Fudan University

MedMNIST v2 – A large-scale lightweight benchmark for 2D and 3D biomedical image classification

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MedMNIST v2 - A large-scale lightweight benchmark for 2D and 3D biomedical image classification We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28 × 28 (2D) or 28 × 28 × 28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 9,998 3D images in total, could support numerous research/educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D/3D neural networks and open-source/commercial AutoML tools. The data and code are publicly available at https://medm...

Corneal thickness measurements with the RTVue, Casia-2, and Pentacam devices in patients with mild-to-moderate keratoconus: a comparative study

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Background To compare the characteristics of corneal thickness measurements among the RTVue, Casia-2, and Pentacam in patients with mild-to-moderate keratoconus. Methods We recruited 46 eyes of 46 patients diagnosed with mild-to-moderate keratoconus at our hospital between January and March 2022. The central corneal thickness (CCT) and thinnest corneal thickness (TCT) were measured using two optical coherence tomography (OCT) instruments (RTVue and Casia-2) and the more conventional Pentacam. Differences and correlations between the CCTs and TCTs, based on the device and influencing factors, were explored. Results The CCTs were highly consistent among the groups (p = 0.434) and correlated with one another (p < 0.001). The TCTs measured by OCTs were thinner than those measured by the Pentacam (p < 0.001); however, all three devices were highly correlated (p < 0.001). The thinnest point location measurements with RTVue and Casia-2 differed significantly from ...

Associations Between the Retinal/Choroidal Microvasculature and Carotid Plaque in Patients with CHD: An Optical Coherence Tomography Angiography Study

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Background To investigate the associations between retinal/choroidal microvasculature and carotid plaque in patients with CHD assessed by optical coherence tomography angiography (OCTA). Methods This study included 127 CHD patients with and 79 without carotid plaque. Each patient had both OCTA taken and digitized to determine retinal/choroidal thickness, vessel density and flow area and carotid ultrasound for carotid plaque size and stability measurement. SCP, DCP, out retina and choriocapillaris vessel density, out retina and choriocapillaris flow area, and full retina thickness were analyzed in the fovea centered 6 × 6 mm area. The association between OCTA measurements and carotid plaque characteristics in patients with CHD were evaluated. Results The duration of hypertension and DM was significantly longer in CHD patients with carotid plaque than that without (p < 0.001). The mean values for vessel density SCP and DCP (except fovea zone), and choriocapillaris na...

Comprehensive comparisons of ocular biometry: A network-based big data analysis

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Purpose To systematically compare and rank ocular measurements with optical and ultrasound biometers based on big data. Methods PubMed, Embase, the Cochrane Library and the US trial registry (www.ClinicalTrial.gov) were used to systematically search trials published up to October 22nd, 2020. We included comparative studies reporting the following parameters measured by at least two devices: axial length (AL), flattest meridian keratometry (Kf), steepest meridian keratometry (Ks), mean keratometry (Km), astigmatism (AST), astigmatism vectors J0 and J45, anterior chamber depth (ACD), aqueous depth (AQD), central corneal thickness (CCT), corneal diameter (CD) and lens thickness (LT). A network-based big data analysis was conducted using STATA version 13.1. Results Across 129 studies involving 17,181 eyes, 12 optical biometers and two ultrasound biometers (with both contact and immersion techniques) were identified. A network meta-analysis for AL and ACD measurements found that...

Biometric measurement with a commercially available swept-source optical coherence tomography in myopia model species

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Background Biometric parameters play an important role in studies on myopia. This study aimed to explore the application of a commercially available two-dimensional visualized swept-source optical coherence tomography (OCT) system, for in vivo biometric measurement in multiple myopia model species. Methods In this study, chickens, guinea pigs, and C57BL/6 mice underwent eye imaging with the commercially available OCT (CASIA2), and the original images were used to calculate the central corneal thickness, anterior chamber depth (ACD), lens thickness (LT), vitreous chamber depth (VCD), and axial length (AL). The retinal thickness and choroidal thickness were also calculated in chicken eyes. The repeatability of the biometric measurement outcomes was analyzed. Results Excellent repeatable AL measurements were obtained for all three species, with an intraclass correlation coefficient (ICC) of ≥0.941 and a within-subject standard deviation of ≤0.055. Excellent repeatability was found...

The observation of anterior segment in children with an R124L mutation corneal dystrophy by anterior segment optical coherence tomography and in vivo confocal microscopy

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Purpose: To evaluate the anterior segment in children with an R124L mutation corneal dystrophy (CD) using anterior segment optical coherence tomography (AS-OCT) and in vivo confocal microscopy (IVCM). Methods: We investigated a family with prevalent CD and an R124L mutation; 59 individuals (14 patients; 6 male and 8 female, aged 2-69 years, 6 children, 2:4 male: female ratio) from four generations were included. We observed corneal lesions through ophthalmologic examinations, AS-OCT, and IVCM. The mean follow-up was 4.60 ± 3.91 years. Results: The mean age for childhood CD onset was 0.90 ± 0.61 years. An Avelino DNA test revealed a heterozygous R124L mutation. Clinical manifestations included recurrent photophobia, tearing, and a foreign body sensation. Recurrence frequency decreased with age. Slit lamp microscopy revealed a rough corneal epithelium. The anterior matrix under the corneal epithelium and the anterior elastic layer were scattered with gray and white opaci...

Early Assessment of Circumferential Anterior Segment Structures Following Implantable Collamer Lens V4c Implantation Via SS-OCT

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Purpose: To explore early changes in circumferential anterior segment structures following Implantable Collamer Lens (ICL) V4c implantation via swept-source optical coherence tomography (SS-OCT). Methods: In 103 eyes of 56 myopic patients undergoing ICL V4c surgery, anterior segments were measured via SS-OCT to compute local anterior chamber angle (ACA) parameters on the nasal-temporal (0°-180°), superior-inferior (90°-270°), and superior nasal-inferior temporal (80°-260°) meridians, including angle-opening distance at 500 µm (AOD500), trabecular-iris space area at 500 µm (TISA500), trabecular-iris angle at 500 µm (TIA500), and circumferential ACA parameters, including AOD area at 500 µm (AODA500), trabecular-iris circumference volume at 500 µm (TICV500), and the index and area of iris-trabecular contact (ITC). ACA parameters were compared preoperatively and at 1 week, 1 month, and 3 months postoperatively and compared among quad...

Baseline retinal nerve fiber layer thickness as a predictor of multiple sclerosis progression

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Objective: To evaluate the potential of retinal nerve fiber layer (RNFL) thickness (RNFLT) measured with optical coherence tomography in predicting disease progression in relapsing-remitting multiple sclerosis (RRMS). Methods: Analyses were conducted post-hoc of this 24-month, phase III, double-blind study, in which RRMS patients were randomized (1:1:1) to once daily oral fingolimod 0.5 mg, 1.25 mg or placebo. The key outcomes were the association between baseline RNFLT and baseline clinical characteristics, and clinical/imaging outcomes up to 24 months. Change of RNFLT with fingolimod versus placebo within 24 months and time-to-RNFL thinning were evaluated. Results: Altogether 885 patients were included. At baseline, lower RNFLT was correlated with higher expanded disability status scale score (r=-1.085, p=0.018), lower brain volume (BV, r=0.025, p=0.006) and deep gray matter volume (r=0.731, p<0.0001), worse visual acuity (r=-19.846, p<0.0001) and longer duration since diagn...

Optical Coherence Tomography following Panretinal Photocoagulation Demonstrating Choroidal Detachment

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Retinal laser therapy such as panretinal photocoagulation can be associated with compli- cations, including rare cases of choroidal detachment. This report describes high-resolution optical coherence tomography (OCT) imaging after retinal laser panretinal photocoagulation (PRP) in pa- tients with proliferative diabetic retinopathy (PDR) demonstrating choroidal detachment. A series of three sequential patients with high-risk proliferative diabetic retinopathy who were PRP laser naïve were examined with spectral-domain OCT immediately after green solid-state laser or PAS- CAL ® PRP treatment. All three patients demonstrated a significant choroidal detachment immedi- ately after PRP treatment. By one month after PRP, the choroidal detachment resolved spontane- ously in all patients. OCT examinations were performed to detect and evaluate the severity and the change of choroidal detachment and thickness measurements were quantified and demonstrated a mean decrease in choroidal t...

Perivascular Flower-Bud-like Lesions on En Face Optical Coherence Tomography Angiography in Patients with Vitreoretinal Lymphoma

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Purpose: To describe perivascular flower-bud-like lesions (PFBLs) as novel characteristics of vitreoretinal lymphoma (VRL) on en face optical coherence tomography (OCT) angiography (OCTA). Methods: A retrospective chart review was performed on 23 consecutive patients (35 eyes), who had biopsy-proven VRL between January 2018 and March 2021. En face OCTA images were analyzed before and after intervention. PFBLs were initially identified on mid-retinal slabs of en face OCTA, and were further characterized by other imaging modalities. Results: PFBLs were detected in 12 eyes (34.3%) of 8 patients, of which 8 eyes had best-corrected visual acuity of 20/40 or better. In 10 of the 12 eyes, PFBLs were detected within 6 months of symptom onset. On en face OCTA, PFBLs presented as either punctate points or confluent bands surrounding retinal vessels, with both arterial and venous involvement. In 4 of the 12 eyes, arteries were mainly affected. On OCT B-scans, PFBLs commonly appeared as hyperre...

Application of artificial intelligence-based dual-modality analysis combining fundus photography and optical coherence tomography in diabetic retinopathy screening in a community hospital

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Background To assess the feasibility and clinical utility of artificial intelligence (AI)-based screening for diabetic retinopathy (DR) and macular edema (ME) by combining fundus photos and optical coherence tomography (OCT) images in a community hospital. Methods Fundus photos and OCT images were taken for 600 diabetic patients in a community hospital. Ophthalmologists graded these fundus photos according to the International Clinical Diabetic Retinopathy (ICDR) Severity Scale as the ground truth. Two existing trained AI models were used to automatically classify the fundus images into DR grades according to ICDR, and to detect concomitant ME from OCT images, respectively. The criteria for referral were DR grades 2–4 and/or the presence of ME. The sensitivity and specificity of AI grading were evaluated. The number of referable DR cases confirmed by ophthalmologists and AI was calculated, respectively. Results DR was detected in 81 (13.5%) participants by ophthalmologists and...

Choroidal and retinal thickness in patients with vitamin C deficiency using swept-source optical coherence tomography

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Background To investigate the effects of vitamin C on central retinal thickness and choroidal thickness. Methods A total of 69 patients diagnosed with vitamin C deficiency and 1:1 age- and gender-matched 69 healthy individuals with normal serum vitamin C were included in this study. Demographic characteristics of the individuals were collected. All patients underwent a comprehensive ophthalmic examination. Subfoveal choroidal thickness and retinal thickness were measured using a swept-source optical coherence tomography (SS-OCT). Results The average retinal thickness was 269.07 ± 13.51 μm in the vitamin C deficiency group and 276.92 ± 13.51 μm in the control group. The average choroidal thickness was 195.62 ± 66.40 μm in the in the vitamin C deficiency group and 238.86 ± 55.08 μm in the control group. There was a significant decrease in both average choroidal t...

Wide-field swept-source OCT angiography of the periarterial capillary-free zone before and after anti-VEGF therapy for branch retinal vein occlusion

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Background: The aim of the study was to investigate the changes in the periarterial capillary-free zone (paCFZ) after anti-vascular endothelial growth factor (VEGF) therapy in patients with branch retinal vein occlusion (BRVO) by wide-field swept-source optical coherence tomography angiography (SS-OCTA) and assess their associations with clinical outcomes. Methods: In this retrospective observational study of 54 treatment-naïve BRVO patients with macular edema, we reviewed the findings of 12 × 12 mm 2 SS-OCTA at baseline, 3, 6, and 12 months after intravitreal ranibizumab injections. The paCFZ and major retinal artery areas were measured on SS-OCTA images. The paCFZ area to artery area (P/A) ratio was calculated. Results: The paCFZ areas and P/A ratios of first- and second-order arteries were significantly greater in BRVO eyes than in contralateral eyes (all P < 0.01), but there were no differences in the first- and second-order artery areas (P = 0.20 and 0.25, respect...

Quantitative evaluation of retinal and choroidal vascularity and retrobulbar blood flow in patients with myopic anisometropia by CDI and OCTA

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Aims To investigate the association between the myopic severity and retinal microvascular density, choroidal vascularity and retrobulbar blood flow in adult anisomyopes. Methods This study comprised 90 eyes of 45 myopic anisomyopes who were recruited for Colour Doppler imaging (CDI) and optical coherence tomography angiography (OCTA). The superficial vessel density (SVD), deep vessel density (DVD), choroidal thickness (ChT) and choroidal vascularity, including total choroidal area (TCA), luminal area (LA), stromal area (SA) and Choroidal Vascularity Index (CVI), were measured using OCTA. Moreover, the Pulsatile Index, peak systolic velocity (PSV) and end diastolic velocity (EDV) of posterior ciliary artery (PCA), central retinal artery (CRA) and ophthalmic artery (OA) were quantified by CDI, and all parameters were compared between two eyes and the correlations among parameters were analysed. Results The mean difference of spherical equivalent (SE) and axial lengths (AL) between eye...

Optical coherence tomography angiography metrics in different stages of diabetic macular edema

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Background: To investigate the optical coherence tomography angiography (OCTA) characteristics of diabetic macular edema (DME) at different stages. Methods: This study was a cross-sectional study. Patients diagnosed with DME were recruited. DME was classified into early, advanced, and severe DME. The vessel density (VD) in the superficial vascular plexus (SVP), deep vascular plexus (DVP) and foveal avascular zone (FAZ) parameters, including FAZ area, FAZ perimeter, acircularity index and foveal VD in a 300-μm-wide region around the FAZ (FD-300), were calculated by the AngioVue software. A multivariate generalized estimating equation was used to evaluate the associations between visual acuity and OCTA metrics. Results: Ninety-two eyes from 74 patients with DME were included in this study. Compared to early (P = 0.006) and advanced DME (P = 0.003), the acircularity index was higher in severe DME. Both whole and parafoveal VD in the DVP decreased in eyes with severe DME compared to ...


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