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Jul 31

Plug-and-Play Regularization on Magnitude with Deep Priors for 3D Near-Field MIMO Imaging

Near-field radar imaging systems are recently used in a wide range of applications, such as medical diagnosis, through-wall imaging, concealed weapon detection, and nondestructive evaluation. In this paper, we consider the problem of reconstructing the three-dimensional (3D) complex-valued reflectivity distribution of the near-field scene from sparse multiple-input multiple-output (MIMO) array measurements. Using the alternating direction method of multipliers (ADMM) framework, we solve this inverse problem by enforcing regularization on the magnitude of the complex-valued reflectivity distribution. For this, we provide a general expression for the proximal mapping associated with such regularization functionals. This equivalently corresponds to the solution of a complex-valued denoising problem which involves regularization on the magnitude. By utilizing this expression, we develop a novel and efficient plug-and-play (PnP) reconstruction method that consists of simple update steps. Due to the success of data-adaptive deep priors in various imaging problems, we also train a 3D deep denoiser to exploit within the developed PnP framework for MIMO imaging. The effectiveness of the developed learning-based PnP approach is illustrated under various compressive and noisy observation scenarios using both simulated data and experimental measurements. The performance is also compared with sparsity priors and the commonly used analytical approaches such as back-projection and Kirchhoff migration. The results demonstrate that the developed technique not only provides state-of-the-art reconstruction performance for 3D real-world targets, but also enables fast computation. Our approach provides a unified general framework to effectively handle arbitrary regularization on the magnitude of a complex-valued unknown and is equally applicable to other radar image formation problems (including SAR).

  • 2 authors
·
Dec 26, 2023

Efficient 3-D Near-Field MIMO-SAR Imaging for Irregular Scanning Geometries

In this article, we introduce a novel algorithm for efficient near-field synthetic aperture radar (SAR) imaging for irregular scanning geometries. With the emergence of fifth-generation (5G) millimeter-wave (mmWave) devices, near-field SAR imaging is no longer confined to laboratory environments. Recent advances in positioning technology have attracted significant interest for a diverse set of new applications in mmWave imaging. However, many use cases, such as automotive-mounted SAR imaging, unmanned aerial vehicle (UAV) imaging, and freehand imaging with smartphones, are constrained to irregular scanning geometries. Whereas traditional near-field SAR imaging systems and quick personnel security (QPS) scanners employ highly precise motion controllers to create ideal synthetic arrays, emerging applications, mentioned previously, inherently cannot achieve such ideal positioning. In addition, many Internet of Things (IoT) and 5G applications impose strict size and computational complexity limitations that must be considered for edge mmWave imaging technology. In this study, we propose a novel algorithm to leverage the advantages of non-cooperative SAR scanning patterns, small form-factor multiple-input multiple-output (MIMO) radars, and efficient monostatic planar image reconstruction algorithms. We propose a framework to mathematically decompose arbitrary and irregular sampling geometries and a joint solution to mitigate multistatic array imaging artifacts. The proposed algorithm is validated through simulations and an empirical study of arbitrary scanning scenarios. Our algorithm achieves high-resolution and high-efficiency near-field MIMO-SAR imaging, and is an elegant solution to computationally constrained irregularly sampled imaging problems.

  • 2 authors
·
May 3, 2023

Efficient Physics-Based Learned Reconstruction Methods for Real-Time 3D Near-Field MIMO Radar Imaging

Near-field multiple-input multiple-output (MIMO) radar imaging systems have recently gained significant attention. In this paper, we develop novel non-iterative deep learning-based reconstruction methods for real-time near-field MIMO imaging. The goal is to achieve high image quality with low computational cost at compressive settings. The developed approaches have two stages. In the first approach, physics-based initial stage performs adjoint operation to back-project the measurements to the image-space, and deep neural network (DNN)-based second stage converts the 3D backprojected measurements to a magnitude-only reflectivity image. Since scene reflectivities often have random phase, DNN processes directly the magnitude of the adjoint result. As DNN, 3D U-Net is used to jointly exploit range and cross-range correlations. To comparatively evaluate the significance of exploiting physics in a learning-based approach, two additional approaches that replace the physics-based first stage with fully connected layers are also developed as purely learning-based methods. The performance is also analyzed by changing the DNN architecture for the second stage to include complex-valued processing (instead of magnitude-only processing), 2D convolution kernels (instead of 3D), and ResNet architecture (instead of U-Net). Moreover, we develop a synthesizer to generate large-scale dataset for training with 3D extended targets. We illustrate the performance through experimental data and extensive simulations. The results show the effectiveness of the developed physics-based learned reconstruction approach in terms of both run-time and image quality at highly compressive settings. Our source codes and dataset are made available at GitHub.

  • 3 authors
·
Dec 28, 2023

Near-Field MIMO-ISAR Millimeter-Wave Imaging

Multiple-input-multiple-output (MIMO) millimeter-wave (mmWave) sensors for synthetic aperture radar (SAR) and inverse SAR (ISAR) address the fundamental challenges of cost-effectiveness and scalability inherent to near-field imaging. In this paper, near-field MIMO-ISAR mmWave imaging systems are discussed and developed. The rotational ISAR (R-ISAR) regime investigated in this paper requires rotating the target at a constant radial distance from the transceiver and scanning the transceiver along a vertical track. Using a 77GHz mmWave radar, a high resolution three-dimensional (3-D) image can be reconstructed from this two-dimensional scanning taking into account the spherical near-field wavefront. While prior work in literature consists of single-input-single-output circular synthetic aperture radar (SISO-CSAR) algorithms or computationally sluggish MIMO-CSAR image reconstruction algorithms, this paper proposes a novel algorithm for efficient MIMO 3-D holographic imaging and details the design of a MIMO R-ISAR imaging system. The proposed algorithm applies a multistatic-to-monostatic phase compensation to the R-ISAR regime allowing for use of highly efficient monostatic algorithms. We demonstrate the algorithm's performance in real-world imaging scenarios on a prototyped MIMO R-ISAR platform. Our fully integrated system, consisting of a mechanical scanner and efficient imaging algorithm, is capable of pairing the scanning efficiency of the MIMO regime with the computational efficiency of single pixel image reconstruction algorithms.

  • 3 authors
·
May 3, 2023

Learning Sub-Sampling and Signal Recovery with Applications in Ultrasound Imaging

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data.

  • 5 authors
·
Aug 15, 2019

Beyond H&E: Unlocking Pathological Insights with Polarization Imaging

Histopathology image analysis is fundamental to digital pathology, with hematoxylin and eosin (H&E) staining as the gold standard for diagnostic and prognostic assessments. While H&E imaging effectively highlights cellular and tissue structures, it lacks sensitivity to birefringence and tissue anisotropy, which are crucial for assessing collagen organization, fiber alignment, and microstructural alterations--key indicators of tumor progression, fibrosis, and other pathological conditions. To bridge this gap, we construct a polarization imaging system and curate a new dataset of over 13,000 paired Polar-H&E images. Visualizations of polarization properties reveal distinctive optical signatures in pathological tissues, underscoring its diagnostic value. Building on this dataset, we propose PolarHE, a dual-modality fusion framework that integrates H&E with polarization imaging, leveraging the latter ability to enhance tissue characterization. Our approach employs a feature decomposition strategy to disentangle common and modality specific features, ensuring effective multimodal representation learning. Through comprehensive validation, our approach significantly outperforms previous methods, achieving an accuracy of 86.70% on the Chaoyang dataset and 89.06% on the MHIST dataset. These results demonstrate that polarization imaging is a powerful and underutilized modality in computational pathology, enriching feature representation and improving diagnostic accuracy. PolarHE establishes a promising direction for multimodal learning, paving the way for more interpretable and generalizable pathology models.

  • 8 authors
·
Nov 14, 2025

The Path to Self-Evolving Clinical Systems: Scaling Medical Agents from Assistance to Autonomy

The growing ability of large language models and vision language models to jointly interpret and reason over images and text is reshaping medical agents, moving them from task specific predictors toward autonomous systems that perceive, reason, plan, remember, and act in clinical environments. This work departs from the capability first perspective of existing literature and instead begins from clinical deployment, asking what tasks, contamination resistant benchmarks, and interactive training environments are required before medical agents can be trusted in practice. Medical agents are formalized as sequential decision making systems under partial observability, together with a three level autonomy taxonomy spanning assisted, cooperative, and fully autonomous operation. The field is organized along a unified scaling spine consisting of framework scaling, capability scaling, and environment scaling. Within this framework, clinical environment scaling, the integration of tools, data, and clinical gyms, is identified as the most actionable yet underexplored direction for agents operating in PACS, EHR, and FHIR ecosystems. Clinical self evolution, where agents improve through interaction with their environments rather than parameter scaling alone, is further positioned as a key research frontier, drawing insights from self improving agents, agent gyms, and test time compute scaling. Applications across radiology, pathology, ophthalmology, and hospital workflows are examined together with deployment challenges including hallucination, cascading failures, and fairness. By consolidating more than 300 references, with particular emphasis on advances from 2025 to 2026, this work provides a roadmap toward trustworthy, self improving medical imaging systems for real clinical practice.

  • 18 authors
·
Jul 12

Polarization aberrations in next-generation Giant Segmented Mirror Telescopes (GSMTs). II. Influence of segment-to-segment coating variations on high-contrast imaging and polarimetry

Direct exo-Earth imaging is a key science goal for astronomy in the next decade. This ambitious task imposes a target contrast of ~10^-7 at wavelengths from I to J-band. In our prior study, we determined that polarization aberrations can limit the achievable contrast to 10^-5 to 10^-6 in the infrared. However, these results assumed a perfect coronagraph coupled to a telescope with an ideal coating on each of the mirrors. In this study we seek to understand the influence of polarization aberrations from segment-to-segment coating variations on coronagraphy and polarimetry. We use the Poke open-source polarization ray tracing package to compute the Jones pupil of each GSMT with spatially-varying coatings applied to the segments. The influence of the resultant polarization aberrations is simulated by propagating the Jones pupil through physical optics models of coronagraphs using HCIPy. After applying wavefront control from an ideal adaptive optics system, we determine that the segment-to-segment variations applied limit the performance of coronagraphy to a raw contrast of approximately 10^-8 in I-band, which is 2-3 orders of magnitude lower the target performance for high-contrast imaging systems on the ground. This is a negligible addition to the nominal polarization aberrations for ground-based systems. We further observe negligible degradation in polarimetric imaging of debris disks from segment-to-segment aberrations above and beyond the impact of nominal polarization aberration.

  • 11 authors
·
Jan 7, 2025

Interferometer response characterization algorithm for multi-aperture Fabry-Perot imaging spectrometers

In recent years, the demand for hyperspectral imaging devices has grown significantly, driven by their ability of capturing high-resolution spectral information. Among the several possible optical designs for acquiring hyperspectral images, there is a growing interest in interferometric spectral imaging systems based on division of aperture. These systems have the advantage of capturing snapshot acquisitions while maintaining a compact design. However, they require a careful calibration to operate properly. In this work, we present the interferometer response characterization algorithm (IRCA), a robust three-step procedure designed to characterize the transmittance response of multi-aperture imaging spectrometers based on the interferometry of Fabry-Perot. Additionally, we propose a formulation of the image formation model for such devices suitable to estimate the parameters of interest by considering the model under various regimes of finesse. The proposed algorithm processes the image output obtained from a set of monochromatic light sources and refines the results using nonlinear regression after an ad-hoc initialization. Through experimental analysis conducted on four different prototypes from the Image SPectrometer On Chip (ImSPOC) family, we validate the performance of our approach for characterization. The associated source code for this paper is available at https://github.com/danaroth83/irca.

  • 5 authors
·
Mar 24, 2023

S3Simulator: A benchmarking Side Scan Sonar Simulator dataset for Underwater Image Analysis

Acoustic sonar imaging systems are widely used for underwater surveillance in both civilian and military sectors. However, acquiring high-quality sonar datasets for training Artificial Intelligence (AI) models confronts challenges such as limited data availability, financial constraints, and data confidentiality. To overcome these challenges, we propose a novel benchmark dataset of Simulated Side-Scan Sonar images, which we term as 'S3Simulator dataset'. Our dataset creation utilizes advanced simulation techniques to accurately replicate underwater conditions and produce diverse synthetic sonar imaging. In particular, the cutting-edge AI segmentation tool i.e. Segment Anything Model (SAM) is leveraged for optimally isolating and segmenting the object images, such as ships and planes, from real scenes. Further, advanced Computer-Aided Design tools i.e. SelfCAD and simulation software such as Gazebo are employed to create the 3D model and to optimally visualize within realistic environments, respectively. Further, a range of computational imaging techniques are employed to improve the quality of the data, enabling the AI models for the analysis of the sonar images. Extensive analyses are carried out on S3simulator as well as real sonar datasets to validate the performance of AI models for underwater object classification. Our experimental results highlight that the S3Simulator dataset will be a promising benchmark dataset for research on underwater image analysis. https://github.com/bashakamal/S3Simulator.

  • 2 authors
·
Aug 22, 2024

Deep Convolutional Neural Network based Classification of Alzheimer's Disease using MRI data

Alzheimer's disease (AD) is a progressive and incurable neurodegenerative disease which destroys brain cells and causes loss to patient's memory. An early detection can prevent the patient from further damage of the brain cells and hence avoid permanent memory loss. In past few years, various automatic tools and techniques have been proposed for diagnosis of AD. Several methods focus on fast, accurate and early detection of the disease to minimize the loss to patients mental health. Although machine learning and deep learning techniques have significantly improved medical imaging systems for AD by providing diagnostic performance close to human level. But the main problem faced during multi-class classification is the presence of highly correlated features in the brain structure. In this paper, we have proposed a smart and accurate way of diagnosing AD based on a two-dimensional deep convolutional neural network (2D-DCNN) using imbalanced three-dimensional MRI dataset. Experimental results on Alzheimer Disease Neuroimaging Initiative magnetic resonance imaging (MRI) dataset confirms that the proposed 2D-DCNN model is superior in terms of accuracy, efficiency, and robustness. The model classifies MRI into three categories: AD, mild cognitive impairment, and normal control: and has achieved 99.89% classification accuracy with imbalanced classes. The proposed model exhibits noticeable improvement in accuracy as compared to the state-fo-the-art methods.

  • 6 authors
·
Jan 8, 2021

Moment-Reenacting: Inverse Motion Degradation with Cross-shutter Guidance

Motion degradation, manifested as blur in global shutter (GS) images or rolling shutter (RS) distortion in RS counterparts, remains a fundamental challenge in computational imaging, especially under fast motion or low-light conditions. While prior works have treated blur decomposition and RS temporal super-resolution as separate tasks, this separation fails to exploit their intrinsic complementarity. In this paper, we propose a unified framework to invert motion degradation and reenact imaging moment by jointly leveraging the complementary characteristics of GS blur and RS distortion. To this end, we introduce a novel dual-shutter setup that captures synchronized blur-RS image pairs and demonstrate that this combination effectively resolves temporal and spatial ambiguities inherent in both modalities. For allowing flexible performance-cost trade-offs, we further extend this dual-shutter setup to a stereo Blur-RS configuration with a narrow baseline. In addition, we construct a triaxial imaging system to collect a real-world dataset with aligned GS-RS pairs and ground-truth high-speed frames, enabling robust training and evaluation beyond synthetic data. Our proposed network explicitly disentangles motion into context-aware and temporally-sensitive representations via a dual-stream motion interpretation module, followed by a self-prompted frame reconstruction stage. Extensive experiments validate the superiority and generalizability of our approach, establishing a new paradigm for realistic high-speed video reconstruction under complex motion degradations. Codes and more resources are available at https://jixiang2016.github.io/dualBR_site/.

  • 5 authors
·
May 21

Multi-interactive Feature Learning and a Full-time Multi-modality Benchmark for Image Fusion and Segmentation

Multi-modality image fusion and segmentation play a vital role in autonomous driving and robotic operation. Early efforts focus on boosting the performance for only one task, e.g., fusion or segmentation, making it hard to reach~`Best of Both Worlds'. To overcome this issue, in this paper, we propose a Multi-interactive Feature learning architecture for image fusion and Segmentation, namely SegMiF, and exploit dual-task correlation to promote the performance of both tasks. The SegMiF is of a cascade structure, containing a fusion sub-network and a commonly used segmentation sub-network. By slickly bridging intermediate features between two components, the knowledge learned from the segmentation task can effectively assist the fusion task. Also, the benefited fusion network supports the segmentation one to perform more pretentiously. Besides, a hierarchical interactive attention block is established to ensure fine-grained mapping of all the vital information between two tasks, so that the modality/semantic features can be fully mutual-interactive. In addition, a dynamic weight factor is introduced to automatically adjust the corresponding weights of each task, which can balance the interactive feature correspondence and break through the limitation of laborious tuning. Furthermore, we construct a smart multi-wave binocular imaging system and collect a full-time multi-modality benchmark with 15 annotated pixel-level categories for image fusion and segmentation. Extensive experiments on several public datasets and our benchmark demonstrate that the proposed method outputs visually appealing fused images and perform averagely 7.66% higher segmentation mIoU in the real-world scene than the state-of-the-art approaches. The source code and benchmark are available at https://github.com/JinyuanLiu-CV/SegMiF.

  • 8 authors
·
Aug 3, 2023

MINIMA: Modality Invariant Image Matching

Image matching for both cross-view and cross-modality plays a critical role in multimodal perception. In practice, the modality gap caused by different imaging systems/styles poses great challenges to the matching task. Existing works try to extract invariant features for specific modalities and train on limited datasets, showing poor generalization. In this paper, we present MINIMA, a unified image matching framework for multiple cross-modal cases. Without pursuing fancy modules, our MINIMA aims to enhance universal performance from the perspective of data scaling up. For such purpose, we propose a simple yet effective data engine that can freely produce a large dataset containing multiple modalities, rich scenarios, and accurate matching labels. Specifically, we scale up the modalities from cheap but rich RGB-only matching data, by means of generative models. Under this setting, the matching labels and rich diversity of the RGB dataset are well inherited by the generated multimodal data. Benefiting from this, we construct MD-syn, a new comprehensive dataset that fills the data gap for general multimodal image matching. With MD-syn, we can directly train any advanced matching pipeline on randomly selected modality pairs to obtain cross-modal ability. Extensive experiments on in-domain and zero-shot matching tasks, including 19 cross-modal cases, demonstrate that our MINIMA can significantly outperform the baselines and even surpass modality-specific methods. The dataset and code are available at https://github.com/LSXI7/MINIMA .

  • 6 authors
·
Dec 26, 2024 2

Toward Generalized Image Quality Assessment: Relaxing the Perfect Reference Quality Assumption

Full-reference image quality assessment (FR-IQA) generally assumes that reference images are of perfect quality. However, this assumption is flawed due to the sensor and optical limitations of modern imaging systems. Moreover, recent generative enhancement methods are capable of producing images of higher quality than their original. All of these challenge the effectiveness and applicability of current FR-IQA models. To relax the assumption of perfect reference image quality, we build a large-scale IQA database, namely DiffIQA, containing approximately 180,000 images generated by a diffusion-based image enhancer with adjustable hyper-parameters. Each image is annotated by human subjects as either worse, similar, or better quality compared to its reference. Building on this, we present a generalized FR-IQA model, namely Adaptive Fidelity-Naturalness Evaluator (A-FINE), to accurately assess and adaptively combine the fidelity and naturalness of a test image. A-FINE aligns well with standard FR-IQA when the reference image is much more natural than the test image. We demonstrate by extensive experiments that A-FINE surpasses standard FR-IQA models on well-established IQA datasets and our newly created DiffIQA. To further validate A-FINE, we additionally construct a super-resolution IQA benchmark (SRIQA-Bench), encompassing test images derived from ten state-of-the-art SR methods with reliable human quality annotations. Tests on SRIQA-Bench re-affirm the advantages of A-FINE. The code and dataset are available at https://tianhewu.github.io/A-FINE-page.github.io/.

  • 4 authors
·
Mar 14, 2025

Towards Scalable Foundation Model for Multi-modal and Hyperspectral Geospatial Data

Geospatial raster data, such as that collected by satellite-based imaging systems at different times and spectral bands, hold immense potential for enabling a wide range of high-impact applications. This potential stems from the rich information that is spatially and temporally contextualized across multiple channels and sensing modalities. Recent work has adapted existing self-supervised learning approaches for such geospatial data. However, they fall short of scalable model architectures, leading to inflexibility and computational inefficiencies when faced with an increasing number of channels and modalities. To address these limitations, we introduce Low-rank Efficient Spatial-Spectral Vision Transformer with three key innovations: i) the LESS Attention Block that approximates high-dimensional spatial-spectral attention through Kronecker's product of the low-dimensional spatial and spectral attention components; ii) the Continuous Positional-Channel Embedding Layer that preserves both the continuity and physical characteristics of each spatial-spectral patch; and iii) the Perception Field Mask that exploits local spatial dependencies by constraining attention to neighboring patches. To evaluate the proposed innovations, we construct GFM-Bench, which serves as a comprehensive benchmark for such geospatial raster data. We pretrain LESS ViT using a Hyperspectral Masked Autoencoder framework with integrated positional and channel masking strategies. Experimental results demonstrate that our proposed method achieves competitive performance against state-of-the-art multi-modal geospatial foundation models while outperforming them on cross-satellite generalization tasks with higher computational efficiency. The flexibility and extensibility of our framework make it a promising direction for future geospatial data analysis tasks that involve a wide range of modalities and channels.

  • 6 authors
·
Mar 17, 2025

PhyMRI-SR: Toward Physics-Aware MRI Image Super-Resolution

Magnetic resonance imaging (MRI) super-resolution is vital for improving diagnostic accessibility, yet most methods treat it as a deterministic mapping from a fixed low-resolution input to a high-resolution target. This overlooks a key property of MRI acquisition physics: spatial resolution and signal-to-noise ratio (SNR) are inherently coupled, making any given low-resolution scan merely one of many possible realizations under varying acquisition trade-offs. We rethink MRI super-resolution as a physics-aware reconstruction problem, in which the goal is to identify the optimal resolution-SNR configuration and then super-resolve it to obtain high-quality MRI results. A key implication of this formulation is that MRI resolution becomes dynamic rather than fixed. To handle such resolution-heterogeneous inputs, we adapt 2D Gaussian Splatting (2D GS) to MRI by formulating reconstruction as a coordinate-based, resolution-agnostic rendering problem. To further enhance fidelity, we introduce three innovations: (1) a prior-aware Gaussian representation that combines an Anatomical Structure Prior for tissue-specific kernel initialization with an Imaging System Prior that captures hardware characteristics via a covariance dictionary; (2) a physics-constrained signal modeling scheme that predicts intrinsic tissue parameters (proton density rho and effective relaxation rate R2) and synthesizes intensities through governing physical equations, ensuring biophysically plausible contrast; and (3) a meta-learning framework that alleviates paired-data scarcity by pretraining on simulated data and adapting to real-world conditions. Extensive experiments on dynamic-resolution datasets and standard benchmarks demonstrate that our method achieves state-of-the-art performance, highlighting its strong potential for clinical deployment.

Planktonzilla: Multimodal dataset and models for understanding plankton ecosystems

Marine plankton underpin aquatic food webs and play a key role in global CO2 sequestration, making reliable species identification critical for understanding ocean health and climate feedbacks. Existing classification models perform well on individual collections but fail to generalize across instruments and environments due to isolated training datasets and inconsistent labels. To address this, we introduce Planktonzilla-17M, a unified dataset consolidating publicly available plankton image collections spanning thirteen imaging systems. It comprises 17.4 million images with standardized taxonomy and geo-environmental metadata, including 3.74 million plankton images spanning over 602 taxonomic classes, of which 201 are identified at the species level, making it the largest and most comprehensive plankton image dataset to date. Using this large-scale dataset, we perform a controlled comparison between supervised and CLIP-style image--text training on a shared ViT backbone. We find that a supervised classifier matches or exceeds CLIP-style training when trained using taxonomic lineage as text. We further observe that BioCLIP and BioCLIP2 perform poorly on plankton in zero-shot and few-shot settings. Leveraging Planktonzilla-17M improves plankton classification performance, highlighting the limitations of current biological foundation models in marine imaging domains.

AdverX-Ray: Ensuring X-Ray Integrity Through Frequency-Sensitive Adversarial VAEs

Ensuring the quality and integrity of medical images is crucial for maintaining diagnostic accuracy in deep learning-based Computer-Aided Diagnosis and Computer-Aided Detection (CAD) systems. Covariate shifts are subtle variations in the data distribution caused by different imaging devices or settings and can severely degrade model performance, similar to the effects of adversarial attacks. Therefore, it is vital to have a lightweight and fast method to assess the quality of these images prior to using CAD models. AdverX-Ray addresses this need by serving as an image-quality assessment layer, designed to detect covariate shifts effectively. This Adversarial Variational Autoencoder prioritizes the discriminator's role, using the suboptimal outputs of the generator as negative samples to fine-tune the discriminator's ability to identify high-frequency artifacts. Images generated by adversarial networks often exhibit severe high-frequency artifacts, guiding the discriminator to focus excessively on these components. This makes the discriminator ideal for this approach. Trained on patches from X-ray images of specific machine models, AdverX-Ray can evaluate whether a scan matches the training distribution, or if a scan from the same machine is captured under different settings. Extensive comparisons with various OOD detection methods show that AdverX-Ray significantly outperforms existing techniques, achieving a 96.2% average AUROC using only 64 random patches from an X-ray. Its lightweight and fast architecture makes it suitable for real-time applications, enhancing the reliability of medical imaging systems. The code and pretrained models are publicly available.

  • 5 authors
·
Feb 23, 2025

Low-Dose CT Image Enhancement Using Deep Learning

The application of ionizing radiation for diagnostic imaging is common around the globe. However, the process of imaging, itself, remains to be a relatively hazardous operation. Therefore, it is preferable to use as low a dose of ionizing radiation as possible, particularly in computed tomography (CT) imaging systems, where multiple x-ray operations are performed for the reconstruction of slices of body tissues. A popular method for radiation dose reduction in CT imaging is known as the quarter-dose technique, which reduces the x-ray dose but can cause a loss of image sharpness. Since CT image reconstruction from directional x-rays is a nonlinear process, it is analytically difficult to correct the effect of dose reduction on image quality. Recent and popular deep-learning approaches provide an intriguing possibility of image enhancement for low-dose artifacts. Some recent works propose combinations of multiple deep-learning and classical methods for this purpose, which over-complicate the process. However, it is observed here that the straight utilization of the well-known U-NET provides very successful results for the correction of low-dose artifacts. Blind tests with actual radiologists reveal that the U-NET enhanced quarter-dose CT images not only provide an immense visual improvement over the low-dose versions, but also become diagnostically preferable images, even when compared to their full-dose CT versions.

  • 9 authors
·
Oct 31, 2023

OmniHD-Scenes: A Next-Generation Multimodal Dataset for Autonomous Driving

The rapid advancement of deep learning has intensified the need for comprehensive data for use by autonomous driving algorithms. High-quality datasets are crucial for the development of effective data-driven autonomous driving solutions. Next-generation autonomous driving datasets must be multimodal, incorporating data from advanced sensors that feature extensive data coverage, detailed annotations, and diverse scene representation. To address this need, we present OmniHD-Scenes, a large-scale multimodal dataset that provides comprehensive omnidirectional high-definition data. The OmniHD-Scenes dataset combines data from 128-beam LiDAR, six cameras, and six 4D imaging radar systems to achieve full environmental perception. The dataset comprises 1501 clips, each approximately 30-s long, totaling more than 450K synchronized frames and more than 5.85 million synchronized sensor data points. We also propose a novel 4D annotation pipeline. To date, we have annotated 200 clips with more than 514K precise 3D bounding boxes. These clips also include semantic segmentation annotations for static scene elements. Additionally, we introduce a novel automated pipeline for generation of the dense occupancy ground truth, which effectively leverages information from non-key frames. Alongside the proposed dataset, we establish comprehensive evaluation metrics, baseline models, and benchmarks for 3D detection and semantic occupancy prediction. These benchmarks utilize surround-view cameras and 4D imaging radar to explore cost-effective sensor solutions for autonomous driving applications. Extensive experiments demonstrate the effectiveness of our low-cost sensor configuration and its robustness under adverse conditions. Data will be released at https://www.2077ai.com/OmniHD-Scenes.

  • 13 authors
·
Dec 14, 2024

Imaging and controlling electron motion and chemical structural dynamics of biological system in real time and space

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

  • 7 authors
·
Oct 2, 2025

When Language Overwrites Vision: Over-Alignment and Geometric Debiasing in Vision-Language Models

Vision-Language Models (VLMs) increasingly power high-stakes applications, from medical imaging to autonomous systems, yet they routinely hallucinate, confidently describing content not present in the input. We investigate the root causes of these failure modes with a mechanistic analysis focusing on the decoder-based VLMs. We trace these failure modes to a geometric over-alignment: to bridge the modality gap required by attention mechanisms, decoder-based VLMs over-align visual embeddings with the text manifold, injecting a statistical linguistic bias that systematically overshadows fine-grained visual evidence. While prior work either aggressively closes this gap or suppresses hallucinations through expensive black-box decoding strategies, none addresses the underlying geometric cause. We provide the first quantitative characterization of this over-alignment, demonstrating that linguistic bias concentrates in the top principal components of a universal, dataset-agnostic text subspace. Building on this insight, we propose two complementary remedies: a training-free inference strategy and a bias-aware fine-tuning paradigm, both of which explicitly project out this subspace from visual representations. Our methods significantly reduce hallucinations across POPE, CHAIR, and AMBER benchmarks, and improve CLAIR scores on long-form captioning tasks, with the training-free variant adding no computational overhead over the base model.

  • 4 authors
·
Jun 22

Radiogenomic biomarkers for immunotherapy in glioblastoma: A systematic review of magnetic resonance imaging studies

Immunotherapy is an effective precision medicine treatment for several cancers. Imaging signatures of the underlying genome (radiogenomics) in glioblastoma patients may serve as preoperative biomarkers of the tumor-host immune apparatus. Validated biomarkers would have the potential to stratify patients during immunotherapy clinical trials, and if trials are beneficial, facilitate personalized neo-adjuvant treatment. The increased use of whole genome sequencing data, and the advances in bioinformatics and machine learning make such developments plausible. We performed a systematic review to determine the extent of development and validation of immune-related radiogenomic biomarkers for glioblastoma. A systematic review was performed following PRISMA guidelines using the PubMed, Medline, and Embase databases. Qualitative analysis was performed by incorporating the QUADAS 2 tool and CLAIM checklist. PROSPERO registered CRD42022340968. Extracted data were insufficiently homogenous to perform a meta-analysis. Results Nine studies, all retrospective, were included. Biomarkers extracted from magnetic resonance imaging volumes of interest included apparent diffusion coefficient values, relative cerebral blood volume values, and image-derived features. These biomarkers correlated with genomic markers from tumor cells or immune cells or with patient survival. The majority of studies had a high risk of bias and applicability concerns regarding the index test performed. Radiogenomic immune biomarkers have the potential to provide early treatment options to patients with glioblastoma. Targeted immunotherapy, stratified by these biomarkers, has the potential to allow individualized neo-adjuvant precision treatment options in clinical trials. However, there are no prospective studies validating these biomarkers, and interpretation is limited due to study bias with little evidence of generalizability.

  • 8 authors
·
May 12, 2024

A co-evolving agentic AI system for medical imaging analysis

Agentic AI is rapidly advancing in healthcare and biomedical research. However, in medical image analysis, their performance and adoption remain limited due to the lack of a robust ecosystem, insufficient toolsets, and the absence of real-time interactive expert feedback. Here we present "TissueLab", a co-evolving agentic AI system that allows researchers to ask direct questions, automatically plan and generate explainable workflows, and conduct real-time analyses where experts can visualize intermediate results and refine them. TissueLab integrates tool factories across pathology, radiology, and spatial omics domains. By standardizing inputs, outputs, and capabilities of diverse tools, the system determines when and how to invoke them to address research and clinical questions. Across diverse tasks with clinically meaningful quantifications that inform staging, prognosis, and treatment planning, TissueLab achieves state-of-the-art performance compared with end-to-end vision-language models (VLMs) and other agentic AI systems such as GPT-5. Moreover, TissueLab continuously learns from clinicians, evolving toward improved classifiers and more effective decision strategies. With active learning, it delivers accurate results in unseen disease contexts within minutes, without requiring massive datasets or prolonged retraining. Released as a sustainable open-source ecosystem, TissueLab aims to accelerate computational research and translational adoption in medical imaging while establishing a foundation for the next generation of medical AI.

  • 14 authors
·
Sep 24, 2025

MetaFormer: High-fidelity Metalens Imaging via Aberration Correcting Transformers

Metalens is an emerging optical system with an irreplaceable merit in that it can be manufactured in ultra-thin and compact sizes, which shows great promise of various applications such as medical imaging and augmented/virtual reality (AR/VR). Despite its advantage in miniaturization, its practicality is constrained by severe aberrations and distortions, which significantly degrade the image quality. Several previous arts have attempted to address different types of aberrations, yet most of them are mainly designed for the traditional bulky lens and not convincing enough to remedy harsh aberrations of the metalens. While there have existed aberration correction methods specifically for metalens, they still fall short of restoration quality. In this work, we propose MetaFormer, an aberration correction framework for metalens-captured images, harnessing Vision Transformers (ViT) that has shown remarkable restoration performance in diverse image restoration tasks. Specifically, we devise a Multiple Adaptive Filters Guidance (MAFG), where multiple Wiener filters enrich the degraded input images with various noise-detail balances, enhancing output restoration quality. In addition, we introduce a Spatial and Transposed self-Attention Fusion (STAF) module, which aggregates features from spatial self-attention and transposed self-attention modules to further ameliorate aberration correction. We conduct extensive experiments, including correcting aberrated images and videos, and clean 3D reconstruction from the degraded images. The proposed method outperforms the previous arts by a significant margin. We further fabricate a metalens and verify the practicality of MetaFormer by restoring the images captured with the manufactured metalens in the wild. Code and pre-trained models are available at https://benhenryl.github.io/MetaFormer

  • 10 authors
·
Dec 5, 2024

MediAug: Exploring Visual Augmentation in Medical Imaging

Data augmentation is essential in medical imaging for improving classification accuracy, lesion detection, and organ segmentation under limited data conditions. However, two significant challenges remain. First, a pronounced domain gap between natural photographs and medical images can distort critical disease features. Second, augmentation studies in medical imaging are fragmented and limited to single tasks or architectures, leaving the benefits of advanced mix-based strategies unclear. To address these challenges, we propose a unified evaluation framework with six mix-based augmentation methods integrated with both convolutional and transformer backbones on brain tumour MRI and eye disease fundus datasets. Our contributions are threefold. (1) We introduce MediAug, a comprehensive and reproducible benchmark for advanced data augmentation in medical imaging. (2) We systematically evaluate MixUp, YOCO, CropMix, CutMix, AugMix, and SnapMix with ResNet-50 and ViT-B backbones. (3) We demonstrate through extensive experiments that MixUp yields the greatest improvement on the brain tumor classification task for ResNet-50 with 79.19% accuracy and SnapMix yields the greatest improvement for ViT-B with 99.44% accuracy, and that YOCO yields the greatest improvement on the eye disease classification task for ResNet-50 with 91.60% accuracy and CutMix yields the greatest improvement for ViT-B with 97.94% accuracy. Code will be available at https://github.com/AIGeeksGroup/MediAug.

  • 7 authors
·
Apr 26, 2025 1

LensNet: An End-to-End Learning Framework for Empirical Point Spread Function Modeling and Lensless Imaging Reconstruction

Lensless imaging stands out as a promising alternative to conventional lens-based systems, particularly in scenarios demanding ultracompact form factors and cost-effective architectures. However, such systems are fundamentally governed by the Point Spread Function (PSF), which dictates how a point source contributes to the final captured signal. Traditional lensless techniques often require explicit calibrations and extensive pre-processing, relying on static or approximate PSF models. These rigid strategies can result in limited adaptability to real-world challenges, including noise, system imperfections, and dynamic scene variations, thus impeding high-fidelity reconstruction. In this paper, we propose LensNet, an end-to-end deep learning framework that integrates spatial-domain and frequency-domain representations in a unified pipeline. Central to our approach is a learnable Coded Mask Simulator (CMS) that enables dynamic, data-driven estimation of the PSF during training, effectively mitigating the shortcomings of fixed or sparsely calibrated kernels. By embedding a Wiener filtering component, LensNet refines global structure and restores fine-scale details, thus alleviating the dependency on multiple handcrafted pre-processing steps. Extensive experiments demonstrate LensNet's robust performance and superior reconstruction quality compared to state-of-the-art methods, particularly in preserving high-frequency details and attenuating noise. The proposed framework establishes a novel convergence between physics-based modeling and data-driven learning, paving the way for more accurate, flexible, and practical lensless imaging solutions for applications ranging from miniature sensors to medical diagnostics. The link of code is https://github.com/baijiesong/Lensnet.

  • 6 authors
·
May 3, 2025

MedBookVQA: A Systematic and Comprehensive Medical Benchmark Derived from Open-Access Book

The accelerating development of general medical artificial intelligence (GMAI), powered by multimodal large language models (MLLMs), offers transformative potential for addressing persistent healthcare challenges, including workforce deficits and escalating costs. The parallel development of systematic evaluation benchmarks emerges as a critical imperative to enable performance assessment and provide technological guidance. Meanwhile, as an invaluable knowledge source, the potential of medical textbooks for benchmark development remains underexploited. Here, we present MedBookVQA, a systematic and comprehensive multimodal benchmark derived from open-access medical textbooks. To curate this benchmark, we propose a standardized pipeline for automated extraction of medical figures while contextually aligning them with corresponding medical narratives. Based on this curated data, we generate 5,000 clinically relevant questions spanning modality recognition, disease classification, anatomical identification, symptom diagnosis, and surgical procedures. A multi-tier annotation system categorizes queries through hierarchical taxonomies encompassing medical imaging modalities (42 categories), body anatomies (125 structures), and clinical specialties (31 departments), enabling nuanced analysis across medical subdomains. We evaluate a wide array of MLLMs, including proprietary, open-sourced, medical, and reasoning models, revealing significant performance disparities across task types and model categories. Our findings highlight critical capability gaps in current GMAI systems while establishing textbook-derived multimodal benchmarks as essential evaluation tools. MedBookVQA establishes textbook-derived benchmarking as a critical paradigm for advancing clinical AI, exposing limitations in GMAI systems while providing anatomically structured performance metrics across specialties.

  • 7 authors
·
Jun 1, 2025

A multi-path 2.5 dimensional convolutional neural network system for segmenting stroke lesions in brain MRI images

Automatic identification of brain lesions from magnetic resonance imaging (MRI) scans of stroke survivors would be a useful aid in patient diagnosis and treatment planning. We propose a multi-modal multi-path convolutional neural network system for automating stroke lesion segmentation. Our system has nine end-to-end UNets that take as input 2-dimensional (2D) slices and examines all three planes with three different normalizations. Outputs from these nine total paths are concatenated into a 3D volume that is then passed to a 3D convolutional neural network to output a final lesion mask. We trained and tested our method on datasets from three sources: Medical College of Wisconsin (MCW), Kessler Foundation (KF), and the publicly available Anatomical Tracings of Lesions After Stroke (ATLAS) dataset. Cross-study validation results (with independent training and validation datasets) were obtained to compare with previous methods based on naive Bayes, random forests, and three recently published convolutional neural networks. Model performance was quantified in terms of the Dice coefficient. Training on the KF and MCW images and testing on the ATLAS images yielded a mean Dice coefficient of 0.54. This was reliably better than the next best previous model, UNet, at 0.47. Reversing the train and test datasets yields a mean Dice of 0.47 on KF and MCW images, whereas the next best UNet reaches 0.45. With all three datasets combined, the current system compared to previous methods also attained a reliably higher cross-validation accuracy. It also achieved high Dice values for many smaller lesions that existing methods have difficulty identifying. Overall, our system is a clear improvement over previous methods for automating stroke lesion segmentation, bringing us an important step closer to the inter-rater accuracy level of human experts.

  • 7 authors
·
May 26, 2019

ServImage: An Image Generation and Editing Benchmark from Real-world Commercial Imaging Services

Recent image generation and editing models demonstrate robust adherence to instructions and high visual quality on academic benchmarks. However, their performance on paid, real-world design projects remains uncertain. We introduce ServImage, a benchmark that explicitly correlates model outputs with economic value in commercial design projects. ServImage consists of (i) \textit{ServImageBench}: a dataset of 1.07k paid commercial design tasks and 2.05k designer deliverables totaling over \$295k, covering portrait, product, and digital content, along with 33k candidate images and 33k human annotations. (ii) \textit{ServImageScore}: an integrated scoring system that combines three quality dimensions: baseline requirements fulfilment, visual execution quality, and commercial necessity satisfaction. These three dimensions are designed to characterize the factors that drive human payment decisions and indicate whether an image is commercially acceptable. (iii) \textit{ServImageModel}: under this scoring system, we propose a payment prediction model trained on the human-annotated candidate images, achieving 82.00\% accuracy in predicting human payment decisions and producing calibrated payment probabilities. ServImage provides a comprehensive foundation for assessing the commercial viability of image generation models and offers a scalable resource for future research on economically grounded vision systems https://github.com/FengxianJi/ServImage{Github.}

  • 8 authors
·
Apr 26

RAVIR: A Dataset and Methodology for the Semantic Segmentation and Quantitative Analysis of Retinal Arteries and Veins in Infrared Reflectance Imaging

The retinal vasculature provides important clues in the diagnosis and monitoring of systemic diseases including hypertension and diabetes. The microvascular system is of primary involvement in such conditions, and the retina is the only anatomical site where the microvasculature can be directly observed. The objective assessment of retinal vessels has long been considered a surrogate biomarker for systemic vascular diseases, and with recent advancements in retinal imaging and computer vision technologies, this topic has become the subject of renewed attention. In this paper, we present a novel dataset, dubbed RAVIR, for the semantic segmentation of Retinal Arteries and Veins in Infrared Reflectance (IR) imaging. It enables the creation of deep learning-based models that distinguish extracted vessel type without extensive post-processing. We propose a novel deep learning-based methodology, denoted as SegRAVIR, for the semantic segmentation of retinal arteries and veins and the quantitative measurement of the widths of segmented vessels. Our extensive experiments validate the effectiveness of SegRAVIR and demonstrate its superior performance in comparison to state-of-the-art models. Additionally, we propose a knowledge distillation framework for the domain adaptation of RAVIR pretrained networks on color images. We demonstrate that our pretraining procedure yields new state-of-the-art benchmarks on the DRIVE, STARE, and CHASE_DB1 datasets. Dataset link: https://ravirdataset.github.io/data/

  • 8 authors
·
Mar 28, 2022

Total Nitrogen Estimation in Agricultural Soils via Aerial Multispectral Imaging and LIBS

Measuring soil health indicators is an important and challenging task that affects farmers' decisions on timing, placement, and quantity of fertilizers applied in the farms. Most existing methods to measure soil health indicators (SHIs) are in-lab wet chemistry or spectroscopy-based methods, which require significant human input and effort, time-consuming, costly, and are low-throughput in nature. To address this challenge, we develop an artificial intelligence (AI)-driven near real-time unmanned aerial vehicle (UAV)-based multispectral sensing (UMS) solution to estimate total nitrogen (TN) of the soil, an important macro-nutrient or SHI that directly affects the crop health. Accurate prediction of soil TN can significantly increase crop yield through informed decision making on the timing of seed planting, and fertilizer quantity and timing. We train two machine learning models including multi-layer perceptron and support vector machine to predict the soil nitrogen using a suite of data classes including multispectral characteristics of the soil and crops in red, near-infrared, and green spectral bands, computed vegetation indices, and environmental variables including air temperature and relative humidity. To generate the ground-truth data or the training data for the machine learning models, we measure the total nitrogen of the soil samples (collected from a farm) using laser-induced breakdown spectroscopy (LIBS).

  • 3 authors
·
Jul 5, 2021

Robust diffraction-limited NIR-to-NUV wide-field imaging from stratospheric balloon-borne platforms -- SuperBIT science telescope commissioning flight & performance

At a fraction the total cost of an equivalent orbital mission, scientific balloon-borne platforms, operating above 99.7% of the Earth's atmosphere, offer attractive, competitive, and effective observational capabilities -- namely space-like resolution, transmission, and backgrounds -- that are well suited for modern astronomy and cosmology. SuperBIT is a diffraction-limited, wide-field, 0.5 m telescope capable of exploiting these observing conditions in order to provide exquisite imaging throughout the near-IR to near-UV. It utilizes a robust active stabilization system that has consistently demonstrated a 1 sigma sky-fixed pointing stability at 48 milliarcseconds over multiple 1 hour observations at float. This is achieved by actively tracking compound pendulations via a three-axis gimballed platform, which provides sky-fixed telescope stability at < 500 milliarcseconds and corrects for field rotation, while employing high-bandwidth tip/tilt optics to remove residual disturbances across the science imaging focal plane. SuperBIT's performance during the 2019 commissioning flight benefited from a customized high-fidelity science-capable telescope designed with exceptional thermo- and opto-mechanical stability as well as tightly constrained static and dynamic coupling between high-rate sensors and telescope optics. At the currently demonstrated level of flight performance, SuperBIT capabilities now surpass the science requirements for a wide variety of experiments in cosmology, astrophysics and stellar dynamics.

  • 29 authors
·
Nov 25, 2019

A Unified Framework for Forward and Inverse Problems in Subsurface Imaging using Latent Space Translations

In subsurface imaging, learning the mapping from velocity maps to seismic waveforms (forward problem) and waveforms to velocity (inverse problem) is important for several applications. While traditional techniques for solving forward and inverse problems are computationally prohibitive, there is a growing interest in leveraging recent advances in deep learning to learn the mapping between velocity maps and seismic waveform images directly from data. Despite the variety of architectures explored in previous works, several open questions still remain unanswered such as the effect of latent space sizes, the importance of manifold learning, the complexity of translation models, and the value of jointly solving forward and inverse problems. We propose a unified framework to systematically characterize prior research in this area termed the Generalized Forward-Inverse (GFI) framework, building on the assumption of manifolds and latent space translations. We show that GFI encompasses previous works in deep learning for subsurface imaging, which can be viewed as specific instantiations of GFI. We also propose two new model architectures within the framework of GFI: Latent U-Net and Invertible X-Net, leveraging the power of U-Nets for domain translation and the ability of IU-Nets to simultaneously learn forward and inverse translations, respectively. We show that our proposed models achieve state-of-the-art (SOTA) performance for forward and inverse problems on a wide range of synthetic datasets, and also investigate their zero-shot effectiveness on two real-world-like datasets. Our code is available at https://github.com/KGML-lab/Generalized-Forward-Inverse-Framework-for-DL4SI

  • 5 authors
·
Oct 15, 2024

Closing the Domain Gap in Biomedical Imaging by In-Context Control Samples

The central problem in biomedical imaging are batch effects: systematic technical variations unrelated to the biological signal of interest. These batch effects critically undermine experimental reproducibility and are the primary cause of failure of deep learning systems on new experimental batches, preventing their practical use in the real world. Despite years of research, no method has succeeded in closing this performance gap for deep learning models. We propose Control-Stabilized Adaptive Risk Minimization via Batch Normalization (CS-ARM-BN), a meta-learning adaptation method that exploits negative control samples. Such unperturbed reference images are present in every experimental batch by design and serve as stable context for adaptation. We validate our novel method on Mechanism-of-Action (MoA) classification, a crucial task for drug discovery, on the large-scale JUMP-CP dataset. The accuracy of standard ResNets drops from 0.939 pm 0.005, on the training domain, to 0.862 pm 0.060 on data from new experimental batches. Foundation models, even after Typical Variation Normalization, fail to close this gap. We are the first to show that meta-learning approaches close the domain gap by achieving 0.935 pm 0.018. If the new experimental batches exhibit strong domain shifts, such as being generated in a different lab, meta-learning approaches can be stabilized with control samples, which are always available in biomedical experiments. Our work shows that batch effects in bioimaging data can be effectively neutralized through principled in-context adaptation, which also makes them practically usable and efficient.

  • 4 authors
·
Apr 21

The Role of AI in Early Detection of Life-Threatening Diseases: A Retinal Imaging Perspective

Retinal imaging has emerged as a powerful, non-invasive modality for detecting and quantifying biomarkers of systemic diseases-ranging from diabetes and hypertension to Alzheimer's disease and cardiovascular disorders but current insights remain dispersed across platforms and specialties. Recent technological advances in optical coherence tomography (OCT/OCTA) and adaptive optics (AO) now deliver ultra-high-resolution scans (down to 5 {\mu}m ) with superior contrast and spatial integration, allowing early identification of microvascular abnormalities and neurodegenerative changes. At the same time, AI-driven and machine learning (ML) algorithms have revolutionized the analysis of large-scale retinal datasets, increasing sensitivity and specificity; for example, deep learning models achieve > 90 \% sensitivity for diabetic retinopathy and AUC = 0.89 for the prediction of cardiovascular risk from fundus photographs. The proliferation of mobile health technologies and telemedicine platforms further extends access, reduces costs, and facilitates community-based screening and longitudinal monitoring. Despite these breakthroughs, translation into routine practice is hindered by heterogeneous imaging protocols, limited external validation of AI models, and integration challenges within clinical workflows. In this review, we systematically synthesize the latest OCT/OCT and AO developments, AI/ML approaches, and mHealth/Tele-ophthalmology initiatives and quantify their diagnostic performance across disease domains. Finally, we propose a roadmap for multicenter protocol standardization, prospective validation trials, and seamless incorporation of retinal screening into primary and specialty care pathways-paving the way for precision prevention, early intervention, and ongoing treatment of life-threatening systemic diseases.

  • 3 authors
·
May 27, 2025

BAAI Cardiac Agent: An intelligent multimodal agent for automated reasoning and diagnosis of cardiovascular diseases from cardiac magnetic resonance imaging

Cardiac magnetic resonance (CMR) is a cornerstone for diagnosing cardiovascular disease. However, it remains underutilized due to complex, time-consuming interpretation across multi-sequences, phases, quantitative measures that heavily reliant on specialized expertise. Here, we present BAAI Cardiac Agent, a multimodal intelligent system designed for end-to-end CMR interpretation. The agent integrates specialized cardiac expert models to perform automated segmentation of cardiac structures, functional quantification, tissue characterization and disease diagnosis, and generates structured clinical reports within a unified workflow. Evaluated on CMR datasets from two hospitals (2413 patients) spanning 7-types of major cardiovascular diseases, the agent achieved an area under the receiver-operating-characteristic curve exceeding 0.93 internally and 0.81 externally. In the task of estimating left ventricular function indices, the results generated by this system for core parameters such as ejection fraction, stroke volume, and left ventricular mass are highly consistent with clinical reports, with Pearson correlation coefficients all exceeding 0.90. The agent outperformed state-of-the-art models in segmentation and diagnostic tasks, and generated clinical reports showing high concordance with expert radiologists (six readers across three experience levels). By dynamically orchestrating expert models for coordinated multimodal analysis, this agent framework enables accurate, efficient CMR interpretation and highlights its potentials for complex clinical imaging workflows. Code is available at https://github.com/plantain-herb/Cardiac-Agent.

  • 21 authors
·
Apr 4

An Integrated AI-Enabled System Using One Class Twin Cross Learning (OCT-X) for Early Gastric Cancer Detection

Early detection of gastric cancer, a leading cause of cancer-related mortality worldwide, remains hampered by the limitations of current diagnostic technologies, leading to high rates of misdiagnosis and missed diagnoses. To address these challenges, we propose an integrated system that synergizes advanced hardware and software technologies to balance speed-accuracy. Our study introduces the One Class Twin Cross Learning (OCT-X) algorithm. Leveraging a novel fast double-threshold grid search strategy (FDT-GS) and a patch-based deep fully convolutional network, OCT-X maximizes diagnostic accuracy through real-time data processing and seamless lesion surveillance. The hardware component includes an all-in-one point-of-care testing (POCT) device with high-resolution imaging sensors, real-time data processing, and wireless connectivity, facilitated by the NI CompactDAQ and LabVIEW software. Our integrated system achieved an unprecedented diagnostic accuracy of 99.70%, significantly outperforming existing models by up to 4.47%, and demonstrated a 10% improvement in multirate adaptability. These findings underscore the potential of OCT-X as well as the integrated system in clinical diagnostics, offering a path toward more accurate, efficient, and less invasive early gastric cancer detection. Future research will explore broader applications, further advancing oncological diagnostics. Code is available at https://github.com/liu37972/Multirate-Location-on-OCT-X-Learning.git.

  • 12 authors
·
Mar 31, 2025

Project Imaging-X: A Survey of 1000+ Open-Access Medical Imaging Datasets for Foundation Model Development

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

Evolving Medical Imaging Agents via Experience-driven Self-skill Discovery

Clinical image interpretation is inherently multi-step and tool-centric: clinicians iteratively combine visual evidence with patient context, quantify findings, and refine their decisions through a sequence of specialized procedures. While LLM-based agents promise to orchestrate such heterogeneous medical tools, existing systems treat tool sets and invocation strategies as static after deployment. This design is brittle under real-world domain shifts, across tasks, and evolving diagnostic requirements, where predefined tool chains frequently degrade and demand costly manual re-design. We propose MACRO, a self-evolving, experience-augmented medical agent that shifts from static tool composition to experience-driven tool discovery. From verified execution trajectories, the agent autonomously identifies recurring effective multi-step tool sequences, synthesizes them into reusable composite tools, and registers these as new high-level primitives that continuously expand its behavioral repertoire. A lightweight image-feature memory grounds tool selection in a visual-clinical context, while a GRPO-like training loop reinforces reliable invocation of discovered composites, enabling closed-loop self-improvement with minimal supervision. Extensive experiments across diverse medical imaging datasets and tasks demonstrate that autonomous composite tool discovery consistently improves multi-step orchestration accuracy and cross-domain generalization over strong baselines and recent state-of-the-art agentic methods, bridging the gap between brittle static tool use and adaptive, context-aware clinical AI assistance. Code will be available upon acceptance.

  • 7 authors
·
Mar 5

Adapting Depth Anything to Adverse Imaging Conditions with Events

Robust depth estimation under dynamic and adverse lighting conditions is essential for robotic systems. Currently, depth foundation models, such as Depth Anything, achieve great success in ideal scenes but remain challenging under adverse imaging conditions such as extreme illumination and motion blur. These degradations corrupt the visual signals of frame cameras, weakening the discriminative features of frame-based depths across the spatial and temporal dimensions. Typically, existing approaches incorporate event cameras to leverage their high dynamic range and temporal resolution, aiming to compensate for corrupted frame features. However, such specialized fusion models are predominantly trained from scratch on domain-specific datasets, thereby failing to inherit the open-world knowledge and robust generalization inherent to foundation models. In this work, we propose ADAE, an event-guided spatiotemporal fusion framework for Depth Anything in degraded scenes. Our design is guided by two key insights: 1) Entropy-Aware Spatial Fusion. We adaptively merge frame-based and event-based features using an information entropy strategy to indicate illumination-induced degradation. 2) Motion-Guided Temporal Correction. We resort to the event-based motion cue to recalibrate ambiguous features in blurred regions. Under our unified framework, the two components are complementary to each other and jointly enhance Depth Anything under adverse imaging conditions. Extensive experiments have been performed to verify the superiority of the proposed method. Our code will be released upon acceptance.

  • 8 authors
·
Jan 4

Robust Single-shot Structured Light 3D Imaging via Neural Feature Decoding

We consider the problem of active 3D imaging using single-shot structured light systems, which are widely employed in commercial 3D sensing devices such as Apple Face ID and Intel RealSense. Traditional structured light methods typically decode depth correspondences through pixel-domain matching algorithms, resulting in limited robustness under challenging scenarios like occlusions, fine-structured details, and non-Lambertian surfaces. Inspired by recent advances in neural feature matching, we propose a learning-based structured light decoding framework that performs robust correspondence matching within feature space rather than the fragile pixel domain. Our method extracts neural features from the projected patterns and captured infrared (IR) images, explicitly incorporating their geometric priors by building cost volumes in feature space, achieving substantial performance improvements over pixel-domain decoding approaches. To further enhance depth quality, we introduce a depth refinement module that leverages strong priors from large-scale monocular depth estimation models, improving fine detail recovery and global structural coherence. To facilitate effective learning, we develop a physically-based structured light rendering pipeline, generating nearly one million synthetic pattern-image pairs with diverse objects and materials for indoor settings. Experiments demonstrate that our method, trained exclusively on synthetic data with multiple structured light patterns, generalizes well to real-world indoor environments, effectively processes various pattern types without retraining, and consistently outperforms both commercial structured light systems and passive stereo RGB-based depth estimation methods. Project page: https://namisntimpot.github.io/NSLweb/.

  • 7 authors
·
Dec 15, 2025

Towards Robust and Generalizable Lensless Imaging with Modular Learned Reconstruction

Lensless cameras disregard the conventional design that imaging should mimic the human eye. This is done by replacing the lens with a thin mask, and moving image formation to the digital post-processing. State-of-the-art lensless imaging techniques use learned approaches that combine physical modeling and neural networks. However, these approaches make simplifying modeling assumptions for ease of calibration and computation. Moreover, the generalizability of learned approaches to lensless measurements of new masks has not been studied. To this end, we utilize a modular learned reconstruction in which a key component is a pre-processor prior to image recovery. We theoretically demonstrate the pre-processor's necessity for standard image recovery techniques (Wiener filtering and iterative algorithms), and through extensive experiments show its effectiveness for multiple lensless imaging approaches and across datasets of different mask types (amplitude and phase). We also perform the first generalization benchmark across mask types to evaluate how well reconstructions trained with one system generalize to others. Our modular reconstruction enables us to use pre-trained components and transfer learning on new systems to cut down weeks of tedious measurements and training. As part of our work, we open-source four datasets, and software for measuring datasets and for training our modular reconstruction.

  • 3 authors
·
Feb 3, 2025

POCOVID-Net: Automatic Detection of COVID-19 From a New Lung Ultrasound Imaging Dataset (POCUS)

With the rapid development of COVID-19 into a global pandemic, there is an ever more urgent need for cheap, fast and reliable tools that can assist physicians in diagnosing COVID-19. Medical imaging such as CT can take a key role in complementing conventional diagnostic tools from molecular biology, and, using deep learning techniques, several automatic systems were demonstrated promising performances using CT or X-ray data. Here, we advocate a more prominent role of point-of-care ultrasound imaging to guide COVID-19 detection. Ultrasound is non-invasive and ubiquitous in medical facilities around the globe. Our contribution is threefold. First, we gather a lung ultrasound (POCUS) dataset consisting of 1103 images (654 COVID-19, 277 bacterial pneumonia and 172 healthy controls), sampled from 64 videos. This dataset was assembled from various online sources, processed specifically for deep learning models and is intended to serve as a starting point for an open-access initiative. Second, we train a deep convolutional neural network (POCOVID-Net) on this 3-class dataset and achieve an accuracy of 89% and, by a majority vote, a video accuracy of 92% . For detecting COVID-19 in particular, the model performs with a sensitivity of 0.96, a specificity of 0.79 and F1-score of 0.92 in a 5-fold cross validation. Third, we provide an open-access web service (POCOVIDScreen) that is available at: https://pocovidscreen.org. The website deploys the predictive model, allowing to perform predictions on ultrasound lung images. In addition, it grants medical staff the option to (bulk) upload their own screenings in order to contribute to the growing public database of pathological lung ultrasound images. Dataset and code are available from: https://github.com/jannisborn/covid19_pocus_ultrasound. NOTE: This preprint is superseded by our paper in Applied Sciences: https://doi.org/10.3390/app11020672

  • 7 authors
·
Apr 25, 2020

StomaD2: An All-in-One System for Intelligent Stomatal Phenotype Analysis via Diffusion-Based Restoration Detection Network

Stomata play a crucial role in regulating plant physiological processes and reflecting environmental responses. However, accurate and high-throughput stomatal phenotyping remains challenging, as conventional approaches rely on destructive sampling and manual annotation, restricting large-scale and field deployment. To overcome these limitations, a noninvasive restoration-detection integrated framework, termed StomaD2, is developed to achieve accurate and fast stomatal phenotyping under complex imaging conditions. The framework incorporates a diffusion-based restoration module to recover degraded images and a specialized rotated object detection network tailored to the small, dense, and cluttered characteristics of stomata. The proposed network enhances feature representation through three key innovations: a column-wise structure for global feature interaction, context-aware resampling and reweighting mechanism to improve multi-scale consistency, and a feature reassembly module to boost discrimination against complex backgrounds. In extensive comparisons, StomaD2 demonstrated state-of-the-art performance. On public Maize and Wheat datasets, it achieved accuracies of 0.994 and 0.992, respectively, significantly outperforming existing benchmarks. When benchmarked against ten other advanced models, including Oriented Former and YOLOv12, StomaD2 achieved a top-tier F1-score/mAP of 0.989. The framework is integrated into a user-friendly, field-operable system that supports the fast extraction of eight stomatal phenotypes, such as density and conductance. Validated on more than 130 plant species, StomaD2's results highlight its strong generalizability and potential for large-scale phenotyping, plant physiology analysis, and precision agriculture applications.

  • 5 authors
·
Apr 17

A Comparative Study on Generative Models for High Resolution Solar Observation Imaging

Solar activity is one of the main drivers of variability in our solar system and the key source of space weather phenomena that affect Earth and near Earth space. The extensive record of high resolution extreme ultraviolet (EUV) observations from the Solar Dynamics Observatory (SDO) offers an unprecedented, very large dataset of solar images. In this work, we make use of this comprehensive dataset to investigate capabilities of current state-of-the-art generative models to accurately capture the data distribution behind the observed solar activity states. Starting from StyleGAN-based methods, we uncover severe deficits of this model family in handling fine-scale details of solar images when training on high resolution samples, contrary to training on natural face images. When switching to the diffusion based generative model family, we observe strong improvements of fine-scale detail generation. For the GAN family, we are able to achieve similar improvements in fine-scale generation when turning to ProjectedGANs, which uses multi-scale discriminators with a pre-trained frozen feature extractor. We conduct ablation studies to clarify mechanisms responsible for proper fine-scale handling. Using distributed training on supercomputers, we are able to train generative models for up to 1024x1024 resolution that produce high quality samples indistinguishable to human experts, as suggested by the evaluation we conduct. We make all code, models and workflows used in this study publicly available at https://github.com/SLAMPAI/generative-models-for-highres-solar-images.

  • 5 authors
·
Apr 14, 2023

Album: executable building blocks for scientific imaging routines, from sharing to LLM-assisted orchestration

Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing routines, adapting them for new use cases, sharing and scaling them across collaborators, and stabilizing them with reproducible execution environments. We present Album, an open-source framework for packaging and sharing scientific routines as executable artifacts through two minimal primitives: (i) the solution, a Python-native executable entry point that combines machine-readable metadata, arguments, environment specifications, and lifecycle hooks; and (ii) the catalog, a decentralized, git-native distribution mechanism with indexed search and optional web rendering for discovery, provenance, and governance. Album uses a two-context execution model in which a host controller evaluates manifests and prepares per-solution environments, while lifecycle hooks execute inside isolated solution environments. This design supports reproducible execution, post-environment setup, and the composition of routines with incompatible dependencies. Album can be used in conjunction with LLM agents: solutions can be drafted and revised with LLM assistance, and a MCP interface exposes cataloged solutions as callable tools for tool-grounded discovery and orchestration. We evaluate Album through four realworld imaging deployments spanning interactive visualization of electron microscopy data, integration of multiple segmentation methods, the orchestration of cryo-electron tomography competition workflows, and mineral quantification pipelines. Overall, Album complements package managers, workflow systems, and container runtimes by making scientific routines executable, shareable artifacts. Documentation and examples are available at https://album.solutions.

  • 5 authors
·
Apr 20

Prompt Triage: Structured Optimization Enhances Vision-Language Model Performance on Medical Imaging Benchmarks

Vision-language foundation models (VLMs) show promise for diverse imaging tasks but often underperform on medical benchmarks. Prior efforts to improve performance include model finetuning, which requires large domain-specific datasets and significant compute, or manual prompt engineering, which is hard to generalize and often inaccessible to medical institutions seeking to deploy these tools. These challenges motivate interest in approaches that draw on a model's embedded knowledge while abstracting away dependence on human-designed prompts to enable scalable, weight-agnostic performance improvements. To explore this, we adapt the Declarative Self-improving Python (DSPy) framework for structured automated prompt optimization in medical vision-language systems through a comprehensive, formal evaluation. We implement prompting pipelines for five medical imaging tasks across radiology, gastroenterology, and dermatology, evaluating 10 open-source VLMs with four prompt optimization techniques. Optimized pipelines achieved a median relative improvement of 53% over zero-shot prompting baselines, with the largest gains ranging from 300% to 3,400% on tasks where zero-shot performance is low. These results highlight the substantial potential of applying automated prompt optimization to medical AI systems, demonstrating significant gains for vision-based applications requiring accurate clinical image interpretation. By reducing dependence on prompt design to elicit intended outputs, these techniques allow clinicians to focus on patient care and clinical decision-making. Furthermore, our experiments offer scalability and preserve data privacy, demonstrating performance improvement on open-source VLMs. We publicly release our evaluation pipelines to support reproducible research on specialized medical tasks, available at https://github.com/DaneshjouLab/prompt-triage-lab.

  • 5 authors
·
Nov 14, 2025

Illicit object detection in X-ray imaging using deep learning techniques: A comparative evaluation

Automated X-ray inspection is crucial for efficient and unobtrusive security screening in various public settings. However, challenges such as object occlusion, variations in the physical properties of items, diversity in X-ray scanning devices, and limited training data hinder accurate and reliable detection of illicit items. Despite the large body of research in the field, reported experimental evaluations are often incomplete, with frequently conflicting outcomes. To shed light on the research landscape and facilitate further research, a systematic, detailed, and thorough comparative evaluation of recent Deep Learning (DL)-based methods for X-ray object detection is conducted. For this, a comprehensive evaluation framework is developed, composed of: a) Six recent, large-scale, and widely used public datasets for X-ray illicit item detection (OPIXray, CLCXray, SIXray, EDS, HiXray, and PIDray), b) Ten different state-of-the-art object detection schemes covering all main categories in the literature, including generic Convolutional Neural Network (CNN), custom CNN, generic transformer, and hybrid CNN-transformer architectures, and c) Various detection (mAP50 and mAP50:95) and time/computational-complexity (inference time (ms), parameter size (M), and computational load (GFLOPS)) metrics. A thorough analysis of the results leads to critical observations and insights, emphasizing key aspects such as: a) Overall behavior of the object detection schemes, b) Object-level detection performance, c) Dataset-specific observations, and d) Time efficiency and computational complexity analysis. To support reproducibility of the reported experimental results, the evaluation code and model weights are made publicly available at https://github.com/jgenc/xray-comparative-evaluation.

  • 8 authors
·
Jul 23, 2025

Generative AI for Synthetic Data Across Multiple Medical Modalities: A Systematic Review of Recent Developments and Challenges

This paper presents a comprehensive systematic review of generative models (GANs, VAEs, DMs, and LLMs) used to synthesize various medical data types, including imaging (dermoscopic, mammographic, ultrasound, CT, MRI, and X-ray), text, time-series, and tabular data (EHR). Unlike previous narrowly focused reviews, our study encompasses a broad array of medical data modalities and explores various generative models. Our search strategy queries databases such as Scopus, PubMed, and ArXiv, focusing on recent works from January 2021 to November 2023, excluding reviews and perspectives. This period emphasizes recent advancements beyond GANs, which have been extensively covered previously. The survey reveals insights from three key aspects: (1) Synthesis applications and purpose of synthesis, (2) generation techniques, and (3) evaluation methods. It highlights clinically valid synthesis applications, demonstrating the potential of synthetic data to tackle diverse clinical requirements. While conditional models incorporating class labels, segmentation masks and image translations are prevalent, there is a gap in utilizing prior clinical knowledge and patient-specific context, suggesting a need for more personalized synthesis approaches and emphasizing the importance of tailoring generative approaches to the unique characteristics of medical data. Additionally, there is a significant gap in using synthetic data beyond augmentation, such as for validation and evaluation of downstream medical AI models. The survey uncovers that the lack of standardized evaluation methodologies tailored to medical images is a barrier to clinical application, underscoring the need for in-depth evaluation approaches, benchmarking, and comparative studies to promote openness and collaboration.

  • 9 authors
·
Jul 1, 2024

Unified Ultrasound Intelligence Toward an End-to-End Agentic System

Clinical ultrasound analysis demands models that generalize across heterogeneous organs, views, and devices, while supporting interpretable workflow-level analysis. Existing methods often rely on task-wise adaptation, and joint learning may be unstable due to cross-task interference, making it hard to deliver workflow-level outputs in practice. To address these challenges, we present USTri, a tri-stage ultrasound intelligence pipeline for unified multi-organ, multi-task analysis. Stage I trains a universal generalist USGen on different domains to learn broad, transferable priors that are robust to device and protocol variability. To better handle domain shifts and reach task-aligned performance while preserving ultrasound shared knowledge, Stage II builds USpec by keeping USGen frozen and finetuning dataset-specific heads. Stage III introduces USAgent, which mimics clinician workflows by orchestrating USpec specialists for multi-step inference and deterministic structured reports. On the FMC\_UIA validation set, our model achieves the best overall performance across 4 task types and 27 datasets, outperforming state-of-the-art methods. Moreover, qualitative results show that USAgent produces clinically structured reports with high accuracy and interpretability. Our study suggests a scalable path to ultrasound intelligence that generalizes across heterogeneous ultrasound tasks and supports consistent end-to-end clinical workflows. The code is publicly available at: https://github.com/MacDunno/USTri.

  • 6 authors
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Apr 21

SpinalSAM-R1: A Vision-Language Multimodal Interactive System for Spine CT Segmentation

The anatomical structure segmentation of the spine and adjacent structures from computed tomography (CT) images is a key step for spinal disease diagnosis and treatment. However, the segmentation of CT images is impeded by low contrast and complex vertebral boundaries. Although advanced models such as the Segment Anything Model (SAM) have shown promise in various segmentation tasks, their performance in spinal CT imaging is limited by high annotation requirements and poor domain adaptability. To address these limitations, we propose SpinalSAM-R1, a multimodal vision-language interactive system that integrates a fine-tuned SAM with DeepSeek-R1, for spine CT image segmentation. Specifically, our SpinalSAM-R1 introduces an anatomy-guided attention mechanism to improve spine segmentation performance, and a semantics-driven interaction protocol powered by DeepSeek-R1, enabling natural language-guided refinement. The SpinalSAM-R1 is fine-tuned using Low-Rank Adaptation (LoRA) for efficient adaptation. We validate our SpinalSAM-R1 on the spine anatomical structure with CT images. Experimental results suggest that our method achieves superior segmentation performance. Meanwhile, we develop a PyQt5-based interactive software, which supports point, box, and text-based prompts. The system supports 11 clinical operations with 94.3\% parsing accuracy and sub-800 ms response times. The software is released on https://github.com/6jm233333/spinalsam-r1.

  • 6 authors
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Oct 30, 2025

OCTCube-M: A 3D multimodal optical coherence tomography foundation model for retinal and systemic diseases with cross-cohort and cross-device validation

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.

  • 12 authors
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Aug 20, 2024

ISLES'24: Final Infarct Prediction with Multimodal Imaging and Clinical Data. Where Do We Stand?

Accurate estimation of brain infarction (i.e., irreversibly damaged tissue) is critical for guiding treatment decisions in acute ischemic stroke. Reliable infarct prediction informs key clinical interventions, including the need for patient transfer to comprehensive stroke centers, the potential benefit of additional reperfusion attempts during mechanical thrombectomy, decisions regarding secondary neuroprotective treatments, and ultimately, prognosis of clinical outcomes. This work introduces the Ischemic Stroke Lesion Segmentation (ISLES) 2024 challenge, which focuses on the prediction of final infarct volumes from pre-interventional acute stroke imaging and clinical data. ISLES24 provides a comprehensive, multimodal setting where participants can leverage all clinically and practically available data, including full acute CT imaging, sub-acute follow-up MRI, and structured clinical information, across a train set of 150 cases. On the hidden test set of 98 cases, the top-performing model, a multimodal nnU-Net-based architecture, achieved a Dice score of 0.285 (+/- 0.213) and an absolute volume difference of 21.2 (+/- 37.2) mL, underlining the significant challenges posed by this task and the need for further advances in multimodal learning. This work makes two primary contributions: first, we establish a standardized, clinically realistic benchmark for post-treatment infarct prediction, enabling systematic evaluation of multimodal algorithmic strategies on a longitudinal stroke dataset; second, we analyze current methodological limitations and outline key research directions to guide the development of next-generation infarct prediction models.

  • 40 authors
·
Aug 20, 2024

EyeFound: A Multimodal Generalist Foundation Model for Ophthalmic Imaging

Artificial intelligence (AI) is vital in ophthalmology, tackling tasks like diagnosis, classification, and visual question answering (VQA). However, existing AI models in this domain often require extensive annotation and are task-specific, limiting their clinical utility. While recent developments have brought about foundation models for ophthalmology, they are limited by the need to train separate weights for each imaging modality, preventing a comprehensive representation of multi-modal features. This highlights the need for versatile foundation models capable of handling various tasks and modalities in ophthalmology. To address this gap, we present EyeFound, a multimodal foundation model for ophthalmic images. Unlike existing models, EyeFound learns generalizable representations from unlabeled multimodal retinal images, enabling efficient model adaptation across multiple applications. Trained on 2.78 million images from 227 hospitals across 11 ophthalmic modalities, EyeFound facilitates generalist representations and diverse multimodal downstream tasks, even for detecting challenging rare diseases. It outperforms previous work RETFound in diagnosing eye diseases, predicting systemic disease incidents, and zero-shot multimodal VQA. EyeFound provides a generalizable solution to improve model performance and lessen the annotation burden on experts, facilitating widespread clinical AI applications for retinal imaging.

  • 9 authors
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May 18, 2024

Euclid Quick Data Release (Q1). AstroVink: A vision transformer approach to find strong gravitational lens systems

We present AstroVink, a vision transformer classifier designed for automated identification of strong lens candidates in Euclid imaging. We build upon the DINOv2 encoder, fine tuned to distinguish between lens and non-lens galaxies. Our base model, trained on simulated strong lens systems and labelled non lenses, recovers 88 of the 110 lens candidates within the top 500 ranked candidates, corresponding to an inspection efficiency of one lens per 5.7 inspected objects in our test set. After the Q1 data release, which yielded about 500 lens candidates, we retrained the model using high confidence lens candidates and new negatives, initially flagged as potential lenses by other classifiers but rejected during visual inspection. The retrained network further improves performance, achieving recovery of all 110 systems within the same ranking and reducing the inspection effort to one lens per 4.5 inspected objects, demonstrating that incorporating real examples significantly enhances model generalisation. An analysis of training subsets revealed that the inclusion of realistic negative examples played a key role in this improvement. Finally, we applied the retrained model to the Q1 original selection of 1.08M targets, followed by a new round of Space Warps citizen science inspection and expert vetting, where we identified a total of eight Grade A and 26 Grade B new lens candidates. These results demonstrate that transformer based architectures can recover strong lens candidates with high efficiency in real Euclid data, while substantially reducing the number of candidates requiring visual inspection.

  • 305 authors
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Apr 22

SilVar-Med: A Speech-Driven Visual Language Model for Explainable Abnormality Detection in Medical Imaging

Medical Visual Language Models have shown great potential in various healthcare applications, including medical image captioning and diagnostic assistance. However, most existing models rely on text-based instructions, limiting their usability in real-world clinical environments especially in scenarios such as surgery, text-based interaction is often impractical for physicians. In addition, current medical image analysis models typically lack comprehensive reasoning behind their predictions, which reduces their reliability for clinical decision-making. Given that medical diagnosis errors can have life-changing consequences, there is a critical need for interpretable and rational medical assistance. To address these challenges, we introduce an end-to-end speech-driven medical VLM, SilVar-Med, a multimodal medical image assistant that integrates speech interaction with VLMs, pioneering the task of voice-based communication for medical image analysis. In addition, we focus on the interpretation of the reasoning behind each prediction of medical abnormalities with a proposed reasoning dataset. Through extensive experiments, we demonstrate a proof-of-concept study for reasoning-driven medical image interpretation with end-to-end speech interaction. We believe this work will advance the field of medical AI by fostering more transparent, interactive, and clinically viable diagnostic support systems. Our code and dataset are publicly available at SiVar-Med.

  • 6 authors
·
Apr 14, 2025 2

ZACH-ViT: Regime-Dependent Inductive Bias in Compact Vision Transformers for Medical Imaging

Vision Transformers rely on positional embeddings and class tokens that encode fixed spatial priors. While effective for natural images, these priors may hinder generalization when spatial layout is weakly informative or inconsistent, a frequent condition in medical imaging and edge-deployed clinical systems. We introduce ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer), a compact Vision Transformer that removes both positional embeddings and the [CLS] token, achieving permutation invariance through global average pooling over patch representations. The term "Zero-token" specifically refers to removing the dedicated [CLS] aggregation token and positional embeddings; patch tokens remain unchanged and are processed normally. Adaptive residual projections preserve training stability in compact configurations while maintaining a strict parameter budget. Evaluation is performed across seven MedMNIST datasets spanning binary and multi-class tasks under a strict few-shot protocol (50 samples per class, fixed hyperparameters, five random seeds). The empirical analysis demonstrates regime-dependent behavior: ZACH-ViT (0.25M parameters, trained from scratch) achieves its strongest advantage on BloodMNIST and remains competitive with TransMIL on PathMNIST, while its relative advantage decreases on datasets with strong anatomical priors (OCTMNIST, OrganAMNIST), consistent with the architectural hypothesis. These findings support the view that aligning architectural inductive bias with data structure can be more important than pursuing universal benchmark dominance. Despite its minimal size and lack of pretraining, ZACH-ViT achieves competitive performance while maintaining sub-second inference times, supporting deployment in resource-constrained clinical environments. Code and models are available at https://github.com/Bluesman79/ZACH-ViT.

  • 1 authors
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Feb 19

M3CoTBench: Benchmark Chain-of-Thought of MLLMs in Medical Image Understanding

Chain-of-Thought (CoT) reasoning has proven effective in enhancing large language models by encouraging step-by-step intermediate reasoning, and recent advances have extended this paradigm to Multimodal Large Language Models (MLLMs). In the medical domain, where diagnostic decisions depend on nuanced visual cues and sequential reasoning, CoT aligns naturally with clinical thinking processes. However, Current benchmarks for medical image understanding generally focus on the final answer while ignoring the reasoning path. An opaque process lacks reliable bases for judgment, making it difficult to assist doctors in diagnosis. To address this gap, we introduce a new M3CoTBench benchmark specifically designed to evaluate the correctness, efficiency, impact, and consistency of CoT reasoning in medical image understanding. M3CoTBench features 1) a diverse, multi-level difficulty dataset covering 24 examination types, 2) 13 varying-difficulty tasks, 3) a suite of CoT-specific evaluation metrics (correctness, efficiency, impact, and consistency) tailored to clinical reasoning, and 4) a performance analysis of multiple MLLMs. M3CoTBench systematically evaluates CoT reasoning across diverse medical imaging tasks, revealing current limitations of MLLMs in generating reliable and clinically interpretable reasoning, and aims to foster the development of transparent, trustworthy, and diagnostically accurate AI systems for healthcare. Project page at https://juntaojianggavin.github.io/projects/M3CoTBench/.

  • 10 authors
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Jan 13

Distilling Photon-Counting CT into Routine Chest CT through Clinically Validated Degradation Modeling

Photon-counting CT (PCCT) provides superior image quality with higher spatial resolution and lower noise compared to conventional energy-integrating CT (EICT), but its limited clinical availability restricts large-scale research and clinical deployment. To bridge this gap, we propose SUMI, a simulated degradation-to-enhancement method that learns to reverse realistic acquisition artifacts in low-quality EICT by leveraging high-quality PCCT as reference. Our central insight is to explicitly model realistic acquisition degradations, transforming PCCT into clinically plausible lower-quality counterparts and learning to invert this process. The simulated degradations were validated for clinical realism by board-certified radiologists, enabling faithful supervision without requiring paired acquisitions at scale. As outcomes of this technical contribution, we: (1) train a latent diffusion model on 1,046 PCCTs, using an autoencoder first pre-trained on both these PCCTs and 405,379 EICTs from 145 hospitals to extract general CT latent features that we release for reuse in other generative medical imaging tasks; (2) construct a large-scale dataset of over 17,316 publicly available EICTs enhanced to PCCT-like quality, with radiologist-validated voxel-wise annotations of airway trees, arteries, veins, lungs, and lobes; and (3) demonstrate substantial improvements: across external data, SUMI outperforms state-of-the-art image translation methods by 15% in SSIM and 20% in PSNR, improves radiologist-rated clinical utility in reader studies, and enhances downstream top-ranking lesion detection performance, increasing sensitivity by up to 15% and F1 score by up to 10%. Our results suggest that emerging imaging advances can be systematically distilled into routine EICT using limited high-quality scans as reference.

  • 13 authors
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Apr 7

CXR-AD: Component X-ray Image Dataset for Industrial Anomaly Detection

Internal defect detection constitutes a critical process in ensuring component quality, for which anomaly detection serves as an effective solution. However, existing anomaly detection datasets predominantly focus on surface defects in visible-light images, lacking publicly available X-ray datasets targeting internal defects in components. To address this gap, we construct the first publicly accessible component X-ray anomaly detection (CXR-AD) dataset, comprising real-world X-ray images. The dataset covers five industrial component categories, including 653 normal samples and 561 defect samples with precise pixel-level mask annotations. We systematically analyze the dataset characteristics and identify three major technical challenges: (1) strong coupling between complex internal structures and defect regions, (2) inherent low contrast and high noise interference in X-ray imaging, and (3) significant variations in defect scales and morphologies. To evaluate dataset complexity, we benchmark three state-of-the-art anomaly detection frameworks (feature-based, reconstruction-based, and zero-shot learning methods). Experimental results demonstrate a 29.78% average performance degradation on CXR-AD compared to MVTec AD, highlighting the limitations of current algorithms in handling internal defect detection tasks. To the best of our knowledge, CXR-AD represents the first publicly available X-ray dataset for component anomaly detection, providing a real-world industrial benchmark to advance algorithm development and enhance precision in internal defect inspection technologies.

  • 6 authors
·
May 5, 2025

WHOI-Plankton- A Large Scale Fine Grained Visual Recognition Benchmark Dataset for Plankton Classification

Planktonic organisms are of fundamental importance to marine ecosystems: they form the basis of the food web, provide the link between the atmosphere and the deep ocean, and influence global-scale biogeochemical cycles. Scientists are increasingly using imaging-based technologies to study these creatures in their natural habit. Images from such systems provide an unique opportunity to model and understand plankton ecosystems, but the collected datasets can be enormous. The Imaging FlowCytobot (IFCB) at Woods Hole Oceanographic Institution, for example, is an in situ system that has been continuously imaging plankton since 2006. To date, it has generated more than 700 million samples. Manual classification of such a vast image collection is impractical due to the size of the data set. In addition, the annotation task is challenging due to the large space of relevant classes, intra-class variability, and inter-class similarity. Methods for automated classification exist, but the accuracy is often below that of human experts. Here we introduce WHOI-Plankton: a large scale, fine-grained visual recognition dataset for plankton classification, which comprises over 3.4 million expert-labeled images across 70 classes. The labeled image set is complied from over 8 years of near continuous data collection with the IFCB at the Martha's Vineyard Coastal Observatory (MVCO). We discuss relevant metrics for evaluation of classification performance and provide results for a traditional method based on hand-engineered features and two methods based on convolutional neural networks.

  • 4 authors
·
Oct 2, 2015

See Through Their Minds: Learning Transferable Neural Representation from Cross-Subject fMRI

Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.

  • 5 authors
·
Mar 10, 2024