medical imaging software developers

Abstract: Computed tomography (CT) and positron emission tomography (PET) provide complementary anatomical and functional information for cancer diagnosis and treatment planning. However, the widespread use of PET is limited by high radiation exposure, elevated costs, and restricted availability. To address these limitations, deep learning-based CT-to-PET translation has emerged as a promising approach for synthesizing PET-like information directly from CT images, although accurately modeling the large cross-modal gap remains challenging. In this work, we propose a 3D CT-to-PET translation framework based on latent Brownian Bridge Diffusion (BBDM). The method consists of two stages. First, a Variational Autoencoder (VAE) is trained on paired CT-PET patches, integrating contrastive learning to improve latent alignment between anatomical and metabolic representations. Second, a BBDM is trained in the latent space to translate CT latent representations into their corresponding PET counterparts. The translated PET latents are then decoded and stitched to reconstruct the final 3D PET volume. We evaluate the proposed approach on two publicly available datasets. Quantitative results based on image fidelity and lesion-level PET-specific metrics demonstrate improved performance compared with competing methods. In particular, the proposed approach improves PET signal fidelity, better preserves clinically relevant uptake patterns, and shows improved performance in preserving small-lesion metabolic activation, paving the way for virtual imaging applications.

Abstract: Bone-marrow cytology is inherently structured: each cell belongs to a hematopoietic lineage, and many cell types lie on ordered maturation trajectories. Standard flat classifiers ignore this structure, treating a mild same-lineage confusion the same as a severe cross-lineage mistake and predicting only discrete labels. We propose HemaHier, an ordinal-hierarchical prediction head for a frozen or lightly adapted cytology foundation model. Its central component is a chain-conditioned maturity score that reads a single maturity value under a per-chain query, supervised only on biologically valid healthy chains, while dysplastic and off-chain cell types remain classes but are excluded from maturity supervision. Fine and lineage predictions are coupled through a shared posterior that guarantees hierarchical consistency, and a staged objective first stabilizes recognition, then adds lineage and maturity supervision. On three bone-marrow datasets under a shared ontology, HemaHier achieves competitive recognition while reducing biologically severe errors and adding a within-lineage maturity ordering that flat classifiers lack. Code is available at https://github.com/xmindflow/HemaHier.

Abstract: Cervical cancer is a major global health challenge, with disease burden falling disproportionately on low- and middle-income countries (LMICs) due to a shortage of trained specialists and the subjective nature of colposcopy-based screening. To address this challenge, we propose a novel deep learning framework for the automated grading of Cervical Intraepithelial Neoplasia (CIN) and the prediction of clinical Swede scores. We also introduce the BUET Multi-Center Colposcopy Dataset, a novel, multi-center cohort designed and annotated for Swede score prediction and CIN grading. Our proposed dual-stream cross-attention architecture mimics the visual reasoning of an expert colposcopist by explicitly fusing paired multimodal cervigrams to evaluate comparative tissue responses. Furthermore, we introduce a custom composite loss function to address severe class imbalances and scoring inconsistencies across the five Swede score components. The proposed framework achieved 71.85% accuracy and an 86.23% AUC-ROC for three-class CIN grading, outperforming existing methods. For Swede score component prediction, the architecture achieved AUC-ROC values ranging from 75.7% to 88.4%, with the composite loss function yielding consistent F1-score improvements. Finally, the total predicted Swede Score, which ranges between 0 and 10, shows a Mean Absolute Error (MAE) of 1.489. The results show that the proposed method can pave the way towards developing AI-assisted colposcopy screening tools to support risk-based triage in resource-limited healthcare settings. The dataset and source code are publicly available(url: https://github.com/mHealthBuet/BUET-colposcopy)

Abstract: Vision-Language Models such as CLIP enable effective few-shot medical anomaly detection (AD) via strong image-text semantic alignment. However, their globally contrastive pretraining lacks explicit spatial supervision, limiting precise lesion localization. In contrast, Vision Foundation Models (VFMs) such as DINO learn spatially coherent patch representations via self-distillation and local-to-global consistency, better capturing fine-grained anatomical structures. Leveraging this complementarity, we propose Spatial-FAD, a spatial-aware few-shot medical AD framework that improves lesion localization by combining VFM spatial priors with CLIP semantics. Specifically, we introduce a VFM-enhanced adapter that injects a structural affinity prior derived from DINO into CLIP features. This structure-guided refinement encourages visual embeddings to better adhere to lesion boundaries while maintaining semantic alignment. To address the loss of spatial detail from patchification and the limited input resolution of CLIP, we adopt a sliding-window aggregation strategy. This generates high-resolution, spatially dense embeddings to further enhance localization granularity. Moreover, we introduce a prototype-enhanced support memory scheme to efficiently exploit the few-shot support set. This module stores compact prototypes for normal and abnormal patterns, reducing memory costs while boosting performance by fusing patch-to-prototype and image-text similarities. Extensive experiments on three benchmark datasets, including Liver CT, Retinal OCT, and Brain MRI, demonstrate that Spatial-FAD significantly outperforms state-of-the-art methods, especially in lesion segmentation. Notably, in the 4-shot scenario, our method achieves an average improvement of over 11.4% in Dice score and 1.8% in AUC. Code is available at: https://github.com/JuzhengMiao/Spatial-FAD.

Abstract: Perineural invasion (PNI) is an adverse histopathologic marker in intrahepatic cholangiocarcinoma (ICC), but it is usually confirmed only after resection. Preoperative T2-weighted MRI may provide noninvasive imaging cues predictive of PNI, although labels are available only at the patient level without slice- or voxel-level annotations. We propose Order-Aware Slab Multiple Instance Learning (OAS-MIL), a weakly supervised framework for patient-level PNI prediction. Each tumor-centered MRI crop is represented as an ordered sequence of overlapping 2.5D slabs formed from contiguous axial slices. A shared encoder extracts slab-level features, which are aggregated by a permutation-invariant set-attention branch and a bidirectional sequence-attention branch. Using five-fold label-stratified cross-validation at the patient level, OAS-MIL achieved a mean AUROC of 0.770, outperforming the evaluated volumetric and MIL baselines. These results suggest that axial order provides a useful inductive bias for weakly supervised PNI prediction from MRI.

Abstract: All-in-One medical image restoration (MedIR) aims to address diverse tasks across modalities and degradation types using a single universal model. Existing methods typically prioritize modeling inter-task heterogeneity (e.g., distinct data distributions and degradation types). However, they largely neglect the inherent homogeneity present in medical images, such as widely shared anatomical structures within and across modalities, which can be leveraged to ease model training and improve generalization. To this end, we propose UniH3, a novel framework that Unifies Hierarchical Homogeneity and Heterogeneity for all-in-one medical image restoration. Specifically, to comprehensively exploit homogeneity, we introduce a Hierarchical Homogeneity Memory (H2M) module that progressively distills intra- and inter-task homogeneity priors from high-quality images during training, and adaptively retrieves the most relevant priors tailored to the input for guided restoration. These retrieved priors are then injected into the restoration pipeline via an efficient Homogeneity-Guided Attention (HGA) mechanism. Furthermore, to comprehensively address heterogeneity, we design a Hierarchical Heterogeneity Balancer (H2B) that mitigates both inter- and intra-task conflicts during optimization, facilitating balanced and effective multi-task learning. Extensive experiments on two large-scale benchmarks, MedIR-2D-500K and MedIR-3D-3K, demonstrate that UniH3 achieves state-of-the-art performance on both all-in-one and single-task medical image restoration. We hope this work establishes a strong benchmark and advances the development of general-purpose medical image restoration models. Code is available at https://github.com/Yaziwel/UniH3.

Abstract: Label-free virtual staining offers a compelling, non-destructive alternative to standard histopathology; however, its clinical adoption is hindered by the computational bottlenecks inherent to processing gigapixel Whole Slide Images (WSIs). Current deep learning approaches require patch-based inference to avoid memory constraints, which disrupts global tissue continuity and introduces tiling artifacts--displaying visible seams and color shifts. To address this, we introduce the Consistency Memory Bank (COMB), a novel label-free virtual staining framework that enforces spatial and channel consistency across tiles without memory bottlenecks. COMB decouples context storage from computation, utilizing a dynamic retrieval mechanism to fetch feature representations from adjacent tiles. This enables a retrieval-based context integration strategy that adopts local padding to resolve spatial discontinuities and neighbor-aware channel attention to stabilize statistical drift. Further optimized with a sliding window schedule to ensure minimal memory overhead, our method demonstrates superior performance over state-of-the-art baselines, achieving significant improvements in both perceptual fidelity and tiling consistency, while suggesting its downstream utility in tumor segmentation. Code is available at https://github.com/dou0000/COMB.

Abstract: Detecting brain metastases in magnetic resonance imaging (MRI) remains challenging because lesions vary widely in size and appearance, with very small metastases occupying only a minute fraction of a three-dimensional input. We investigate whether combining different spatial fields of view (FOVs) improves lesion detection in multimodal MRI and present a scale-aware 3D deep-learning framework. The method uses independently trained $96^3$ and $64^3$ 3D U-Nets whose whole-volume probability maps are combined by weighted late fusion. This design allows us to study the effect of spatial context separately from image resolution and modality choice. On a 97-patient development cohort, cross-FOV fusion improved lesion-level precision and F1 while substantially reducing false positives relative to the individual models. A same-FOV ensemble control showed that these gains were not explained solely by averaging independently trained networks, supporting a contribution from complementary spatial context. An exploratory cross-FOV agreement filter reduced false positives but did not improve overall F1. These results support cross-FOV probability fusion as a simple and computationally practical strategy for improving the precision-false-positive trade-off in 3D brain-metastasis detection.

Abstract: Few-shot medical image segmentation (FSMIS) seeks to delineate unseen structures from a small support set, but its standard formulation fixes task-defining evidence before inference. This assumption is fragile when query cases exhibit acquisition shift, atypical pathology, ambiguous boundaries, or poor image quality. Prototype learning, cross-domain matching, interactive segmentation, uncertainty estimation, test-time adaptation, and promptable foundation models address parts of this problem, yet have not been jointly evaluated under a common model of expert attention and clinical risk. This Perspective reframes FSMIS as a sequential clinician-model decision problem with a static support budget $K$ and a distinct interaction budget $B$. At each step, a system accepts the current segmentation, requests feedback, or defers to full expert review. Queries vary in location and modality and are selected by response-conditioned net expected value of information; clinician-provided feedback informs bounded adaptation only after prespecified provenance, consistency, and safety gates. The framework separates distributional atypicality from predicted clinical failure and treats clinician responses as informative but fallible observations. We synthesize the transition from few-shot and cross-domain segmentation to interactive and selective adaptation, delineate the integration gap, and define four research directions with falsifiable hypotheses. Evaluation spans external-domain calibration, quality-effort trade-offs, reader studies, and prospective workflow assessment. The central claim is not that interaction alone resolves domain shift, but that scarce expert attention should be allocated only when it is expected to reduce clinically relevant risk.

Abstract: Reconstructing volumetric Computed Tomography (CT) from a single 2D chest radiograph (CXR) is an ill-posed inverse problem, further complicated by the scarcity of paired CXR-CT training data. Prior approaches address this by training on Digitally Reconstructed Radiographs (DRRs), which are synthetic projections derived from CT volumes. However, the domain gap between DRRs and real CXRs limits generalization, often resulting in coarse or anatomically inconsistent reconstructions when applied to clinical images. To address this challenging problem, this study introduces a Multi-Pass Multi-View Blended Learning framework for synthesizing high-fidelity volumetric CT directly from real chest X-ray (CXR) images. The proposed approach progressively decomposes the synthesis task into two distinct, complementary learning stages. Stage 1 is an unsupervised CXR-to-DRR Domain Adaptation, while Stage 2 includes three passes, namely, (a) supervised DRR-to-CT Transformation, (b) unsupervised Multi-View Slice Refinement, followed by (c) Progressive Transfer Learning (PTL). With such a blended learning paradigm, the proposed approach mitigates the synthetic-to-real domain gap while enhancing both the structural integrity and anatomical detail of the final output. On the LIDC-IDRI dataset, where paired DRR-CT ground truth is available for quantitative evaluation, the proposed method improves upon prior methods by up to 14% in PSNR and 7.6% in SSIM. The framework successfully generates structurally consistent and anatomically realistic high-fidelity CT volumes from real CXRs, marking a significant advancement toward clinical viability of CT reconstruction from standard radiographic images.

Abstract: Real-time MRI (rtMRI) captures the dynamics of the entire vocal tract during speech, but labeled data are scarce and the modality - single-slice, grayscale, low-resolution - differs substantially from the natural videos that video foundation models are trained on. We introduce Arti-JEPA, a joint embedding predictive architecture to model vocal tract rtMRI by continuing its self-supervised objective on about 62h of unlabelled vocal-tract videos, and evaluate the frozen representation on three tasks: cross-domain phoneme prediction (on typical speakers), fluent-vs-disfluent classification (a corpus containing stuttered speech), and characterizing pre/post-operative transfer (after partial glossectomy). Three key findings emerge. (1) A temporal video prior decisively outperforms per-frame image encoders, and latent prediction (V-JEPA) is at least as strong as pixel reconstruction (VideoMAE), with the edge on fine-grained phonemes. (2) Domain adaptation is \emph{task-dependent}: it roughly doubles cross-domain phoneme prediction $κ$ (to 0.352) but does not help binary stuttering classification. (3) Arti-JEPA was able to recover phoneme signal from pre/post glossectomy speech --- an in-domain probe decodes patients at least as well as a typical speaker, indicating that the residual transfer gap is cross-speaker/domain misalignment, not surgical signal loss, and post-operative decoding does not fall below performance on pre-operative speech. Together, these position a frozen, domain-adapted rtMRI encoder as a reusable measurement tool for articulatory and clinical speech science.

Abstract: Large networks and ensembles often lead medical image segmentation challenges, but their storage and inference demands complicate deployment. We present LightMedSeg-ISLES, a 1.26-million-parameter pipeline for T1-weighted stroke lesion segmentation in ISLES'26. On a 146-case held-out cohort, flip test-time augmentation produces 0.618 mean Dice and 0.599 lesion-wise F1. A 102.35-million-parameter nnU-Net ResEnc-L produces 0.634 Dice and 0.544 lesion-wise F1 after size filtering. LightMedSeg therefore retains 97.5\% of nnU-Net's Dice with 81.4$\times$ fewer parameters while improving lesion-wise F1 by 0.055. Its four-pass TTA operating point requires 4.7$\times$ fewer FLOPs per standardized patch than nnU-Net. It also slightly exceeds filtered UNETR++ and nnFormer. Longer training and stronger augmentation add 0.0358 Dice without increasing capacity, establishing a strong single-checkpoint alternative to much larger models.

Abstract: Delineating lung tumours on computed tomography (CT) takes a considerable share of the time spent on radiotherapy planning, and a contour proposed by a model can be refined interactively by the clinician. Promptable foundation models such as SAM 3 support this workflow by writing each correction into a session memory that conditions the remaining slices, while the model weights stay fixed. On 690 test cases from five public CT cohorts, fine-tuning SAM 3 on lung tumours raises the Dice obtained from a single point prompt from 0.298 to 0.757, and seven rounds of corrections raise it further to 0.765, but under memory conditioning alone the accuracy on slices the annotator has not touched stops improving after six rounds. We therefore treat each correction as a training signal and propose LeCor, which performs test-time training on a small set of case adapters that are reset for every case and meta-learned such that a single gradient step driven by a click improves the slices that were not clicked. On the 133 test cases that span at least eight slices, LeCor raises the Dice reached after seven correction rounds from 0.787 with the fine-tuned model to 0.827, reduces the number of cases that never reach a Dice of 0.80 from 47 to 27, and reaches in three correction rounds the accuracy that the fine-tuned model attains in seven.

Abstract: Longitudinal characterization of multiple sclerosis (MS) lesions remains constrained by the lack of frameworks capable of establishing consistent instance-level correspondences across time. Conventional segmentation approaches produce semantic lesion masks at each visit and therefore fail to capture the complex instance temporal patterns associated with lesion appearance, disappearance, splitting, or merging. This study presents a comparative evaluation of five strategies for automated tracking of spinal cord MS lesions in longitudinal MRI data from a multi-site cohort. The investigated strategies rely either on deformable registration or on a spinal anatomical reference system, and encompass overlap-based matching, coordinate-based Hungarian algorithm, gradient-boosted classification, and Siamese model classification. Tracking accuracy is quantified using instance-level true positives, false positives, and false negatives, allowing to assess the presence of one-to-many and many-to-one associations. Results show best performance for the registration-based overlap method. This study provides the first systematic analysis of lesion-instance correspondence in the spinal cord and outlines the strengths and limitations of registration-based and registration-free paradigms for longitudinal MS assessment. The code is available at http://github.com/ivadomed/longitudinal-sc-ms-lesion-tracking .

Abstract: In proton therapy, plans are typically optimized on a single planning CT, making robustness evaluation essential under anatomical changes. However, current scenarios often rely on simplified perturbations that poorly capture complex, patient-specific variability. We propose SynthRCT, a scalable conditional generative framework for 3D anatomical deformation synthesis. Based on a conditional variational autoencoder, SynthRCT learns a latent deformation space and decodes sampled latent codes into local stationary velocity fields conditioned on an input anatomy. Local fields are assembled into coherent full-volume transformations, enabling memory-scalable generation for large field-of-view CT data. We validate the approach on respiratory 4DCT data with multiple breathing-phase anatomies per subject. SynthRCT enables patient-specific sampling of plausible anatomical transformations beyond predefined robustness scenarios. Code available at: https://github.com/TomasGuija/SynthRCT.

Abstract: Purpose: Accurate CT protocol selection is critical for diagnostic quality and patient safety, yet the current process is manual, time-consuming, and prone to inconsistencies. Prior Machine Learning methods using keywords or bag-of-words lack contextual understanding and perform poorly on rare protocols. We propose a decision support system using large language model (LLM) features to recommend protocols from free-text clinical indications, capturing clinical nuance and phrasing variation for more consistent, efficient selection. Methods: In this REB-approved retrospective study, 285,123 chest CT imaging requests from a large academic medical center (2017-2024) were split into training (228,099, 80%) and held-out test (57,024, 20%) sets. Each request included procedure names, clinical indication, HIS comments, and the selected protocol. Clinical text was embedded using a fine-tuned LLM, Meta's LLaMA-3.1-70B; these features input a logistic regression classifier predicting 18 protocol labels (e.g., PE, LDCT). Results: The pipeline achieved a weighted precision of 0.84, weighted F1-score of 0.81, and overall accuracy of 79% across 18 CT protocols. On 300 independent cases with expert consensus, the LLM reached an overall accuracy of 80% versus 83% for radiologists, with no significant difference (p = 0.263). Performance was comparable across most classes, with the LLM exceeding radiologists for some challenging categories, and entropy analyses indicated more balanced protocol use, suggesting reduced variability. Conclusion: An LLM-based recommendation system can leverage general knowledge from a large natural-text corpus to accurately assign chest CT protocols from free-text imaging requests, and may serve as a viable foundation for protocol recommendation tools where inputs require language understanding.

Abstract: Cranial nerves (CNs) play essential roles in sensory, motor, and autonomic functions. Accurate CN parcellation from multimodal magnetic resonance imaging (MRI) is crucial for neuroanatomical analysis and neurosurgical planning. However, accurate CN parcellation remains extremely challenging because CNs are very small, exhibit low image contrast, and have slender tubular morphologies and complex anatomical trajectories. Moreover, the lack of publicly available, expert-annotated datasets has impeded the development and fair benchmarking of learning-based CN analysis methods. In this work, we introduce CNsEMD, an expert-annotated multimodal dataset for CN parcellation. It comprises data from 202 subjects acquired on 3T, 5T, and 7T MRI scanners. We further propose the projective hyperspherical manifold network (PHM-Net), which learns cross-modal representations by capturing angular relationships in a shared hyperspherical embedding space. Rather than performing multimodal fusion in Euclidean space, the proposed Hyperspherical cross-modal interaction (HCI) module enables bidirectional feature exchange between T1-weighted (T1w) and direction-encoded color (DEC) representations on a unit hypersphere. The Magnitude-preserving projective hyperspherical orientation representation (PHOR) captures the axial nature of DEC orientations while preserving diffusion magnitude. The hyperspherical prototype segmentation head (HPSH) further extends angular similarity to voxel-wise classification using normalized voxel embeddings and learnable class prototypes. Extensive experimental results on the CNsEMD dataset demonstrate the effectiveness of our PHM-Net against state-of-the-art methods. CNsEMD establishes a reproducible benchmark for multimodal CN imaging, while PHM-Net provides a geometry-consistent solution for CN parcellation across diverse MRI acquisitions.

Abstract: Invasive coronary angiography (CAG) is the gold standard for diagnosing coronary artery disease, but interpretation varies substantially among observers. Existing AI systems can improve consistency but lack auditable decision processes and are limited in comprehensive open-ended assessment, undermining clinician trust and clinical adoption readiness. We developed CARDEA, a unified large vision-language model that serves as the inference core of a CAG pipeline. It was trained solely on public datasets and closed-ended tasks in three stages: visual feature alignment, a self-distilled Chain-of-Box (CoB) cold start, and reinforcement learning with verifiable rewards (RLVR) with a CoB reward encouraging bounding-box use in the reasoning trace. We assessed its two study-level diagnoses, dominance classification and complexity assessment, against a dedicated classifier and two interventional cardiologists. Report generation was excluded from training and evaluated zero-shot across stages on an external cohort using vessel-severity macro-$F_1$. CARDEA trailed the classifier on in-distribution dominance but drew level under domain shift (accuracy, 0.91 [95% confidence interval (CI), 0.86 to 0.95]) and was comparable to the cardiologists on complexity assessment (accuracy, 0.90 [CI, 0.82 to 0.97]). Only RLVR improved zero-shot report generation, raising its vessel-severity macro-$F_1$ (0.686 [CI, 0.664 to 0.707]) above the untuned base model (0.513) and over twice the always-normal floor (0.312). CARDEA runs an end-to-end CAG pipeline from raw multi-view videos through keyframe selection to study-level diagnosis while exposing auditable spatial evidence behind its conclusions. RLVR on verifiable closed-ended tasks surfaced open-ended reporting ability that supervised imitation did not. Clinical use requires prospective validation against expert cardiologists.