Image and Video Processing
LoRCA: LoRA Cycle Adaptation for Histology to HiP-CT Translation with DINOv3
Yang Zhou, Edoardo Occhipinti, Banboye Kidzeru Elvis et al. (+11 more)
Hierarchical Phase-Contrast
Tomography (HiP-CT) is a synchrotron based X-ray imaging technique that enables non-destructive, volumetric imaging of intact organs with multi-resolutions bridging 20 $\mu m$/voxel for whole organs to near-cellular resolution ($\sim$0.8 $\mu m$/voxel) in local regions. This offers the opportunity to bring volumetric whole-organ context to histology. However, nonlinear registration between H&E histology and HiP-CT volumes is challenging due to the differences in feature representations of different colour spaces. Synthesis-before-registration methods have shown strong results in histology-to-MRI and histology-to-CT
alignment. However, existing approaches either rely on manual anatomical contours or are trained from scratch without semantic constraints, limiting their generalisability to soft tissue organs and novel modalities. We propose LoRCA (LoRA Cycle Adaptation), a cycle consistent style translation framework built on a shared frozen DINOv3 with modality-specific LoRA adapters, learning modality-specific representations that are decoded and adversarially trained. LoRCA enables structure-preserving translation without requiring paired training data. The frozen backbone is intended to be a structural anchor that prevents content drift by preserving pretrained semantic-extraction capability. We evaluate translation quality using Fréchet Inception Distance (FID) and structural fidelity via mutual information and Canny edge preservation. LoRCA outperforms CycleGAN in both translation quality and structural consistency. As a preliminary indicator of downstream registration utility, we find that style-translated images yield increased feature correspondences under MatchAnything on manually aligned HiP-CT and histology test pairs, suggesting that LoRCA-style translation is a promising step towards 2D histological sections to 3D HiP-CT volumes registration.
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All authors Yang Zhou, Edoardo Occhipinti, Banboye Kidzeru Elvis, Jishizhan Chen, Stathis Megas, Joseph Brunet, Joanna Purzycka, Theresa Urban, Hector Dejea, Sarah Amalia Teichmann, Menna R Clatworthy, Paul Tafforeau, Peter D Lee, Claire L Walsh
Image and Video Processing
Implicit representations are dead. Long live explicit primitives!
Nil Stolt-Ansó, Maik Dannecker, Wenqi Huang et al. (+2 more)
Continuous parameterization of medical data has emerged as a powerful paradigm for resolution-independent image representation. While Implicit Neural Representations offer high fidelity and compact storage, their reliance on global Multi-Layer Perceptrons incurs sizeable computational costs, large
memory requirements, and extensive optimization times. As medical imaging trends towards ever-more detailed, high-resolution volumes, these costs impose significant bottlenecks in the applicability of implicit approaches. Recently, explicit Gaussian-based primitives have revolutionized the representation learning paradigm by trading deep network evaluations for localized, rasterization-friendly primitives. In this paper, we present a comprehensive, cross-dimensional evaluation of Gaussian representations against implicit approaches for medical imaging applications. First, we outline a theoretical overview on the mathematical properties offered by explicit primitives beyond what is capable under the implicit neural paradigm. Subsequently, we
benchmark the computational performance on two demanding image
datasets: 2D microscopy histology and 3D lung Computed
Tomography (CT). Our experiments demonstrate that Gaussian representations consistently match or surpass reconstruction metrics compared to implicit methods across all compression factors, while displaying significantly lower optimization times, and
memory requirements. Together with the compelling mathematical properties offered by explicit primitives, these findings motivate the wider adoption of Gaussian representations and position them as an attractive direction for future research in medical imaging.
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All authors Nil Stolt-Ansó, Maik Dannecker, Wenqi Huang, Andras Jakab, Daniel Rueckert
Image and Video Processing
Pre- to Post-Contrast Synthesis of Breast DCE-MRI using Latent Bridge Matching
Sina Amirrajab, Zohaib Salahuddin, Henry C Woodruff et al. (+1 more)
Dynamic contrast-enhanced
magnetic resonance imaging (DCE-MRI) is central to breast cancer imaging, but gadolinium administration increases scan burden and motivates contrast-reduced alternatives, including synthetic contrast generation. We propose a latent bridge matching (LBM) framework for synthesizing peak-enhanced breast DCE-MRI from pre-contrast images in the MAMA-SYNTH challenge setting. Instead of starting from Gaussian noise as in conventional latent
diffusion models (LDMs), the proposed model learns a conditional bridge between paired pre-contrast and peak-enhanced VAE latents. A latent UNet predicts the remaining correction from intermediate bridge states to the peak-enhanced latent, enabling iterative refinement while keeping the trajectory anchored to patient-specific anatomy. We evaluated two LBM conditioning variants on 91 DUKE validation cases. For the tumor-conditioned variant, tumor masks were used as conditioning inputs. Tumor-conditioning improved performance compared with pre-contrast conditioning, reducing MSE from 1.023 to 0.940 and FRD from 7.523 to 4.716, while increasing tumor SSIM from 0.355 to 0.429. The tumor-conditioned LBM also outperformed the evaluated LDM baseline on this validation cohort. These results suggest that latent bridge matching is a promising pre-contrast-anchored formulation for virtual contrast enhancement, while further work is needed to validate generalization and remove dependence on ground-truth tumor masks at inference.
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All authors Sina Amirrajab, Zohaib Salahuddin, Henry C Woodruff, Philippe Lambin
Image and Video Processing
Robustness of transferability estimation metrics for medical imaging
Niclas Claßen, Théo Sourget, Dovile Juodelyte et al. (+2 more)
In transfer learning, the choice of source model largely influences the performance on a target
dataset. Still, selecting a fitting source remains a challenging task, especially in medical imaging where one has to decide between models pre-trained on off-the-shelf options, such as ImageNet, and domain specific
datasets. Transferability estimation (TE) metrics address this problem by aiming to predict the best performing source model in a computationally cost effective way. However, previous work has reported conflicting TE metric performances due to differences in experimental setups. Moreover, most TE metrics are designed for and evaluated on natural images, while being optimized for accuracy, whereas in medical imaging metrics that are more robust to class imbalance are typically used. We study the impact of varying the target
dataset as an isolated factor, by constructing miniature populations of different sample sizes and random seeds. In addition, we investigate the influence of the evaluation metric used to obtain the reference ranking. We find that small modifications to the target
dataset change the rankings. Furthermore, we show that the choice of evaluation metric affects the reference rankings and therefore the evaluation of TE metrics. Overall, we observe a low agreement between rankings from TE metrics and reference. The code, model checkpoints and data splits used in this work are available through https://github.com/niclasclassen/robustness-of-transferability-estimation-metrics-for-medical-imaging.
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All authors Niclas Claßen, Théo Sourget, Dovile Juodelyte, Rob van der Goot, Veronika Cheplygina
Image and Video Processing
Energy and Performance Benchmarking of Deep Learning Models for Breast Cancer Detection
Samar Garrab and Ghada Achour
Recent advances in machine learning have greatly improved breast cancer detection, enabling more accurate and timely diagnosis. Deep learning (DL) models show strong potential for medical image analysis; however, as their architectural complexity increases, their environmental impacts are becoming a growing concern. In this paper, we present a comparative analysis of seven DL models for breast cancer detection on two medical
datasets: Breast Ultrasound and BreakHis 400X. The evaluated architectures range from Convolutional Neural Networks (CNNs) and
transformers to hybrid models. In addition to performance metrics, we assess CO2 emissions during both training and inference. Our results show that EfficientNet and ResNet consistently deliver strong performance, although with higher CO2 emissions. The selected
transformers, such as DeiT-Tiny, perform competitively on both
datasets, whereas DenseNet121 achieves lower accuracy. On the Breast Ultrasound
Dataset, DeiT provides the most favourable balance between accuracy and energy consumption, whereas on the BreakHis
dataset, the ViT and Swin models achieve the best results. Overall, our findings indicate that no single architecture category from the evaluated ones consistently dominates across the two selected
datasets. Our results highlight the importance of jointly considering performance, emissions, and
dataset characteristics when selecting models for medical applications.
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Image and Video Processing
Structural Guidance for Unified Joint Demosaicing and Denoising
Qixin Zheng, Ping Chen, Qiangqiang Shen et al. (+1 more)
Joint demosaicing and denoising is a fundamental step in camera image signal processing, yet remains challenging because different Bayer-like color filter arrays (CFAs) and sensor noise jointly corrupt both color sampling and image content. Existing unified restoration networks explicitly model CFA geometry but are still driven primarily by pixel-level supervision, making them prone to structural degradation around edges, repetitive textures, and moiré patterns where local evidence is unreliable. We attribute this limitation partly to the absence of explicit structural guidance beyond pixel-level reconstruction supervision. Motivated by this observation, we propose a structural-guided unified restoration framework that injects pretrained structural knowledge into CFA-aware image restoration. Our model receives a unified five-channel observation consisting of the raw mosaic, CFA masks, and a noise-level map. A SwinIR restoration branch reconstructs pixel details under CFA-conditioned modulation, while a parallel structural
reasoning branch extracts complementary structural cues from a sparse pseudo-RGB observation. To bridge the substantial domain gap between sparse noisy sensor data and the natural-image pretraining domain of the structural encoder, we introduce a lightweight trainable adapter before residually fusing structural and restoration features. A shared decoder jointly predicts the restored RGB image and an auxiliary clean mosaic, providing supervision in both image and sensor domains. Extensive experiments across multiple CFA patterns and noise levels demonstrate consistent improvements over state-of-the-art unified and CFA-specific methods, indicating that adapted structural priors can enhance robust camera image restoration. The source codes and
dataset are provided in the supplementary material.
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All authors Qixin Zheng, Ping Chen, Qiangqiang Shen, Haijin Zeng
Image and Video Processing
SpecF2M: A Spectral-Aware Multi-task Network Estimating Axial Length and Refractive Error from Pediatric Fundus Photographs
Mengxian He, Xinyue Liu, Yunyun Sun et al. (+5 more)
Spherical Equivalent Refraction (SER) and Axial Length (AL) are core indicators for pediatric myopia screening, yet their measurements require dedicated biometry and cycloplegic refraction. Fundus photography offers an accessible imaging modality, as myopia-related posterior-pole changes are visible in 45$^\circ$ fundus images. However, these cues are often low-contrast, spatially diffuse, and multi-scale. Moreover, AL, Sphere (SPH), and Cylinder (CYL) share partially overlapping but non-identical anatomical correlates. We propose SpecF2M, a spectral-aware multi-task network for estimating AL and SER components from pediatric fundus photographs. SpecF2M integrates a deterministic anatomy-guided enhancement module, a hybrid spatial–spectral backbone combining MixCNN and Hybrid Spectral Learning (HSL) blocks, and an expert-routing head for component-level estimation of AL, SPH, and CYL. On a pediatric cohort of 4,359 eligible child visits and 6,966 fundus images, SpecF2M outperforms controlled CNN/ViT baselines for AL and SPH estimation, achieving MAEs of 0.5347 mm and 0.7062 D, respectively. Component-level analysis further reveals asymmetric task coupling, where CYL exhibits weaker association with fundus-derived myopic patterns than AL/SPH. These results support fundus-based, screening-oriented estimation of pediatric myopia indicators, while external validation remains necessary before deployment.
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All authors Mengxian He, Xinyue Liu, Yunyun Sun, Wei Hao, Minqing Zhang, Lichun Wang, Shunyi Zhang, Wu Yuan
Image and Video Processing
APCReg: Anatomical-Prior-Guided Coarse-to-Fine CBCT–IOS Registration via Multi-View Projection and Reliability-Controlled Residual Correction
Xincan Zheng, Yaqi Wang, Zhi Li et al. (+4 more)
Registration between cone-beam computed
tomography (CBCT) and intraoral scans (IOS) is essential for patient-specific surgical planning. However, disparate imaging modalities, limited overlap, and large pose offsets make automated registration unreliable. Consequently, clinical registration remains dependent on conventional geometry pipelines and manual clinician adjustment. To address these challenges, we propose APCReg, an anatomical-prior-guided coarse-to-fine framework for global registration and reliability-controlled residual correction. Specifically, multi-view anatomical coarse registration (MACR) performs ordered orthogonal projection
alignment (buccal, proximal, and occlusal) to decompose the six-degree-of-freedom search before three-dimensional refinement. Overlap-aware residual registration (OARR) combines shared KPConv features, a folded arch-length cue, overlap-gated cross-
attention, and Sinkhorn matching. Finally, dental-arch-structured hypothesis selection evaluates diverse poses on held-out reliable correspondences, while a ground-truth-free coarse-retention guard conditionally retains a geometrically reliable coarse pose. On 60 held-out jaw pairs, APCReg achieves a submillimeter mean Chamfer distance of 0.87 mm and a Hausdorff distance of 2.92 mm under this evaluation protocol, and ranks first across the six reported metrics among the evaluated open-source baselines.
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All authors Xincan Zheng, Yaqi Wang, Zhi Li, Jiahao Bao, Lan Feng, Yiru Xia, Shuai Wang
Image and Video Processing
Knowledge-Guided 3D CT Generation: A Conditioning-Centric Taxonomy
Francesca Pia Panaccione, Eugenio Lomurno and Matteo Matteucci
Controllable generation guided by external knowledge is a key requirement in modern generative deep learning applications, enabling the synthesis of samples with explicit constraints on semantic content, structural properties, and variability. In 3D Computed
Tomography (CT), such control is essential for clinical applications, including data augmentation,
privacy-preserving data sharing, and the simulation of specific anatomical or pathological scenarios. While research on conditional 3D CT generation has expanded rapidly, the diversity of existing approaches makes systematic comparison difficult and obscures fundamental design choices. In this survey, we propose a conditioning-centric taxonomy that organizes the literature along three orthogonal dimensions: the type of external knowledge (K), the knowledge integration paradigm (I), and the generative architecture (A). This factorization defines an explicit design space (K x I x A) that provides a unified perspective on prior work. Using this framework, we systematize existing methods, identify dominant trends and recurring design patterns, and highlight underexplored regions of the design space that point toward promising directions for future research.
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Image and Video Processing
Longitudinal 3D Foundation Modeling for Neoadjuvant Breast Cancer Response Prediction from Serial DCE-MRI
Fidel Omar Tito Cruz, Neda Ghafouri, Zengyan Wang et al. (+3 more)
Pathologic complete response (pCR) is an important endpoint in neoadjuvant chemotherapy (NAC) for breast cancer, and predicting pCR from imaging during treatment could support treatment response assessment. Many existing imaging-based approaches rely on a single static timepoint, which fails to capture changes that occur during treatment. In this work, we present a longitudinal framework that combines a frozen 3D foundation encoder (Pillar-0) with our Temporal Dynamics Network (TDN) to predict treatment response from serial Dynamic Contrast-Enhanced (DCE) MRI acquired across four clinical timepoints from pre-treatment to pre-surgery. The TDN combines time-aware volumetric
embeddings with clinical and treatment data to predict pCR. Evaluated on 982 patients from the combined I-SPY2 and ACRIN-6698 cohort, the proposed model achieves strong performance across all reported metrics when longitudinal 3D imaging is fused with clinical data (test AUROC: 73.6%, balanced accuracy: 69.1%). While clinical variables provide the strongest individual predictive signal, longitudinal 3D imaging contributes complementary information when fused with clinical data, improving pCR prediction. Our source code is available at: https://github.com/omarftt/longitudinal_temporal_pillar.
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All authors Fidel Omar Tito Cruz, Neda Ghafouri, Zengyan Wang, Pegah Khosravi, Yu Tian, Chen Chen
Image and Video Processing
Integrating spectral and morphological plant features with decision-tree models for early-season cotton biomass and nitrogen status estimation from multi-year UAV data
Vaishali Swaminathan, Nithya Rajan, J Alex Thomasson et al. (+4 more)
Precision nitrogen (N) management (PNM) for cotton requires in-season monitoring of crop growth parameters and N status indicators to decide fertilizer timing, placement, and application rates for optimal canopy development and yield. This study developed remote sensing and machine learning-based methods to estimate cotton dry biomass weight (DBW), plant N uptake (PNU), plant N concentration (PNC), critical N dilution (Nc), and nitrogen nutrition index (NNI) to support PNM. To achieve this, a three-year field-based N-management study was conducted and unmanned aerial vehicle (
UAV)-based multispectral images were acquired between early vegetative growth and flowering stages, critical for fertilizer applications. Spatiotemporally consistent spectral and morphological plant features, including plant height (PH) and fractional canopy cover (FCC), provided reliable model training inputs. DBW, PNU, and PNC estimates from simple regression using vegetation indices (VIs), multiple linear regression (MLR) combining VIs, PH, and FCC, and decision-tree models, random forest regression (RFR) and extreme gradient boosting (XGB), combining spectral reflectance, PH, and FCC were evaluated using trial-held-out (THO) and leave-one-year-out (LOYO) validation methods. The best validation accuracies were from RFRTHO (R2 = 0.88 and MAPE = 23.14% for DBW; R2 = 0.84 and MAPE = 20.61% for PNU; R2 = 0.85 and MAPE = 7.82% for PNC) and XGBTHO (R2 = 0.87 and MAPE = 21.91% for DBW; R2 = 0.81 and MAPE = 21.40% for PNU; R2 = 0.86 and MAPE = 7.66% for PNC). Nc was calculated from model estimated DBW and PNC for high-yielding, medium-to-tall cotton varieties grown in the Texas Coastal Plains and validated using ground-truth biomass measurements. NNI derived from XGBTHO outputs performed marginally better than NNI from RFRTHO in identifying N-deficient plots and multi-level N-stress categorization.
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All authors Vaishali Swaminathan, Nithya Rajan, J Alex Thomasson, Amrit Shrestha, Karem Meza Capcha, Robert Hardin, Pramod Pokhrel
Image and Video Processing
Bit Allocation Transfer for Perceptual Quality Enhancement of Traditional Video Codecs
Runyu Yang and Ivan V. Bajić
Traditional block-based
video codecs, such as H.264/AVC, H.265/HEVC and H.266/VVC, rely on hand-crafted Rate-Distortion Optimization (RDO) processes that primarily minimize Mean Squared Error (MSE), which correlates poorly with human perceptual quality. While neural
video compression methods can easily optimize perceptually aligned metrics like MS-SSIM, their high computational complexity limits practical deployment. This paper proposes a novel bit allocation transfer framework that bridges these two paradigms to enhance the perceptual quality of conventional
video codecs. Specifically, we train a quantization step generation model using a perceptual loss within a neural
video compression framework (DCVC-FM). The model takes the original frame and a motion-compensated prediction as input and outputs a quantization step map. We then derive a block-wise bit ratio from this map and convert it into a Quantization Parameter (QP) map for a traditional
video codec. Experimental results on the HEVC B$\sim$D
dataset demonstrate that our method achieves 20.20%, 8.25%, and 8.37% bitrate savings in terms of MS-SSIM compared with the standard reference software JM-19.0, HM-16.20, and VTM-23.0, respectively, with additional gains when utilizing predicted frames. Our approach effectively transfers the implicit perceptual importance learned by neural
video compression models to guide block-level bit allocation in traditional
video codecs without modifying their core decoding syntax.
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Image and Video Processing · Cross-listed from q-bio.QM
JUMP-lite: Compact, reproducible benchmarking of cell representations
Alán F. Muñoz, Johan Fredin Haslum, Runxi Shen et al. (+2 more)
Image-based profiling captures rich phenotypic signatures for drug discovery and functional genomics. Large public
datasets like JUMP
Cell Painting now provide millions of images for systematic study. However, JUMP alone occupies 115 TB, and fragmented evaluation practices make systematic comparisons of representation methods impractical for many researchers. Here we present Nahual, an open-source framework for reproducible model deployment, and JUMP-lite, a 92.0 GB subset of JUMP that is approximately 1,250-fold smaller, selected to cover genetic modalities and compound annotations and reduced via lossy JPEG XL compression. Using these resources, we
benchmark five representation methods, including classical features (CellProfiler) and deep learning models (MorphEM, OpenPhenom, SubCell, DINOv2). Moderate compression broadly retains signal relative to uncompressed images. Standardized phenotypic activity and consistency metrics reveal meaningful performance differences across methods. Together, JUMP-lite and Nahual provide a foundation for accessible, reproducible benchmarking of image-based
cell representations.
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All authors Alán F. Muñoz, Johan Fredin Haslum, Runxi Shen, Anne E. Carpenter, Shantanu Singh
Image and Video Processing
IceHorizon: A Dataset for Horizon Detection in Ice-Covered Maritime Environments and Comparative Evaluation of Detection Methods
Alisa Pesotskaia and Emin Zerman
Horizon detection in images of ice-covered waters is a challenging problem for maritime navigation due to low contrast between water and sky, cluttered ice structures, and varying illumination conditions. This paper presents a comparative evaluation of six horizon detection
algorithms, including four classical computer
vision methods and two hybrid approaches combining deep learning with classical line detection. A new bespoke IceHorizon
dataset consisting of 30 ship-based and 8 drone-based
videos is used to evaluate detection accuracy, horizon coverage, and computational performance. The results show that hybrid methods achieve the highest accuracy and most reliable horizon estimates. In contrast, purely classical methods exhibit reduced robustness, particularly in visually ambiguous scenes. Performance on ship-based imagery was consistently higher than on drone-based imagery, indicating a strong dependency on acquisition characteristics. The created
dataset and codes used in this study are made publicly available to support further research on this topic. The code is available at https://github.com/allythe/HorizonDetection. The
dataset is available at https://doi.org/10.5281/zenodo.20411867
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Image and Video Processing
Spatial Masked-Set Learning for Sparse Multi-Shell Diffusion MRI Signal Synthesis
Yousef Sadegheih, Pratibha Kumari and Dorit Merhof
Dense multi-shell
diffusion MRI provides rich q-space information but requires long acquisition times. We propose a spatial masked-set framework for sparse multi-shell
diffusion MRI signal synthesis. The model treats observed measurements as an unordered set, uses a local $3 \times 3 \times 3$ neighborhood for spatial context, and predicts radial-order-6 SHORE coefficients for the center voxel. The coefficients can then be decoded analytically to synthesize signals at arbitrary q-space locations. Training combines shell-wise gradient dropping, dense signal supervision, and rotation-consistent SHORE targets so that sparse input signals remain aligned with their coefficient supervision under augmentation. We evaluate on held-out HCP100 white-matter voxels by retaining limited subsets of measured
diffusion-weighted signals from the reference acquisition. The proposed method achieves lower signal NMSE than both analytical q-space models and a state-of-the-art continuous dMRI signal synthesis model designed for arbitrary input and output q-space sampling. In the $b=1000$ setting with 10 input gradients, it achieves $2.70\%$ NMSE, a $22.4\%$ relative reduction over this continuous model. Fractional anisotropy on reconstructed $b=1000$ signals provides a complementary tensor-derived endpoint, with analytical models remaining competitive for FA despite higher dense-signal NMSE across the evaluated q-space. The implementation is available on \href{https://github.com/xmindflow/SHOREPred}{https://github.com/xmindflow/SHOREPred}.
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