Daily Papers

Optical coherence tomography (OCT) imaging from different camera devices causes challenging domain shifts and can cause a severe drop in accuracy for machine learning models. In this work, we introduce a minimal noise adaptation method based on a singular value decomposition (SVDNA) to overcome the domain gap between target domains from three different device manufacturers in retinal OCT imaging. Our method utilizes the difference in noise structure to successfully bridge the domain gap between different OCT devices and transfer the style from unlabeled target domain images to source images for which manual annotations are available. We demonstrate how this method, despite its simplicity, compares or even outperforms state-of-the-art unsupervised domain adaptation methods for semantic segmentation on a public OCT dataset. SVDNA can be integrated with just a few lines of code into the augmentation pipeline of any network which is in contrast to many state-of-the-art domain adaptation methods which often need to change the underlying model architecture or train a separate style transfer model. The full code implementation for SVDNA is available at https://github.com/ValentinKoch/SVDNA.

Automated segmentation of retinal optical coherence tomography (OCT) images has become an important recent direction in machine learning for medical applications. We hypothesize that the anatomic structure of layers and their high-frequency variation in OCT images make retinal OCT a fitting choice for extracting spectral-domain features and combining them with spatial domain features. In this work, we present Upsilon-Net, an architecture that combines the frequency domain features with the image domain to improve the segmentation performance of OCT images. The results of this work demonstrate that the introduction of two branches, one for spectral and one for spatial domain features, brings a very significant improvement in fluid segmentation performance and allows outperformance as compared to the well-known U-Net model. Our improvement was 13% on the fluid segmentation dice score and 1.9% on the average dice score. Finally, removing selected frequency ranges in the spectral domain demonstrates the impact of these features on the fluid segmentation outperformance.

Recent research in medical image analysis with deep learning almost exclusively focuses on grid- or voxel-based data representations. We challenge this common choice by introducing MedFuncta, a modality-agnostic continuous data representation based on neural fields. We demonstrate how to scale neural fields from single instances to large datasets by exploiting redundancy in medical signals and by applying an efficient meta-learning approach with a context reduction scheme. We further address the spectral bias in commonly used SIREN activations, by introducing an omega_0-schedule, improving reconstruction quality and convergence speed. We validate our proposed approach on a large variety of medical signals of different dimensions and modalities (1D: ECG; 2D: Chest X-ray, Retinal OCT, Fundus Camera, Dermatoscope, Colon Histopathology, Cell Microscopy; 3D: Brain MRI, Lung CT) and successfully demonstrate that we can solve relevant downstream tasks on these representations. We additionally release a large-scale dataset of > 550k annotated neural fields to promote research in this direction.

Optical coherence tomography (OCT) is a non-invasive imaging technique with extensive clinical applications in ophthalmology. OCT enables the visualization of the retinal layers, playing a vital role in the early detection and monitoring of retinal diseases. OCT uses the principle of light wave interference to create detailed images of the retinal microstructures, making it a valuable tool for diagnosing ocular conditions. This work presents an open-access OCT dataset (OCTDL) comprising over 1600 high-resolution OCT images labeled according to disease group and retinal pathology. The dataset consists of OCT records of patients with Age-related Macular Degeneration (AMD), Diabetic Macular Edema (DME), Epiretinal Membrane (ERM), Retinal Artery Occlusion (RAO), Retinal Vein Occlusion (RVO), and Vitreomacular Interface Disease (VID). The images were acquired with an Optovue Avanti RTVue XR using raster scanning protocols with dynamic scan length and image resolution. Each retinal b-scan was acquired by centering on the fovea and interpreted and cataloged by an experienced retinal specialist. In this work, we applied Deep Learning classification techniques to this new open-access dataset.

We present OCTCube-M, a 3D OCT-based multi-modal foundation model for jointly analyzing OCT and en face images. OCTCube-M first developed OCTCube, a 3D foundation model pre-trained on 26,685 3D OCT volumes encompassing 1.62 million 2D OCT images. It then exploits a novel multi-modal contrastive learning framework COEP to integrate other retinal imaging modalities, such as fundus autofluorescence and infrared retinal imaging, into OCTCube, efficiently extending it into multi-modal foundation models. OCTCube achieves best performance on predicting 8 retinal diseases, demonstrating strong generalizability on cross-cohort, cross-device and cross-modality prediction. OCTCube can also predict cross-organ nodule malignancy (CT) and low cardiac ejection fraction as well as systemic diseases, such as diabetes and hypertension, revealing its wide applicability beyond retinal diseases. We further develop OCTCube-IR using COEP with 26,685 OCT and IR image pairs. OCTCube-IR can accurately retrieve between OCT and IR images, allowing joint analysis between 3D and 2D retinal imaging modalities. Finally, we trained a tri-modal foundation model OCTCube-EF from 4 million 2D OCT images and 400K en face retinal images. OCTCube-EF attains the best performance on predicting the growth rate of geographic atrophy (GA) across datasets collected from 6 multi-center global trials conducted in 23 countries. This improvement is statistically equivalent to running a clinical trial with more than double the size of the original study. Our analysis based on another retrospective case study reveals OCTCube-EF's ability to avoid false positive Phase-III results according to its accurate treatment effect estimation on the Phase-II results. In sum, OCTCube-M is a 3D multi-modal foundation model framework that integrates OCT and other retinal imaging modalities revealing substantial diagnostic and prognostic benefits.

Retinal foundation models aim to learn generalizable representations from diverse retinal images, facilitating label-efficient model adaptation across various ophthalmic tasks. Despite their success, current retinal foundation models are generally restricted to a single imaging modality, such as Color Fundus Photography (CFP) or Optical Coherence Tomography (OCT), limiting their versatility. Moreover, these models may struggle to fully leverage expert annotations and overlook the valuable domain knowledge essential for domain-specific representation learning. To overcome these limitations, we introduce UrFound, a retinal foundation model designed to learn universal representations from both multimodal retinal images and domain knowledge. UrFound is equipped with a modality-agnostic image encoder and accepts either CFP or OCT images as inputs. To integrate domain knowledge into representation learning, we encode expert annotation in text supervision and propose a knowledge-guided masked modeling strategy for model pre-training. It involves reconstructing randomly masked patches of retinal images while predicting masked text tokens conditioned on the corresponding retinal image. This approach aligns multimodal images and textual expert annotations within a unified latent space, facilitating generalizable and domain-specific representation learning. Experimental results demonstrate that UrFound exhibits strong generalization ability and data efficiency when adapting to various tasks in retinal image analysis. By training on ~180k retinal images, UrFound significantly outperforms the state-of-the-art retinal foundation model trained on up to 1.6 million unlabelled images across 8 public retinal datasets. Our code and data are available at https://github.com/yukkai/UrFound.

The oxygen saturation level in the blood (SaO2) is crucial for health, particularly in relation to sleep-related breathing disorders. However, continuous monitoring of SaO2 is time-consuming and highly variable depending on patients' conditions. Recently, optical coherence tomography angiography (OCTA) has shown promising development in rapidly and effectively screening eye-related lesions, offering the potential for diagnosing sleep-related disorders. To bridge this gap, our paper presents three key contributions. Firstly, we propose JointViT, a novel model based on the Vision Transformer architecture, incorporating a joint loss function for supervision. Secondly, we introduce a balancing augmentation technique during data preprocessing to improve the model's performance, particularly on the long-tail distribution within the OCTA dataset. Lastly, through comprehensive experiments on the OCTA dataset, our proposed method significantly outperforms other state-of-the-art methods, achieving improvements of up to 12.28% in overall accuracy. This advancement lays the groundwork for the future utilization of OCTA in diagnosing sleep-related disorders. See project website https://steve-zeyu-zhang.github.io/JointViT

Glaucoma is the number one cause of irreversible blindness globally. A major challenge for accurate glaucoma detection and progression forecasting is the bottleneck of limited labeled patients with the state-of-the-art (SOTA) 3D retinal imaging data of optical coherence tomography (OCT). To address the data scarcity issue, this paper proposes two solutions. First, we develop a novel generalization-reinforced semi-supervised learning (SSL) model called pseudo supervisor to optimally utilize unlabeled data. Compared with SOTA models, the proposed pseudo supervisor optimizes the policy of predicting pseudo labels with unlabeled samples to improve empirical generalization. Our pseudo supervisor model is evaluated with two clinical tasks consisting of glaucoma detection and progression forecasting. The progression forecasting task is evaluated both unimodally and multimodally. Our pseudo supervisor model demonstrates superior performance than SOTA SSL comparison models. Moreover, our model also achieves the best results on the publicly available LAG fundus dataset. Second, we introduce the Harvard Glaucoma Detection and Progression (Harvard-GDP) Dataset, a multimodal multitask dataset that includes data from 1,000 patients with OCT imaging data, as well as labels for glaucoma detection and progression. This is the largest glaucoma detection dataset with 3D OCT imaging data and the first glaucoma progression forecasting dataset that is publicly available. Detailed sex and racial analysis are provided, which can be used by interested researchers for fairness learning studies. Our released dataset is benchmarked with several SOTA supervised CNN and transformer deep learning models. The dataset and code are made publicly available via https://ophai.hms.harvard.edu/datasets/harvard-gdp1000.

Clinicians spend a significant amount of time reviewing medical images and transcribing their findings regarding patient diagnosis, referral and treatment in text form. Vision-language models (VLMs), which automatically interpret images and summarize their findings as text, have enormous potential to alleviate clinical workloads and increase patient access to high-quality medical care. While foundational models have stirred considerable interest in the medical community, it is unclear whether their general capabilities translate to real-world clinical utility. In this work, we show that foundation VLMs markedly underperform compared to practicing ophthalmologists on specialist tasks crucial to the care of patients with age-related macular degeneration (AMD). To address this, we initially identified the essential capabilities required for image-based clinical decision-making, and then developed a curriculum to selectively train VLMs in these skills. The resulting model, RetinaVLM, can be instructed to write reports that significantly outperform those written by leading foundation medical VLMs in disease staging (F1 score of 0.63 vs. 0.11) and patient referral (0.67 vs. 0.39), and approaches the diagnostic performance of junior ophthalmologists (who achieve 0.77 and 0.78 on the respective tasks). Furthermore, in a reader study involving two senior ophthalmologists with up to 32 years of experience, RetinaVLM's reports were found to be similarly correct (78.6% vs. 82.1%) and complete (both 78.6%) as reports written by junior ophthalmologists with up to 10 years of experience. These results demonstrate that our curriculum-based approach provides a blueprint for specializing generalist foundation medical VLMs to handle real-world clinical tasks.

The retina is the only part of the human body in which blood vessels can be accessed non-invasively using imaging techniques such as digital fundus images (DFI). The spatial distribution of the retinal microvasculature may change with cardiovascular diseases and thus the eyes may be regarded as a window to our hearts. Computerized segmentation of the retinal arterioles and venules (A/V) is essential for automated microvasculature analysis. Using active learning, we created a new DFI dataset containing 240 crowd-sourced manual A/V segmentations performed by fifteen medical students and reviewed by an ophthalmologist, and developed LUNet, a novel deep learning architecture for high resolution A/V segmentation. LUNet architecture includes a double dilated convolutional block that aims to enhance the receptive field of the model and reduce its parameter count. Furthermore, LUNet has a long tail that operates at high resolution to refine the segmentation. The custom loss function emphasizes the continuity of the blood vessels. LUNet is shown to significantly outperform two state-of-the-art segmentation algorithms on the local test set as well as on four external test sets simulating distribution shifts across ethnicity, comorbidities, and annotators. We make the newly created dataset open access (upon publication).

Deep learning is currently the state-of-the-art for automated detection of referable diabetic retinopathy (DR) from color fundus photographs (CFP). While the general interest is put on improving results through methodological innovations, it is not clear how good these approaches perform compared to standard deep classification models trained with the appropriate settings. In this paper we propose to model a strong baseline for this task based on a simple and standard ResNet-18 architecture. To this end, we built on top of prior art by training the model with a standard preprocessing strategy but using images from several public sources and an empirically calibrated data augmentation setting. To evaluate its performance, we covered multiple clinically relevant perspectives, including image and patient level DR screening, discriminating responses by input quality and DR grade, assessing model uncertainties and analyzing its results in a qualitative manner. With no other methodological innovation than a carefully designed training, our ResNet model achieved an AUC = 0.955 (0.953 - 0.956) on a combined test set of 61007 test images from different public datasets, which is in line or even better than what other more complex deep learning models reported in the literature. Similar AUC values were obtained in 480 images from two separate in-house databases specially prepared for this study, which emphasize its generalization ability. This confirms that standard networks can still be strong baselines for this task if properly trained.

Diabetic retinopathy (DR) is a growing health problem worldwide and is a leading cause of visual impairment and blindness, especially among working people aged 20-65. Its incidence is increasing along with the number of diabetes cases, and it is more common in developed countries than in developing countries. Recent research in the field of diabetic retinopathy diagnosis is using advanced technologies, such as analysis of images obtained by ophthalmoscopy. Automatic methods for analyzing eye images based on neural networks, deep learning and image analysis algorithms can improve the efficiency of diagnosis. This paper describes an automatic DR diagnosis method that includes processing and analysis of ophthalmoscopic images of the eye. It uses morphological algorithms to identify the optic disc and lesions characteristic of DR, such as microaneurysms, hemorrhages and exudates. Automated DR diagnosis has the potential to improve the efficiency of early detection of this disease and contribute to reducing the number of cases of diabetes-related visual impairment. The final step was to create an application with a graphical user interface that allowed retinal images taken at cooperating ophthalmology offices to be uploaded to the server. These images were then analyzed using a developed algorithm to make a diagnosis.

We propose a novel framework for retinal feature point alignment, designed for learning cross-modality features to enhance matching and registration across multi-modality retinal images. Our model draws on the success of previous learning-based feature detection and description methods. To better leverage unlabeled data and constrain the model to reproduce relevant keypoints, we integrate a keypoint-based segmentation task. It is trained in a self-supervised manner by enforcing segmentation consistency between different augmentations of the same image. By incorporating a keypoint augmented self-supervised layer, we achieve robust feature extraction across modalities. Extensive evaluation on two public datasets and one in-house dataset demonstrates significant improvements in performance for modality-agnostic retinal feature alignment. Our code and model weights are publicly available at https://github.com/MedICL-VU/RetinaIPA.

Recently two-stage detectors have surged ahead of single-shot detectors in the accuracy-vs-speed trade-off. Nevertheless single-shot detectors are immensely popular in embedded vision applications. This paper brings single-shot detectors up to the same level as current two-stage techniques. We do this by improving training for the state-of-the-art single-shot detector, RetinaNet, in three ways: integrating instance mask prediction for the first time, making the loss function adaptive and more stable, and including additional hard examples in training. We call the resulting augmented network RetinaMask. The detection component of RetinaMask has the same computational cost as the original RetinaNet, but is more accurate. COCO test-dev results are up to 41.4 mAP for RetinaMask-101 vs 39.1mAP for RetinaNet-101, while the runtime is the same during evaluation. Adding Group Normalization increases the performance of RetinaMask-101 to 41.7 mAP. Code is at:https://github.com/chengyangfu/retinamask

Scarcity of large publicly available retinal fundus image datasets for automated glaucoma detection has been the bottleneck for successful application of artificial intelligence towards practical Computer-Aided Diagnosis (CAD). A few small datasets that are available for research community usually suffer from impractical image capturing conditions and stringent inclusion criteria. These shortcomings in already limited choice of existing datasets make it challenging to mature a CAD system so that it can perform in real-world environment. In this paper we present a large publicly available retinal fundus image dataset for glaucoma classification called G1020. The dataset is curated by conforming to standard practices in routine ophthalmology and it is expected to serve as standard benchmark dataset for glaucoma detection. This database consists of 1020 high resolution colour fundus images and provides ground truth annotations for glaucoma diagnosis, optic disc and optic cup segmentation, vertical cup-to-disc ratio, size of neuroretinal rim in inferior, superior, nasal and temporal quadrants, and bounding box location for optic disc. We also report baseline results by conducting extensive experiments for automated glaucoma diagnosis and segmentation of optic disc and optic cup.

Effectively representing medical images, especially retinal images, presents a considerable challenge due to variations in appearance, size, and contextual information of pathological signs called lesions. Precise discrimination of these lesions is crucial for diagnosing vision-threatening issues such as diabetic retinopathy. While visual attention-based neural networks have been introduced to learn spatial context and channel correlations from retinal images, they often fall short in capturing localized lesion context. Addressing this limitation, we propose a novel attention mechanism called Guided Context Gating, an unique approach that integrates Context Formulation, Channel Correlation, and Guided Gating to learn global context, spatial correlations, and localized lesion context. Our qualitative evaluation against existing attention mechanisms emphasize the superiority of Guided Context Gating in terms of explainability. Notably, experiments on the Zenodo-DR-7 dataset reveal a substantial 2.63% accuracy boost over advanced attention mechanisms & an impressive 6.53% improvement over the state-of-the-art Vision Transformer for assessing the severity grade of retinopathy, even with imbalanced and limited training samples for each class.

WHO has declared that more than 2.2 billion people worldwide are suffering from visual disorders, such as media haze, glaucoma, and drusen. At least 1 billion of these cases could have been either prevented or successfully treated, yet they remain unaddressed due to poverty, a lack of specialists, inaccurate ocular fundus diagnoses by ophthalmologists, or the presence of a rare disease. To address this, the research has developed the Hybrid Trio-Network Model Algorithm for accurately diagnosing 12 distinct common and rare eye diseases. This algorithm utilized the RFMiD dataset of 3,200 fundus images and the Binary Relevance Method to detect diseases separately, ensuring expandability and avoiding incorrect correlations. Each detector, incorporating finely tuned hyperparameters to optimize performance, consisted of three feature components: A classical transfer learning CNN model, a two-stage CNN model, and a Siamese Network. The diagnosis was made using features extracted through this Trio-Model with Ensembled Machine Learning algorithms. The proposed model achieved an average accuracy of 97% and an AUC score of 0.96. Compared to past benchmark studies, an increase of over 10% in the F1-score was observed for most diseases. Furthermore, using the Siamese Network, the model successfully made predictions in diseases like optic disc pallor, which past studies failed to predict due to low confidence. This diagnostic tool presents a stable, adaptive, cost-effective, efficient, accessible, and fast solution for globalizing early detection of both common and rare diseases.

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 37 open-access, mostly categorical fundus imaging datasets from various sources, with up to 97 different target conditions and 284,660 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a large margin more generalist, larger-scale image-language models, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.

Diabetic Retinopathy (DR), induced by diabetes, poses a significant risk of visual impairment. Accurate and effective grading of DR aids in the treatment of this condition. Yet existing models experience notable performance degradation on unseen domains due to domain shifts. Previous methods address this issue by simulating domain style through simple visual transformation and mitigating domain noise via learning robust representations. However, domain shifts encompass more than image styles. They overlook biases caused by implicit factors such as ethnicity, age, and diagnostic criteria. In our work, we propose a novel framework where representations of paired data from different domains are decoupled into semantic features and domain noise. The resulting augmented representation comprises original retinal semantics and domain noise from other domains, aiming to generate enhanced representations aligned with real-world clinical needs, incorporating rich information from diverse domains. Subsequently, to improve the robustness of the decoupled representations, class and domain prototypes are employed to interpolate the disentangled representations while data-aware weights are designed to focus on rare classes and domains. Finally, we devise a robust pixel-level semantic alignment loss to align retinal semantics decoupled from features, maintaining a balance between intra-class diversity and dense class features. Experimental results on multiple benchmarks demonstrate the effectiveness of our method on unseen domains. The code implementations are accessible on https://github.com/richard-peng-xia/DECO.

Accurate retinal vessel (RV) segmentation is a crucial step in the quantitative assessment of retinal vasculature, which is needed for the early detection of retinal diseases and other conditions. Numerous studies have been conducted to tackle the problem of segmenting vessels automatically using a pixel-wise classification approach. The common practice of creating ground truth labels is to categorize pixels as foreground and background. This approach is, however, biased, and it ignores the uncertainty of a human annotator when it comes to annotating e.g. thin vessels. In this work, we propose a simple and effective method that casts the RV segmentation task as an image-level regression. For this purpose, we first introduce a novel Segmentation Annotation Uncertainty-Aware (SAUNA) transform, which adds pixel uncertainty to the ground truth using the pixel's closeness to the annotation boundary and vessel thickness. To train our model with soft labels, we generalize the earlier proposed Jaccard metric loss to arbitrary hypercubes for soft Jaccard index (Intersection-over-Union) optimization. Additionally, we employ a stable version of the Focal-L1 loss for pixel-wise regression. We conduct thorough experiments and compare our method to a diverse set of baselines across 5 retinal image datasets. Our empirical results indicate that the integration of the SAUNA transform and these segmentation losses led to significant performance boosts for different segmentation models. Particularly, our methodology enables UNet-like architectures to substantially outperform computational-intensive baselines. Our implementation is available at https://github.com/Oulu-IMEDS/SAUNA.

In the field of medical imaging, the scarcity of large-scale datasets due to privacy restrictions stands as a significant barrier to develop large models for medical. To address this issue, we introduce SynFundus-1M, a high-quality synthetic dataset with over 1 million retinal fundus images and extensive disease and pathologies annotations, which is generated by a Denoising Diffusion Probabilistic Model. The SynFundus-Generator and SynFundus-1M achieve superior Frechet Inception Distance (FID) scores compared to existing methods on main-stream public real datasets. Furthermore, the ophthalmologists evaluation validate the difficulty in discerning these synthetic images from real ones, confirming the SynFundus-1M's authenticity. Through extensive experiments, we demonstrate that both CNN and ViT can benifit from SynFundus-1M by pretraining or training directly. Compared to datasets like ImageNet or EyePACS, models train on SynFundus-1M not only achieve better performance but also faster convergence on various downstream tasks.

Automatic diabetic retinopathy (DR) lesions segmentation makes great sense of assisting ophthalmologists in diagnosis. Although many researches have been conducted on this task, most prior works paid too much attention to the designs of networks instead of considering the pathological association for lesions. Through investigating the pathogenic causes of DR lesions in advance, we found that certain lesions are closed to specific vessels and present relative patterns to each other. Motivated by the observation, we propose a relation transformer block (RTB) to incorporate attention mechanisms at two main levels: a self-attention transformer exploits global dependencies among lesion features, while a cross-attention transformer allows interactions between lesion and vessel features by integrating valuable vascular information to alleviate ambiguity in lesion detection caused by complex fundus structures. In addition, to capture the small lesion patterns first, we propose a global transformer block (GTB) which preserves detailed information in deep network. By integrating the above blocks of dual-branches, our network segments the four kinds of lesions simultaneously. Comprehensive experiments on IDRiD and DDR datasets well demonstrate the superiority of our approach, which achieves competitive performance compared to state-of-the-arts.

A large-scale labeled dataset is a key factor for the success of supervised deep learning in computer vision. However, a limited number of annotated data is very common, especially in ophthalmic image analysis, since manual annotation is time-consuming and labor-intensive. Self-supervised learning (SSL) methods bring huge opportunities for better utilizing unlabeled data, as they do not need massive annotations. With an attempt to use as many as possible unlabeled ophthalmic images, it is necessary to break the dimension barrier, simultaneously making use of both 2D and 3D images. In this paper, we propose a universal self-supervised Transformer framework, named Uni4Eye, to discover the inherent image property and capture domain-specific feature embedding in ophthalmic images. Uni4Eye can serve as a global feature extractor, which builds its basis on a Masked Image Modeling task with a Vision Transformer (ViT) architecture. We employ a Unified Patch Embedding module to replace the origin patch embedding module in ViT for jointly processing both 2D and 3D input images. Besides, we design a dual-branch multitask decoder module to simultaneously perform two reconstruction tasks on the input image and its gradient map, delivering discriminative representations for better convergence. We evaluate the performance of our pre-trained Uni4Eye encoder by fine-tuning it on six downstream ophthalmic image classification tasks. The superiority of Uni4Eye is successfully established through comparisons to other state-of-the-art SSL pre-training methods.

Introduction: Blood vessels can be non-invasively visualized from a digital fundus image (DFI). Several studies have shown an association between cardiovascular risk and vascular features obtained from DFI. Recent advances in computer vision and image segmentation enable automatising DFI blood vessel segmentation. There is a need for a resource that can automatically compute digital vasculature biomarkers (VBM) from these segmented DFI. Methods: In this paper, we introduce a Python Vasculature BioMarker toolbox, denoted PVBM. A total of 11 VBMs were implemented. In particular, we introduce new algorithmic methods to estimate tortuosity and branching angles. Using PVBM, and as a proof of usability, we analyze geometric vascular differences between glaucomatous patients and healthy controls. Results: We built a fully automated vasculature biomarker toolbox based on DFI segmentations and provided a proof of usability to characterize the vascular changes in glaucoma. For arterioles and venules, all biomarkers were significant and lower in glaucoma patients compared to healthy controls except for tortuosity, venular singularity length and venular branching angles. Conclusion: We have automated the computation of 11 VBMs from retinal blood vessel segmentation. The PVBM toolbox is made open source under a GNU GPL 3 license and is available on physiozoo.com (following publication).

We introduce VascX models, a comprehensive set of model ensembles for analyzing retinal vasculature from color fundus images (CFIs). Annotated CFIs were aggregated from public datasets for vessel, artery-vein, and disc segmentation; and fovea localization. Additional CFIs from the population-based Rotterdam Study were, with arteries and veins annotated by graders at pixel level. Our models achieved robust performance across devices from different vendors, varying levels of image quality levels, and diverse pathologies. Our models demonstrated superior segmentation performance compared to existing systems under a variety of conditions. Significant enhancements were observed in artery-vein and disc segmentation performance, particularly in segmentations of these structures on CFIs of intermediate quality, a common characteristic of large cohorts and clinical datasets. Our model outperformed human graders in segmenting vessels with greater precision. With VascX models we provide a robust, ready-to-use set of model ensembles and inference code aimed at simplifying the implementation and enhancing the quality of automated retinal vasculature analyses. The precise vessel parameters generated by the model can serve as starting points for the identification of disease patterns in and outside of the eye.

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

Redundancies and correlations in the responses of sensory neurons seem to waste neural resources but can carry cues about structured stimuli and may help the brain to correct for response errors. To assess how the retina negotiates this tradeoff, we measured simultaneous responses from populations of ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure. We found that pairwise correlations in the retinal output remained similar across stimuli with widely different spatio-temporal correlations including white noise and natural movies. Meanwhile, purely spatial correlations tended to increase correlations in the retinal response. Responding to more correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the similarity of pairwise correlations across stimuli where receptive field measurements were possible.

Although the preservation of shape continuity and physiological anatomy is a natural assumption in the segmentation of medical images, it is often neglected by deep learning methods that mostly aim for the statistical modeling of input data as pixels rather than interconnected structures. In biological structures, however, organs are not separate entities; for example, in reality, a severed vessel is an indication of an underlying problem, but traditional segmentation models are not designed to strictly enforce the continuity of anatomy, potentially leading to inaccurate medical diagnoses. To address this issue, we propose a graph-based approach that enforces the continuity and connectivity of anatomical topology in medical images. Our method encodes the continuity of shapes as a graph constraint, ensuring that the network's predictions maintain this continuity. We evaluate our method on two public benchmarks on retinal vessel segmentation, showing significant improvements in connectivity metrics compared to traditional methods while getting better or on-par performance on segmentation metrics.

Image restoration is a challenging and ill-posed problem which also has been a long-standing issue. However, most of learning based restoration methods are proposed to target one degradation type which means they are lack of generalization. In this paper, we proposed a multi-branch restoration model inspired from the Human Visual System (i.e., Retinal Ganglion Cells) which can achieve multiple restoration tasks in a general framework. The experiments show that the proposed multi-branch architecture, called CMFNet, has competitive performance results on four datasets, including image dehazing, deraindrop, and deblurring, which are very common applications for autonomous cars. The source code and pretrained models of three restoration tasks are available at https://github.com/FanChiMao/CMFNet.

Automatic estimation of cardiac ultrasound image quality can be beneficial for guiding operators and ensuring the accuracy of clinical measurements. Previous work often fails to distinguish the view correctness of the echocardiogram from the image quality. Additionally, previous studies only provide a global image quality value, which limits their practical utility. In this work, we developed and compared three methods to estimate image quality: 1) classic pixel-based metrics like the generalized contrast-to-noise ratio (gCNR) on myocardial segments as region of interest and left ventricle lumen as background, obtained using a U-Net segmentation 2) local image coherence derived from a U-Net model that predicts coherence from B-Mode images 3) a deep convolutional network that predicts the quality of each region directly in an end-to-end fashion. We evaluate each method against manual regional image quality annotations by three experienced cardiologists. The results indicate poor performance of the gCNR metric, with Spearman correlation to the annotations of rho = 0.24. The end-to-end learning model obtains the best result, rho = 0.69, comparable to the inter-observer correlation, rho = 0.63. Finally, the coherence-based method, with rho = 0.58, outperformed the classical metrics and is more generic than the end-to-end approach.

Segmentation of blood vessels in murine cerebral 3D OCTA images is foundational for in vivo quantitative analysis of the effects of neurovascular disorders, such as stroke or Alzheimer's, on the vascular network. However, to accurately segment blood vessels with state-of-the-art deep learning methods, a vast amount of voxel-level annotations is required. Since cerebral 3D OCTA images are typically plagued by artifacts and generally have a low signal-to-noise ratio, acquiring manual annotations poses an especially cumbersome and time-consuming task. To alleviate the need for manual annotations, we propose utilizing synthetic data to supervise segmentation algorithms. To this end, we extract patches from vessel graphs and transform them into synthetic cerebral 3D OCTA images paired with their matching ground truth labels by simulating the most dominant 3D OCTA artifacts. In extensive experiments, we demonstrate that our approach achieves competitive results, enabling annotation-free blood vessel segmentation in cerebral 3D OCTA images.

Though tremendous strides have been made in uncontrolled face detection, accurate and efficient face localisation in the wild remains an open challenge. This paper presents a robust single-stage face detector, named RetinaFace, which performs pixel-wise face localisation on various scales of faces by taking advantages of joint extra-supervised and self-supervised multi-task learning. Specifically, We make contributions in the following five aspects: (1) We manually annotate five facial landmarks on the WIDER FACE dataset and observe significant improvement in hard face detection with the assistance of this extra supervision signal. (2) We further add a self-supervised mesh decoder branch for predicting a pixel-wise 3D shape face information in parallel with the existing supervised branches. (3) On the WIDER FACE hard test set, RetinaFace outperforms the state of the art average precision (AP) by 1.1% (achieving AP equal to 91.4%). (4) On the IJB-C test set, RetinaFace enables state of the art methods (ArcFace) to improve their results in face verification (TAR=89.59% for FAR=1e-6). (5) By employing light-weight backbone networks, RetinaFace can run real-time on a single CPU core for a VGA-resolution image. Extra annotations and code have been made available at: https://github.com/deepinsight/insightface/tree/master/RetinaFace.

Point-spread-function (PSF) engineering is a powerful computational imaging techniques wherein a custom phase mask is integrated into an optical system to encode additional information into captured images. Used in combination with deep learning, such systems now offer state-of-the-art performance at monocular depth estimation, extended depth-of-field imaging, lensless imaging, and other tasks. Inspired by recent advances in spatial light modulator (SLM) technology, this paper answers a natural question: Can one encode additional information and achieve superior performance by changing a phase mask dynamically over time? We first prove that the set of PSFs described by static phase masks is non-convex and that, as a result, time-averaged PSFs generated by dynamic phase masks are fundamentally more expressive. We then demonstrate, in simulation, that time-averaged dynamic (TiDy) phase masks can offer substantially improved monocular depth estimation and extended depth-of-field imaging performance.

While models derived from Vision Transformers (ViTs) have been phonemically surging, pre-trained models cannot seamlessly adapt to arbitrary resolution images without altering the architecture and configuration, such as sampling the positional encoding, limiting their flexibility for various vision tasks. For instance, the Segment Anything Model (SAM) based on ViT-Huge requires all input images to be resized to 1024times1024. To overcome this limitation, we propose the Multi-Head Self-Attention Convolution (MSA-Conv) that incorporates Self-Attention within generalized convolutions, including standard, dilated, and depthwise ones. Enabling transformers to handle images of varying sizes without retraining or rescaling, the use of MSA-Conv further reduces computational costs compared to global attention in ViT, which grows costly as image size increases. Later, we present the Vision Transformer in Convolution (TiC) as a proof of concept for image classification with MSA-Conv, where two capacity enhancing strategies, namely Multi-Directional Cyclic Shifted Mechanism and Inter-Pooling Mechanism, have been proposed, through establishing long-distance connections between tokens and enlarging the effective receptive field. Extensive experiments have been carried out to validate the overall effectiveness of TiC. Additionally, ablation studies confirm the performance improvement made by MSA-Conv and the two capacity enhancing strategies separately. Note that our proposal aims at studying an alternative to the global attention used in ViT, while MSA-Conv meets our goal by making TiC comparable to state-of-the-art on ImageNet-1K. Code will be released at https://github.com/zs670980918/MSA-Conv.

Several recent studies have demonstrated that attention-based networks, such as Vision Transformer (ViT), can outperform Convolutional Neural Networks (CNNs) on several computer vision tasks without using convolutional layers. This naturally leads to the following questions: Can a self-attention layer of ViT express any convolution operation? In this work, we prove that a single ViT layer with image patches as the input can perform any convolution operation constructively, where the multi-head attention mechanism and the relative positional encoding play essential roles. We further provide a lower bound on the number of heads for Vision Transformers to express CNNs. Corresponding with our analysis, experimental results show that the construction in our proof can help inject convolutional bias into Transformers and significantly improve the performance of ViT in low data regimes.

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

Semantic segmentation models classify pixels into a set of known (``in-distribution'') visual classes. When deployed in an open world, the reliability of these models depends on their ability not only to classify in-distribution pixels but also to detect out-of-distribution (OoD) pixels. Historically, the poor OoD detection performance of these models has motivated the design of methods based on model re-training using synthetic training images that include OoD visual objects. Although successful, these re-trained methods have two issues: 1) their in-distribution segmentation accuracy may drop during re-training, and 2) their OoD detection accuracy does not generalise well to new contexts (e.g., country surroundings) outside the training set (e.g., city surroundings). In this paper, we mitigate these issues with: (i) a new residual pattern learning (RPL) module that assists the segmentation model to detect OoD pixels without affecting the inlier segmentation performance; and (ii) a novel context-robust contrastive learning (CoroCL) that enforces RPL to robustly detect OoD pixels among various contexts. Our approach improves by around 10\% FPR and 7\% AuPRC the previous state-of-the-art in Fishyscapes, Segment-Me-If-You-Can, and RoadAnomaly datasets. Our code is available at: https://github.com/yyliu01/RPL.

High-resolution images offer more information about scenes that can improve model accuracy. However, the dominant model architecture in computer vision, the vision transformer (ViT), cannot effectively leverage larger images without finetuning -- ViTs poorly extrapolate to more patches at test time, although transformers offer sequence length flexibility. We attribute this shortcoming to the current patch position encoding methods, which create a distribution shift when extrapolating. We propose a drop-in replacement for the position encoding of plain ViTs that restricts attention heads to fixed fields of view, pointed in different directions, using 2D attention masks. Our novel method, called LookHere, provides translation-equivariance, ensures attention head diversity, and limits the distribution shift that attention heads face when extrapolating. We demonstrate that LookHere improves performance on classification (avg. 1.6%), against adversarial attack (avg. 5.4%), and decreases calibration error (avg. 1.5%) -- on ImageNet without extrapolation. With extrapolation, LookHere outperforms the current SoTA position encoding method, 2D-RoPE, by 21.7% on ImageNet when trained at 224^2 px and tested at 1024^2 px. Additionally, we release a high-resolution test set to improve the evaluation of high-resolution image classifiers, called ImageNet-HR.

The goal of this work is to characterize the representational impact that foveation operations have for machine vision systems, inspired by the foveated human visual system, which has higher acuity at the center of gaze and texture-like encoding in the periphery. To do so, we introduce models consisting of a first-stage fixed image transform followed by a second-stage learnable convolutional neural network, and we varied the first stage component. The primary model has a foveated-textural input stage, which we compare to a model with foveated-blurred input and a model with spatially-uniform blurred input (both matched for perceptual compression), and a final reference model with minimal input-based compression. We find that: 1) the foveated-texture model shows similar scene classification accuracy as the reference model despite its compressed input, with greater i.i.d. generalization than the other models; 2) the foveated-texture model has greater sensitivity to high-spatial frequency information and greater robustness to occlusion, w.r.t the comparison models; 3) both the foveated systems, show a stronger center image-bias relative to the spatially-uniform systems even with a weight sharing constraint. Critically, these results are preserved over different classical CNN architectures throughout their learning dynamics. Altogether, this suggests that foveation with peripheral texture-based computations yields an efficient, distinct, and robust representational format of scene information, and provides symbiotic computational insight into the representational consequences that texture-based peripheral encoding may have for processing in the human visual system, while also potentially inspiring the next generation of computer vision models via spatially-adaptive computation. Code + Data available here: https://github.com/ArturoDeza/EmergentProperties

Gaze following aims to interpret human-scene interactions by predicting the person's focal point of gaze. Prevailing approaches often adopt a two-stage framework, whereby multi-modality information is extracted in the initial stage for gaze target prediction. Consequently, the efficacy of these methods highly depends on the precision of the preceding modality extraction. Others use a single-modality approach with complex decoders, increasing network computational load. Inspired by the remarkable success of pre-trained plain vision transformers (ViTs), we introduce a novel single-modality gaze following framework called ViTGaze. In contrast to previous methods, it creates a novel gaze following framework based mainly on powerful encoders (relative decoder parameters less than 1%). Our principal insight is that the inter-token interactions within self-attention can be transferred to interactions between humans and scenes. Leveraging this presumption, we formulate a framework consisting of a 4D interaction encoder and a 2D spatial guidance module to extract human-scene interaction information from self-attention maps. Furthermore, our investigation reveals that ViT with self-supervised pre-training has an enhanced ability to extract correlation information. Many experiments have been conducted to demonstrate the performance of the proposed method. Our method achieves state-of-the-art (SOTA) performance among all single-modality methods (3.4% improvement in the area under curve (AUC) score, 5.1% improvement in the average precision (AP)) and very comparable performance against multi-modality methods with 59% number of parameters less.

In this paper, we present a novel methodology we call MDS-ViTNet (Multi Decoder Saliency by Vision Transformer Network) for enhancing visual saliency prediction or eye-tracking. This approach holds significant potential for diverse fields, including marketing, medicine, robotics, and retail. We propose a network architecture that leverages the Vision Transformer, moving beyond the conventional ImageNet backbone. The framework adopts an encoder-decoder structure, with the encoder utilizing a Swin transformer to efficiently embed most important features. This process involves a Transfer Learning method, wherein layers from the Vision Transformer are converted by the Encoder Transformer and seamlessly integrated into a CNN Decoder. This methodology ensures minimal information loss from the original input image. The decoder employs a multi-decoding technique, utilizing dual decoders to generate two distinct attention maps. These maps are subsequently combined into a singular output via an additional CNN model. Our trained model MDS-ViTNet achieves state-of-the-art results across several benchmarks. Committed to fostering further collaboration, we intend to make our code, models, and datasets accessible to the public.

Echocardiography is the most widely used cardiac imaging modality, capturing ultrasound video data to assess cardiac structure and function. Artificial intelligence (AI) in echocardiography has the potential to streamline manual tasks and improve reproducibility and precision. However, most echocardiography AI models are single-view, single-task systems that do not synthesize complementary information from multiple views captured during a full exam, and thus lead to limited performance and scope of applications. To address this problem, we introduce EchoPrime, a multi-view, view-informed, video-based vision-language foundation model trained on over 12 million video-report pairs. EchoPrime uses contrastive learning to train a unified embedding model for all standard views in a comprehensive echocardiogram study with representation of both rare and common diseases and diagnoses. EchoPrime then utilizes view-classification and a view-informed anatomic attention model to weight video-specific interpretations that accurately maps the relationship between echocardiographic views and anatomical structures. With retrieval-augmented interpretation, EchoPrime integrates information from all echocardiogram videos in a comprehensive study and performs holistic comprehensive clinical echocardiography interpretation. In datasets from two independent healthcare systems, EchoPrime achieves state-of-the art performance on 23 diverse benchmarks of cardiac form and function, surpassing the performance of both task-specific approaches and prior foundation models. Following rigorous clinical evaluation, EchoPrime can assist physicians in the automated preliminary assessment of comprehensive echocardiography.