arXiv subjects

Morteza Ghahremani

Publications and source records attributed to Morteza Ghahremani.

At least 19 recordsLinked to original sources

arXiv2026

SomaNet: Weakly Supervised Learning for Instance Soma Segmentation in 3D Electron Microscopy with Partial Annotations

Soma instance segmentation, i.e., identifying and delineating individual cell somas as distinct instances, is crucial for cellular analysis and connectomic reconstruction. Three-dimensional electron microscopy (3D EM) provides nanometer-scale resolution for capturing fine-grained soma morphology. However, dense instance-level manual annotation is prohibitively costly, limiting the scalability of fully supervised methods. To address this challenge, we propose SomaNet, a weakly supervised framework for 3D EM soma instance segmentation under partial annotation constraints. SomaNet adopts a teacher--student learning paradigm tailored to partial labels. The teacher is trained using partially annotated data to generate pseudo-labels, while the student jointly learns from the partial ground-truth annotations and the generated pseudo-labels, progressively recovering dense instance segmentations. To accurately delineate cell somas under limited supervision with varying instance counts, SomaNet incorporates affinity learning, which encourages high similarity within instances and low similarity across instance boundaries. Semantic-guided affinity decoding and 2D-to-3D reconstruction then produce volumetrically consistent 3D soma instances while preserving the large receptive fields of 2D backbones. The framework is architecture-flexible and supports diverse backbones, including vision transformers and foundation models, enabling direct transfer of pretrained visual representations to volumetric EM segmentation. Experiments on 3D EM brain datasets demonstrate that SomaNet achieves accurate and robust soma instance segmentation across regions with diverse soma morphologies under partial annotation. Code is available at https://github.com/mkhateri/SomaNet.

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arXiv2026

Generating Reports or Repeating Templates? Measuring and Mitigating Template Collapse in 3D CT Report Generation

Modern 3D medical vision-language models (VLMs) can generate fluent radiology-style text while exhibit critically low pathology detection and output diversity, collapsing to generic templates that under-report rare yet critical findings. We identify this failure mode as Template Collapse. This failure stems from the unique constraints of 3D medical imaging, e.g., limited data, severe label imbalance, and weak signals from volumetric encoders. Under these constraints, text-generation objectives encourage shortcut learning and fluent but weakly grounded reports. We systematically diagnose the Template Collapse through clinical fidelity, output diversity, normal-template bias, and rare-finding survival. To mitigate it, we propose CLarGen, a decoupled framework that separates what to say (clinical detection) from how to say it (language synthesis). CLarGen uses (i) a Latent Query Transformer for multi-label pathology detection, (ii) pathology-guided retrieval for clinically matched exemplars, and (iii) a medical language model to synthesize the final report from detected findings and retrieved context. Across state-of-the-art 3D CT report generation baselines, CLarGen mitigates Template Collapse and substantially improves clinical accuracy (macro-F1 0.487 vs. 0.189; CRG 0.472 vs. 0.368) while maintaining fluent reporting. Our results suggest that explicit, measurable clinical grounding is essential for template-collapse-resistant 3D CT report generation. Code is available at https://github.com/ai-med/CLarGen.

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arXiv2026

Conditional Diffusion for 3D CT Volume Reconstruction from 2D X-rays

Computed tomography (CT) provides rich 3D anatomical detail but is often constrained by high radiation exposure, substantial costs, and limited availability. Standard chest X-rays are cost-effective and widely accessible, but provide only 2D projections with limited pathological information. Reconstructing 3D CT volumes from 2D X-rays could markedly increase diagnostic accessibility, yet existing methods rely predominantly on synthetic X-ray projections, limiting clinical generalization. We propose AXON, a multi-stage diffusion-based framework that reconstructs 3D CT volumes directly from real X-rays with substantially improved fidelity over existing approaches. AXON follows a coarse-to-fine paradigm: a Brownian Bridge diffusion model first captures global anatomical structure, and a ControlNet-guided refinement stage then enhances local intensity detail and anatomical realism. To alleviate the depth ambiguity inherent in 2D-to-3D reconstruction, AXON incorporates bi-planar X-ray views, enabling more accurate spatial reasoning and structural recovery. A dedicated super-resolution module further increases the spatial resolution of the generated volumes. Experiments on public and external datasets show that AXON consistently surpasses state-of-the-art approaches while generalizing across diverse clinical distributions. At our highest-resolution bi-planar setting, AXON achieves an 11.9% improvement in PSNR and an 11.0% increase in SSIM over the strongest baseline evaluated at that resolution. In the $128^3$ single-planar setting, it maintains a lead of 7.8% in PSNR on LIDC-IDRI, with larger margins on the external clinical dataset of 8.0% in PSNR and 16.9% in SSIM. Our code is available at https://github.com/ai-med/AXON/.

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arXiv2026

Adapting Foundation Vision-Language Models to Medical Diagnosis via Query-Driven Expert Bridging

Vision-language foundation models achieve promising performance in natural image classification, yet their direct application to medical imaging is limited by severe domain shifts, resolution mismatches, and the multi-label nature of clinical diagnosis. Training dedicated medical foundation models from scratch, however, is costly and data-intensive. Here, we propose MedBridge, a lightweight adaptation framework that opens a new direction in domain-gap mitigation by jointly combining domain alignment, resolution preservation, and multi-label reasoning via complementary VLM experts for medical image diagnosis. Specifically, MedBridge transforms pretrained VLMs into multi-view query encoders that inject a compact set of learnable query tokens into intermediate layers, enabling non-destructive domain alignment while preserving fine-grained pathological cues via multi-view high-resolution sampling. These query tokens further act as routing signals for a mixture-of-experts, dynamically integrating heterogeneous foundation models for multi-label reasoning without requiring a shared representation space. We evaluated MedBridge on five chest radiograph benchmarks in three key adaptation tasks. MedBridge demonstrates superior performance in both cross-domain generalization (out-of-distribution transfer) and in-domain specialization (same-distribution tuning) settings, yielding a significant 6-15% AUC improvement over state-of-the-art adaptation methods for multi-label thoracic disease diagnosis. Furthermore, MedBridge is model-agnostic and demonstrates broad extensibility across eight diverse VLMs (e.g., CLIP, LLaVA, Qwen-VL, MedGemma), highlighting its ability to flexibly adapt arbitrary foundation models into a powerful medical diagnostic tool. Our code will be released upon acceptance.

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arXiv2026

Controllable Complex Human Motion Video Generation via Text-to-Skeleton Cascades

Generating videos of complex human motions such as flips, cartwheels, and martial arts remains challenging for current video diffusion models. Text-only conditioning is temporally ambiguous for fine-grained motion control, while explicit pose-based controls, though effective, require users to provide complete skeleton sequences that are costly to produce for long and dynamic actions. We propose a two-stage cascaded framework that addresses both limitations. First, an autoregressive text-to-skeleton model generates 2D pose sequences from natural language descriptions by predicting each joint conditioned on previously generated poses. This design captures long-range temporal dependencies and inter-joint coordination required for complex motions. Second, a pose-conditioned video diffusion model synthesizes videos from a reference image and the generated skeleton sequence. It employs DINO-ALF (Adaptive Layer Fusion), a multi-level reference encoder that preserves appearance and clothing details under large pose changes and self-occlusions. To address the lack of publicly available datasets for complex human motion video generation, we introduce a Blender-based synthetic dataset containing 2,000 videos with diverse characters performing acrobatic and stunt-like motions. The dataset provides full control over appearance, motion, and environment. It fills an important gap because existing benchmarks significantly under-represent acrobatic motions while web-collected datasets raise copyright and privacy concerns. Experiments on our synthetic dataset and the Motion-X Fitness benchmark show that our text-to-skeleton model outperforms prior methods on FID, R-precision, and motion diversity. Our pose-to-video model also achieves the best results among all compared methods on VBench metrics for temporal consistency, motion smoothness, and subject preservation.

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arXiv2026

USFetal: Tools for Fetal Brain Ultrasound Compounding

Ultrasound offers a safe, cost-effective, and widely accessible technology for fetal brain imaging, making it especially suitable for routine clinical use. However, it suffers from view-dependent artifacts, operator variability, and a limited field of view, which make interpretation and quantitative evaluation challenging. Ultrasound compounding aims to overcome these limitations by integrating complementary information from multiple 3D acquisitions into a single, coherent volumetric representation. This work provides four main contributions: (1) We present the first systematic categorization of computational strategies for fetal brain ultrasound compounding, including both classical techniques and modern learning-based frameworks. (2) We implement and compare representative methods across four key categories - multi-scale, transformation-based, variational, and deep learning approaches - emphasizing their core principles and practical advantages. (3) Motivated by the lack of full-view, artifact-free ground truth required for supervised learning, we focus on unsupervised and self-supervised strategies and introduce two new deep learning based approaches: a self-supervised compounding framework and an adaptation of unsupervised deep plug-and-play priors for compounding. (4) We conduct a comprehensive evaluation on ten multi-view fetal brain ultrasound datasets, using both expert radiologist scoring and standard quantitative image-quality metrics. We also release the USFetal Compounding Toolbox, publicly available to support benchmarking and future research. Keywords: Ultrasound compounding, fetal brain, deep learning, self-supervised, unsupervised.

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arXiv2025

MRI Super-Resolution with Deep Learning: A Comprehensive Survey

High-resolution (HR) magnetic resonance imaging (MRI) is crucial for many clinical and research applications. However, achieving it remains costly and constrained by technical trade-offs and experimental limitations. Super-resolution (SR) presents a promising computational approach to overcome these challenges by generating HR images from more affordable low-resolution (LR) scans, potentially improving diagnostic accuracy and efficiency without requiring additional hardware. This survey reviews recent advances in MRI SR techniques, with a focus on deep learning (DL) approaches. It examines DL-based MRI SR methods from the perspectives of computer vision, computational imaging, inverse problems, and MR physics, covering theoretical foundations, architectural designs, learning strategies, benchmark datasets, and performance metrics. We propose a systematic taxonomy to categorize these methods and present an in-depth study of both established and emerging SR techniques applicable to MRI, considering unique challenges in clinical and research contexts. We also highlight open challenges and directions that the community needs to address. Additionally, we provide a collection of essential open-access resources, tools, and tutorials, available on our GitHub: https://github.com/mkhateri/Awesome-MRI-Super-Resolution. IEEE keywords: MRI, Super-Resolution, Deep Learning, Computational Imaging, Inverse Problem, Survey.

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arXiv2025

Disentangling Progress in Medical Image Registration: Beyond Trend-Driven Architectures towards Domain-Specific Strategies

Medical image registration drives quantitative analysis across organs, modalities, and patient populations. Recent deep learning methods often combine low-level "trend-driven" computational blocks from computer vision, such as large-kernel CNNs, Transformers, and state-space models, with high-level registration-specific designs like motion pyramids, correlation layers, and iterative refinement. Yet, their relative contributions remain unclear and entangled. This raises a central question: should future advances in registration focus on importing generic architectural trends or on refining domain-specific design principles? Through a modular framework spanning brain, lung, cardiac, and abdominal registration, we systematically disentangle the influence of these two paradigms. Our evaluation reveals that low-level "trend-driven" computational blocks offer only marginal or inconsistent gains, while high-level registration-specific designs consistently deliver more accurate, smoother, and more robust deformations. These domain priors significantly elevate the performance of a standard U-Net baseline, far more than variants incorporating "trend-driven" blocks, achieving an average relative improvement of $\sim3\%$. All models and experiments are released within a transparent, modular benchmark that enables plug-and-play comparison for new architectures and registration tasks (https://github.com/BailiangJ/rethink-reg). This dynamic and extensible platform establishes a common ground for reproducible and fair evaluation, inviting the community to isolate genuine methodological contributions from domain priors. Our findings advocate a shift in research emphasis: from following architectural trends to embracing domain-specific design principles as the true drivers of progress in learning-based medical image registration.

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arXiv2025

LatentMove: Towards Complex Human Movement Video Generation

Image-to-video (I2V) generation seeks to produce realistic motion sequences from a single reference image. Although recent methods exhibit strong temporal consistency, they often struggle when dealing with complex, non-repetitive human movements, leading to unnatural deformations. To tackle this issue, we present LatentMove, a DiT-based framework specifically tailored for highly dynamic human animation. Our architecture incorporates a conditional control branch and learnable face/body tokens to preserve consistency as well as fine-grained details across frames. We introduce Complex-Human-Videos (CHV), a dataset featuring diverse, challenging human motions designed to benchmark the robustness of I2V systems. We also introduce two metrics to assess the flow and silhouette consistency of generated videos with their ground truth. Experimental results indicate that LatentMove substantially improves human animation quality--particularly when handling rapid, intricate movements--thereby pushing the boundaries of I2V generation. The code, the CHV dataset, and the evaluation metrics will be available at https://github.com/ --.

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arXiv2024

Stable-Pose: Leveraging Transformers for Pose-Guided Text-to-Image Generation

Controllable text-to-image (T2I) diffusion models have shown impressive performance in generating high-quality visual content through the incorporation of various conditions. Current methods, however, exhibit limited performance when guided by skeleton human poses, especially in complex pose conditions such as side or rear perspectives of human figures. To address this issue, we present Stable-Pose, a novel adapter model that introduces a coarse-to-fine attention masking strategy into a vision Transformer (ViT) to gain accurate pose guidance for T2I models. Stable-Pose is designed to adeptly handle pose conditions within pre-trained Stable Diffusion, providing a refined and efficient way of aligning pose representation during image synthesis. We leverage the query-key self-attention mechanism of ViTs to explore the interconnections among different anatomical parts in human pose skeletons. Masked pose images are used to smoothly refine the attention maps based on target pose-related features in a hierarchical manner, transitioning from coarse to fine levels. Additionally, our loss function is formulated to allocate increased emphasis to the pose region, thereby augmenting the model's precision in capturing intricate pose details. We assessed the performance of Stable-Pose across five public datasets under a wide range of indoor and outdoor human pose scenarios. Stable-Pose achieved an AP score of 57.1 in the LAION-Human dataset, marking around 13% improvement over the established technique ControlNet. The project link and code is available at https://github.com/ai-med/StablePose.

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arXiv2024

DiaMond: Dementia Diagnosis with Multi-Modal Vision Transformers Using MRI and PET

Diagnosing dementia, particularly for Alzheimer's Disease (AD) and frontotemporal dementia (FTD), is complex due to overlapping symptoms. While magnetic resonance imaging (MRI) and positron emission tomography (PET) data are critical for the diagnosis, integrating these modalities in deep learning faces challenges, often resulting in suboptimal performance compared to using single modalities. Moreover, the potential of multi-modal approaches in differential diagnosis, which holds significant clinical importance, remains largely unexplored. We propose a novel framework, DiaMond, to address these issues with vision Transformers to effectively integrate MRI and PET. DiaMond is equipped with self-attention and a novel bi-attention mechanism that synergistically combine MRI and PET, alongside a multi-modal normalization to reduce redundant dependency, thereby boosting the performance. DiaMond significantly outperforms existing multi-modal methods across various datasets, achieving a balanced accuracy of 92.4% in AD diagnosis, 65.2% for AD-MCI-CN classification, and 76.5% in differential diagnosis of AD and FTD. We also validated the robustness of DiaMond in a comprehensive ablation study. The code is available at https://github.com/ai-med/DiaMond.

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arXiv2024

Faster Image2Video Generation: A Closer Look at CLIP Image Embedding's Impact on Spatio-Temporal Cross-Attentions

This paper investigates the role of CLIP image embeddings within the Stable Video Diffusion (SVD) framework, focusing on their impact on video generation quality and computational efficiency. Our findings indicate that CLIP embeddings, while crucial for aesthetic quality, do not significantly contribute towards the subject and background consistency of video outputs. Moreover, the computationally expensive cross-attention mechanism can be effectively replaced by a simpler linear layer. This layer is computed only once at the first diffusion inference step, and its output is then cached and reused throughout the inference process, thereby enhancing efficiency while maintaining high-quality outputs. Building on these insights, we introduce the VCUT, a training-free approach optimized for efficiency within the SVD architecture. VCUT eliminates temporal cross-attention and replaces spatial cross-attention with a one-time computed linear layer, significantly reducing computational load. The implementation of VCUT leads to a reduction of up to 322T Multiple-Accumulate Operations (MACs) per video and a decrease in model parameters by up to 50M, achieving a 20% reduction in latency compared to the baseline. Our approach demonstrates that conditioning during the Semantic Binding stage is sufficient, eliminating the need for continuous computation across all inference steps and setting a new standard for efficient video generation.

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arXiv2024

Mamba? Catch The Hype Or Rethink What Really Helps for Image Registration

Our findings indicate that adopting "advanced" computational elements fails to significantly improve registration accuracy. Instead, well-established registration-specific designs offer fair improvements, enhancing results by a marginal 1.5\% over the baseline. Our findings emphasize the importance of rigorous, unbiased evaluation and contribution disentanglement of all low- and high-level registration components, rather than simply following the computer vision trends with "more advanced" computational blocks. We advocate for simpler yet effective solutions and novel evaluation metrics that go beyond conventional registration accuracy, warranting further research across diverse organs and modalities. The code is available at \url{https://github.com/BailiangJ/rethink-reg}.

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arXiv2024

Adversarial Distortion Learning for Medical Image Denoising

We present a novel adversarial distortion learning (ADL) for denoising two- and three-dimensional (2D/3D) biomedical image data. The proposed ADL consists of two auto-encoders: a denoiser and a discriminator. The denoiser removes noise from input data and the discriminator compares the denoised result to its noise-free counterpart. This process is repeated until the discriminator cannot differentiate the denoised data from the reference. Both the denoiser and the discriminator are built upon a proposed auto-encoder called Efficient-Unet. Efficient-Unet has a light architecture that uses the residual blocks and a novel pyramidal approach in the backbone to efficiently extract and re-use feature maps. During training, the textural information and contrast are controlled by two novel loss functions. The architecture of Efficient-Unet allows generalizing the proposed method to any sort of biomedical data. The 2D version of our network was trained on ImageNet and tested on biomedical datasets whose distribution is completely different from ImageNet; so, there is no need for re-training. Experimental results carried out on magnetic resonance imaging (MRI), dermatoscopy, electron microscopy and X-ray datasets show that the proposed method achieved the best on each benchmark. Our implementation and pre-trained models are available at https://github.com/mogvision/ADL.

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arXiv2024

Box It to Bind It: Unified Layout Control and Attribute Binding in T2I Diffusion Models

While latent diffusion models (LDMs) excel at creating imaginative images, they often lack precision in semantic fidelity and spatial control over where objects are generated. To address these deficiencies, we introduce the Box-it-to-Bind-it (B2B) module - a novel, training-free approach for improving spatial control and semantic accuracy in text-to-image (T2I) diffusion models. B2B targets three key challenges in T2I: catastrophic neglect, attribute binding, and layout guidance. The process encompasses two main steps: i) Object generation, which adjusts the latent encoding to guarantee object generation and directs it within specified bounding boxes, and ii) attribute binding, guaranteeing that generated objects adhere to their specified attributes in the prompt. B2B is designed as a compatible plug-and-play module for existing T2I models, markedly enhancing model performance in addressing the key challenges. We evaluate our technique using the established CompBench and TIFA score benchmarks, demonstrating significant performance improvements compared to existing methods. The source code will be made publicly available at https://github.com/nextaistudio/BoxIt2BindIt.

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arXiv2024

No-Clean-Reference Image Super-Resolution: Application to Electron Microscopy

The inability to acquire clean high-resolution (HR) electron microscopy (EM) images over a large brain tissue volume hampers many neuroscience studies. To address this challenge, we propose a deep-learning-based image super-resolution (SR) approach to computationally reconstruct clean HR 3D-EM with a large field of view (FoV) from noisy low-resolution (LR) acquisition. Our contributions are I) Investigating training with no-clean references for $\ell_2$ and $\ell_1$ loss functions; II) Introducing a novel network architecture, named EMSR, for enhancing the resolution of LR EM images while reducing inherent noise; and, III) Comparing different training strategies including using acquired LR and HR image pairs, i.e., real pairs with no-clean references contaminated with real corruptions, the pairs of synthetic LR and acquired HR, as well as acquired LR and denoised HR pairs. Experiments with nine brain datasets showed that training with real pairs can produce high-quality super-resolved results, demonstrating the feasibility of training with non-clean references for both loss functions. Additionally, comparable results were observed, both visually and numerically, when employing denoised and noisy references for training. Moreover, utilizing the network trained with synthetically generated LR images from HR counterparts proved effective in yielding satisfactory SR results, even in certain cases, outperforming training with real pairs. The proposed SR network was compared quantitatively and qualitatively with several established SR techniques, showcasing either the superiority or competitiveness of the proposed method in mitigating noise while recovering fine details.

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arXiv2023

RegBN: Batch Normalization of Multimodal Data with Regularization

Recent years have witnessed a surge of interest in integrating high-dimensional data captured by multisource sensors, driven by the impressive success of neural networks in the integration of multimodal data. However, the integration of heterogeneous multimodal data poses a significant challenge, as confounding effects and dependencies among such heterogeneous data sources introduce unwanted variability and bias, leading to suboptimal performance of multimodal models. Therefore, it becomes crucial to normalize the low- or high-level features extracted from data modalities before their fusion takes place. This paper introduces a novel approach for the normalization of multimodal data, called RegBN, that incorporates regularization. RegBN uses the Frobenius norm as a regularizer term to address the side effects of confounders and underlying dependencies among different data sources. The proposed method generalizes well across multiple modalities and eliminates the need for learnable parameters, simplifying training and inference. We validate the effectiveness of RegBN on eight databases from five research areas, encompassing diverse modalities such as language, audio, image, video, depth, tabular, and 3D MRI. The proposed method demonstrates broad applicability across different architectures such as multilayer perceptrons, convolutional neural networks, and vision transformers, enabling effective normalization of both low- and high-level features in multimodal neural networks. RegBN is available at \url{https://github.com/mogvision/regbn}.

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arXiv2023

Self-Supervised Super-Resolution Approach for Isotropic Reconstruction of 3D Electron Microscopy Images from Anisotropic Acquisition

Three-dimensional electron microscopy (3DEM) is an essential technique to investigate volumetric tissue ultra-structure. Due to technical limitations and high imaging costs, samples are often imaged anisotropically, where resolution in the axial direction ($z$) is lower than in the lateral directions $(x,y)$. This anisotropy 3DEM can hamper subsequent analysis and visualization tasks. To overcome this limitation, we propose a novel deep-learning (DL)-based self-supervised super-resolution approach that computationally reconstructs isotropic 3DEM from the anisotropic acquisition. The proposed DL-based framework is built upon the U-shape architecture incorporating vision-transformer (ViT) blocks, enabling high-capability learning of local and global multi-scale image dependencies. To train the tailored network, we employ a self-supervised approach. Specifically, we generate pairs of anisotropic and isotropic training datasets from the given anisotropic 3DEM data. By feeding the given anisotropic 3DEM dataset in the trained network through our proposed framework, the isotropic 3DEM is obtained. Importantly, this isotropic reconstruction approach relies solely on the given anisotropic 3DEM dataset and does not require pairs of co-registered anisotropic and isotropic 3DEM training datasets. To evaluate the effectiveness of the proposed method, we conducted experiments using three 3DEM datasets acquired from brain. The experimental results demonstrated that our proposed framework could successfully reconstruct isotropic 3DEM from the anisotropic acquisition.

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