened, and the boundary between the choroid and sclera (sclerochoroidal junction) is blurred, which makes the segmentation more challenging. The proposed method was designed based on the U-Net model, and a ne...
Background: Despite the benefits of radioactive iodine (RAI) therapy as an adjunctive treatment f... more Background: Despite the benefits of radioactive iodine (RAI) therapy as an adjunctive treatment for thyroid cancer, it can be associated with several side effects. The main purpose of this study was to determine the changes in serum alkaline phosphatase (ALP), calcium (Ca), and parathyroid hormone (PTH) at different doses of RAI therapy among patients who were referred to the nuclear medicine department of Namazi Hospital, Shiraz. Materials and Methods: This cross-sectional study was conducted on 60 patients with papillary thyroid cancer who underwent RAI therapy at different doses of 100, 150, and 200 mCi. The ALP, Ca, and PTH levels of patients were measured before and 60 days after RAI therapy. Results: Our study revealed that RAI therapy at all doses significantly increased ALP level in comparison with baseline amounts (P≤0.05). However, changes in PTH and Ca levels were not significant among patients who received different doses of RAI (P˃0.05). Conclusion: RAI therapy could af...
Given the capacity of Optical Coherence Tomography (OCT) imaging to display symptoms of a wide va... more Given the capacity of Optical Coherence Tomography (OCT) imaging to display symptoms of 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 (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, deman...
Background To assess the impact of brachytherapy on macular microvasculature utilizing optical co... more Background To assess the impact of brachytherapy on macular microvasculature utilizing optical coherence tomography angiography (OCTA) in treated choroidal melanoma. Methods In this retrospective observational case series, we reviewed the recorded data of the patients with unilateral extramacular choroidal melanoma treated with ruthenium − 106 (106Ru) plaque radiotherapy with a follow-up period of more than 6 months. Automatically measured OCTA retinal parameters were analysed after image processing. Results Thirty-one eyes of 31 patients with the mean age of 51.1 years were recruited. Six eyes had no radiation maculopathy (RM). From 25 eyes with RM, nine eyes (36%) revealed a burnout macular microvasculature with imperceptible vascular details. Twenty-one non-irradiated fellow eyes from the enrolled patients were considered as the control group. Foveal and optic disc radiation dose had the highest value to predict the burnout pattern (ROC, AUC: 0.763, 0.727). Superficial and deep f...
Fuchs uveitis (FU) is a chronic and often unilateral ocular inflammation and characteristic iris ... more Fuchs uveitis (FU) is a chronic and often unilateral ocular inflammation and characteristic iris atrophic changes, other than heterochromia, are common in FU and are key to the correct diagnosis in many cases. With the advent of anterior segment optical coherence tomography (AS-OCT), some investigators attempted to quantitatively study these atrophic changes; mostly by introducing various methods to measure iris thickness in AS-OCT images. We aimed to present an automated method in an observational case series to measure the smoothness index (SI) of the iris surface in AS-OCT images. The ratio of the length of the straight line connecting the most peripheral and central points of the anterior iris border (in nasal and temporal sides) to the actual length of this border on AS-OCT images, was defined as SI. In a uveitis referral center, twenty-two eyes of 11 patients with unilateral Fuchs uveitis (FU) (7 female) and 22 eyes of 11 healthy control subjects underwent AS-OCT imaging. Imag...
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