Large-scale text-to-image foundation models have achieved remarkable visual realism, yet generating human images with correct anatomical structures remains challenging. Existing approaches enforce anatomical constraints through part-specific modules or localized loss weighting during supervised fine-tuning on high-quality human photos, but such datasets are limited and often provide ambiguous optimization signals due to confounding factors such as lighting, pose, and background. Preference-based alignment offers an alternative, but standard Direct Preference Optimization (DPO) treats all pixels equally and therefore fails to exploit the localized nature of anatomical artifacts. To address this, we propose the framework of Alignment via Synthetic Anatomical Preference (ASAP), which constructs controlled preference pairs through a localized degradation mechanism applied to high-fidelity human images. This mechanism performs a controlled experiment on images by introducing explicit anatomical errors in targeted regions while preserving the remaining content. With this mechanism, we create the Human Anatomical Preference (HAP) dataset with over 10K curated pairs for effective anatomica
Text-conditioned generative models for volumetric medical imaging provide semantic control but lack explicit anatomical guidance, often resulting in outputs that are spatially ambiguous or anatomically inconsistent. In contrast, structure-driven methods ensure strong anatomical consistency but typically assume access to ground-truth annotations, which are unavailable when the target image is to be synthesized. We propose a retrieval-augmented approach for Text-to-CT generation that integrates semantic and anatomical information under a realistic inference setting. Given a radiology report, our method retrieves a semantically related clinical case using a 3D vision-language encoder and leverages its associated anatomical annotation as a structural proxy. This proxy is injected into a text-conditioned latent diffusion model via a ControlNet branch, providing coarse anatomical guidance while maintaining semantic flexibility. Experiments on the CT-RATE dataset show that retrieval-augmented generation improves image fidelity and clinical consistency compared to text-only baselines, while additionally enabling explicit spatial controllability, a capability inherently absent in such appro
Diffusion models have enabled remarkably high-quality medical image generation, yet it is challenging to enforce anatomical constraints in generated images. To this end, we propose a diffusion model-based method that supports anatomically-controllable medical image generation, by following a multi-class anatomical segmentation mask at each sampling step. We additionally introduce a random mask ablation training algorithm to enable conditioning on a selected combination of anatomical constraints while allowing flexibility in other anatomical areas. We compare our method ("SegGuidedDiff") to existing methods on breast MRI and abdominal/neck-to-pelvis CT datasets with a wide range of anatomical objects. Results show that our method reaches a new state-of-the-art in the faithfulness of generated images to input anatomical masks on both datasets, and is on par for general anatomical realism. Finally, our model also enjoys the extra benefit of being able to adjust the anatomical similarity of generated images to real images of choice through interpolation in its latent space. SegGuidedDiff has many applications, including cross-modality translation, and the generation of paired or counte
Video transformers have recently demonstrated strong potential for echocardiogram (echo) analysis, leveraging self-supervised pre-training and flexible adaptation across diverse tasks. However, like other models operating on videos, they are prone to learning spurious correlations from non-diagnostic regions such as image backgrounds. To overcome this limitation, we propose the Video Anatomically Constrained Transformer (ViACT), a novel framework that integrates anatomical priors directly into the transformer architecture. ViACT represents a deforming anatomical structure as a point set and encodes both its spatial geometry and corresponding image patches into transformer tokens. During pre-training, ViACT follows a masked autoencoding strategy that masks and reconstructs only anatomical patches, enforcing that representation learning is focused on the anatomical region. The pre-trained model can then be fine-tuned for tasks localized to this region. In this work we focus on the myocardium, demonstrating the framework on echo analysis tasks such as left ventricular ejection fraction (EF) regression and cardiac amyloidosis (CA) detection. The anatomical constraint focuses transforme
Multi-modal Magnetic Resonance Imaging (MRI) is imperative for accurate brain tumor segmentation, offering indispensable complementary information. Nonetheless, the absence of modalities poses significant challenges in achieving precise segmentation. Recognizing the shared anatomical structures between mono-modal and multi-modal representations, it is noteworthy that mono-modal images typically exhibit limited features in specific regions and tissues. In response to this, we present Anatomical Consistency Distillation and Inconsistency Synthesis (ACDIS), a novel framework designed to transfer anatomical structures from multi-modal to mono-modal representations and synthesize modality-specific features. ACDIS consists of two main components: Anatomical Consistency Distillation (ACD) and Modality Feature Synthesis Block (MFSB). ACD incorporates the Anatomical Feature Enhancement Block (AFEB), meticulously mining anatomical information. Simultaneously, Anatomical Consistency ConsTraints (ACCT) are employed to facilitate the consistent knowledge transfer, i.e., the richness of information and the similarity in anatomical structure, ensuring precise alignment of structural features acro
Deep-learning-based denoising methods have significantly improved Low-Dose CT (LDCT) image quality. However, existing models often over-smooth important anatomical details due to their purely data-driven attention mechanisms. To address this challenge, we propose a novel LDCT denoising framework, BioAtt. The key innovation lies in attending anatomical prior distributions extracted from the pretrained vision-language model BiomedCLIP. These priors guide the denoising model to focus on anatomically relevant regions to suppress noise while preserving clinically relevant structures. We highlight three main contributions: BioAtt outperforms baseline and attention-based models in SSIM, PSNR, and RMSE across multiple anatomical regions. The framework introduces a new architectural paradigm by embedding anatomic priors directly into spatial attention. Finally, BioAtt attention maps provide visual confirmation that the improvements stem from anatomical guidance rather than increased model complexity.
Intravoxel incoherent motion (IVIM) is a diffusion-weighted magnetic resonance imaging (MRI) method that may be applied to the placenta to help diagnose abnormal pregnancies. IVIM requires prolonged scan times, followed by a model-based estimation procedure. Maternal or fetal motion during the scan affects the accuracy of this estimation. In this work, we proposed to address this challenging motion correction and data fitting problem by using additional anatomical information that is routinely collected at the beginning of the examination. Super-resolution reconstruction (SRR) was applied to these anatomical data, to provide a patient-specific, 3D isotropic, anatomic reference. Our first contribution is a novel framework with a two-step motion correction that uses both IVIM and the SRR anatomic data, accounting for both intra- and inter-scan, non-rigid motion. Our second contribution is an automation and acceleration of the IVIM data fitting, using a state-of-the-art Bayesian-type algorithm, modified with a preconditioned Crank-Nicholson (pCN) sampling strategy. The accuracy of the IVIM parameter fitting was improved by the proposed motion correction strategy, as assessed by the me
Generative modeling of anatomical structures plays a crucial role in virtual imaging trials, which allow researchers to perform studies without the costs and constraints inherent to in vivo and phantom studies. For clinical relevance, generative models should allow targeted control to simulate specific patient populations rather than relying on purely random sampling. In this work, we propose a steerable generative model based on implicit neural representations. Implicit neural representations naturally support topology changes, making them well-suited for anatomical structures with varying topology, such as the thyroid. Our model learns a disentangled latent representation, enabling fine-grained control over shape variations. Evaluation includes reconstruction accuracy and anatomical plausibility. Our results demonstrate that the proposed model achieves high-quality shape generation while enabling targeted anatomical modifications.
3D brain MRI studies often examine subtle morphometric differences between cohorts that are hard to detect visually. Given the high cost of MRI acquisition, these studies could greatly benefit from image syntheses, particularly counterfactual image generation, as seen in other domains, such as computer vision. However, counterfactual models struggle to produce anatomically plausible MRIs due to the lack of explicit inductive biases to preserve fine-grained anatomical details. This shortcoming arises from the training of the models aiming to optimize for the overall appearance of the images (e.g., via cross-entropy) rather than preserving subtle, yet medically relevant, local variations across subjects. To preserve subtle variations, we propose to explicitly integrate anatomical constraints on a voxel-level as prior into a generative diffusion framework. Called Probabilistic Causal Graph Model (PCGM), the approach captures anatomical constraints via a probabilistic graph module and translates those constraints into spatial binary masks of regions where subtle variations occur. The masks (encoded by a 3D extension of ControlNet) constrain a novel counterfactual denoising UNet, whose
Anatomical mesh segmentation requires models that operate directly on irregular surface geometry while remaining robust to arbitrary patient pose and mesh resolution variation. Existing task-specific mesh and point-cloud methods are not equivariant, and can degrade sharply under test-time perturbation, for example dropping by 25-26 IoU points on intraoral scan segmentation at $40^\circ$ tilt. We present EAMS, an Equivariant Anatomical Mesh Segmentor built on Equivariant Mesh Neural Networks (EMNN), and evaluate it across four clinically distinct tasks spanning edge-, vertex-, and face-level supervision. We combine intrinsic mesh descriptors with anatomy-aware priors, including PCA-derived frames for dental arches and liver surfaces, and augment message passing to provide lightweight global context. Across intracranial aneurysm and intraoral segmentation, EAMS variants are competitive with specialized baselines on unperturbed inputs while remaining stable under geometric perturbations, and on liver surfaces they expose a favorable trade-off between canonical-pose accuracy and rotation robustness. These results show that a lightweight ($<2$M parameters) equivariant framework can d
Medical Phrase Grounding (MPG) maps radiological findings described in medical reports to specific regions in medical images. The primary obstacle hindering progress in MPG is the scarcity of annotated data available for training and validation. We propose anatomical grounding as an in-domain pre-training task that aligns anatomical terms with corresponding regions in medical images, leveraging large-scale datasets such as Chest ImaGenome. Our empirical evaluation on MS-CXR demonstrates that anatomical grounding pre-training significantly improves performance in both a zero-shot learning and fine-tuning setting, outperforming state-of-the-art MPG models. Our fine-tuned model achieved state-of-the-art performance on MS-CXR with an mIoU of 61.2, demonstrating the effectiveness of anatomical grounding pre-training for MPG.
Anatomical trees play a central role in clinical diagnosis and treatment planning. However, accurately representing anatomical trees is challenging due to their varying and complex topology and geometry. Traditional methods for representing tree structures, captured using medical imaging, while invaluable for visualizing vascular and bronchial networks, exhibit drawbacks in terms of limited resolution, flexibility, and efficiency. Recently, implicit neural representations (INRs) have emerged as a powerful tool for representing shapes accurately and efficiently. We propose a novel approach, $TrIND$, for representing anatomical trees using INR, while also capturing the distribution of a set of trees via denoising diffusion in the space of INRs. We accurately capture the intricate geometries and topologies of anatomical trees at any desired resolution. Through extensive qualitative and quantitative evaluation, we demonstrate high-fidelity tree reconstruction with arbitrary resolution yet compact storage, and versatility across anatomical sites and tree complexities. The code is available at: \texttt{\url{https://github.com/sinashish/TreeDiffusion}}.
Curation is a significant barrier to using 'big data' radiotherapy planning databases of 100,000+ patients. Anatomic site stratification is essential for downstream analyses, but current methods rely on inconsistent plan labels or target nomenclature, which is unreliable for multi-institutional data. We developed software to automate labeling by inferring anatomic regions directly from dose-volume overlap with deep-learning segmentations, eliminating metadata reliance. The software processes DICOM files in bulk, utilizing deep learning to segment 118 structures (organs, glands, and bones) categorized into six regions: Cranial, Head and Neck, Pelvis, Abdomen, Thorax, Extremity. The 85% and 50% isodose lines are converted to structures to compute organ-specific dose-overlap metrics. Plans are assigned ranked regional labels based on these intersections. The algorithm was refined using 109 expert-labeled cases and validated on 100 consecutive clinical plans. On the 100-plan test dataset, the algorithm achieved 91% Exact Accuracy (matching all expert labels and order), 94% Top-2 Accuracy (matching the top two expert regions regardless of order), and 95% Top-1 Accuracy (matching the pri
Cardiac amyloidosis (CA) is a rare cardiomyopathy, with typical abnormalities in clinical measurements from echocardiograms such as reduced global longitudinal strain of the myocardium. An alternative approach for detecting CA is via neural networks, using video classification models such as convolutional neural networks. These models process entire video clips, but provide no assurance that classification is based on clinically relevant features known to be associated with CA. An alternative paradigm for disease classification is to apply models to quantitative features such as strain, ensuring that the classification relates to clinically relevant features. Drawing inspiration from this approach, we explicitly constrain a transformer model to the anatomical region where many known CA abnormalities occur -- the myocardium, which we embed as a set of deforming points and corresponding sampled image patches into input tokens. We show that our anatomical constraint can also be applied to the popular self-supervised learning masked autoencoder pre-training, where we propose to mask and reconstruct only anatomical patches. We show that by constraining both the transformer and pre-train
Progress in anatomical 3D shape classification is limited by the complexity of mesh data and the lack of standardized benchmarks, highlighting the need for robust learning methods and reproducible evaluation. We introduce two key steps toward clinically and benchmark-ready anatomical shape classification via self-supervised graph autoencoding. We propose Precomputed Structural Pooling (PSPooling), a non-learnable mesh pooling operator designed for efficient and structure-preserving graph coarsening in 3D anatomical shape analysis. PSPooling precomputes node correspondence sets based on geometric proximity, enabling parallelizable and reversible pooling and unpooling operations with guaranteed support structure. This design avoids the sparsity and reconstruction issues of selection-based methods and the sequential overhead of edge contraction approaches, making it particularly suitable for high-resolution medical meshes. To demonstrate its effectiveness, we integrate PSPooling into a self-supervised graph autoencoder that learns anatomy-aware representations from unlabeled surface meshes. We evaluate the downstream benefits on MedShapeNet19, a new curated benchmark dataset we derive
We propose a self-supervised model producing 3D anatomical positional embeddings (APE) of individual medical image voxels. APE encodes voxels' anatomical closeness, i.e., voxels of the same organ or nearby organs always have closer positional embeddings than the voxels of more distant body parts. In contrast to the existing models of anatomical positional embeddings, our method is able to efficiently produce a map of voxel-wise embeddings for a whole volumetric input image, which makes it an optimal choice for different downstream applications. We train our APE model on 8400 publicly available CT images of abdomen and chest regions. We demonstrate its superior performance compared with the existing models on anatomical landmark retrieval and weakly-supervised few-shot localization of 13 abdominal organs. As a practical application, we show how to cheaply train APE to crop raw CT images to different anatomical regions of interest with 0.99 recall, while reducing the image volume by 10-100 times. The code and the pre-trained APE model are available at https://github.com/mishgon/ape .
We introduce a novel Region-based contrastive pretraining for Medical Image Retrieval (RegionMIR) that demonstrates the feasibility of medical image retrieval with similar anatomical regions. RegionMIR addresses two major challenges for medical image retrieval i) standardization of clinically relevant searching criteria (e.g., anatomical, pathology-based), and ii) localization of anatomical area of interests that are semantically meaningful. In this work, we propose an ROI image retrieval image network that retrieves images with similar anatomy by extracting anatomical features (via bounding boxes) and evaluate similarity between pairwise anatomy-categorized features between the query and the database of images using contrastive learning. ROI queries are encoded using a contrastive-pretrained encoder that was fine-tuned for anatomy classification, which generates an anatomical-specific latent space for region-correlated image retrieval. During retrieval, we compare the anatomically encoded query to find similar features within a feature database generated from training samples, and retrieve images with similar regions from training samples. We evaluate our approach on both anatomy
Symmetry detection and morphological classification of anatomical structures play pivotal roles in medical image analysis. The application of kinematic surface fitting, a method for characterizing shapes through parametric stationary velocity fields, has shown promising results in computer vision and computer-aided design. However, existing research has predominantly focused on first order rotational velocity fields, which may not adequately capture the intricate curved and twisted nature of anatomical structures. To address this limitation, we propose an innovative approach utilizing a second order velocity field for kinematic surface fitting. This advancement accommodates higher rotational shape complexity and improves the accuracy of symmetry detection in anatomical structures. We introduce a robust fitting technique and validate its performance through testing on synthetic shapes and real anatomical structures. Our method not only enables the detection of curved rotational symmetries (core lines) but also facilitates morphological classification by deriving intrinsic shape parameters related to curvature and torsion. We illustrate the usefulness of our technique by categorizing
Anatomic tracer studies are critical for validating and improving diffusion MRI (dMRI) tractography. However, large-scale analysis of data from such studies is hampered by the labor-intensive process of annotating fiber bundles manually on histological slides. Existing automated methods often miss sparse bundles or require complex post-processing across consecutive sections, limiting their flexibility and generalizability. We present a streamlined, fully automated framework for fiber bundle segmentation in macaque tracer data, based on a U-Net architecture with large patch sizes, foreground aware sampling, and semisupervised pre-training. Our approach eliminates common errors such as mislabeling terminals as bundles, improves detection of sparse bundles by over 20% and reduces the False Discovery Rate (FDR) by 40% compared to the state-of-the-art, all while enabling analysis of standalone slices. This new framework will facilitate the automated analysis of anatomic tracing data at a large scale, generating more ground-truth data that can be used to validate and optimize dMRI tractography methods.
Coordinate based implicit neural representations have gained rapid popularity in recent years as they have been successfully used in image, geometry and scene modeling tasks. In this work, we present a novel use case for such implicit representations in the context of learning anatomically constrained face models. Actor specific anatomically constrained face models are the state of the art in both facial performance capture and performance retargeting. Despite their practical success, these anatomical models are slow to evaluate and often require extensive data capture to be built. We propose the anatomical implicit face model; an ensemble of implicit neural networks that jointly learn to model the facial anatomy and the skin surface with high-fidelity, and can readily be used as a drop in replacement to conventional blendshape models. Given an arbitrary set of skin surface meshes of an actor and only a neutral shape with estimated skull and jaw bones, our method can recover a dense anatomical substructure which constrains every point on the facial surface. We demonstrate the usefulness of our approach in several tasks ranging from shape fitting, shape editing, and performance reta