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Mar 16

Med-Banana-50K: A Cross-modality Large-Scale Dataset for Text-guided Medical Image Editing

Medical image editing has emerged as a pivotal technology with broad applications in data augmentation, model interpretability, medical education, and treatment simulation. However, the lack of large-scale, high-quality, and openly accessible datasets tailored for medical contexts with strict anatomical and clinical constraints has significantly hindered progress in this domain. To bridge this gap, we introduce Med-Banana-50K, a comprehensive dataset of over 50k medically curated image edits spanning chest X-ray, brain MRI, and fundus photography across 23 diseases. Each sample supports bidirectional lesion editing (addition and removal) and is constructed using Gemini-2.5-Flash-Image based on real clinical images. A key differentiator of our dataset is the medically grounded quality control protocol: we employ an LLM-as-Judge evaluation framework with criteria such as instruction compliance, structural plausibility, image realism, and fidelity preservation, alongside iterative refinement over up to five rounds. Additionally, Med-Banana-50K includes around 37,000 failed editing attempts with full evaluation logs to support preference learning and alignment research. By offering a large-scale, medically rigorous, and fully documented resource, Med-Banana-50K establishes a critical foundation for developing and evaluating reliable medical image editing systems. Our dataset and code are publicly available. [https://github.com/richardChenzhihui/med-banana-50k].

  • 2 authors
·
Nov 2, 2025

PIE: Simulating Disease Progression via Progressive Image Editing

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

  • 6 authors
·
Sep 20, 2023 1

Pixel Perfect MegaMed: A Megapixel-Scale Vision-Language Foundation Model for Generating High Resolution Medical Images

Medical image synthesis presents unique challenges due to the inherent complexity and high-resolution details required in clinical contexts. Traditional generative architectures such as Generative Adversarial Networks (GANs) or Variational Auto Encoder (VAEs) have shown great promise for high-resolution image generation but struggle with preserving fine-grained details that are key for accurate diagnosis. To address this issue, we introduce Pixel Perfect MegaMed, the first vision-language foundation model to synthesize images at resolutions of 1024x1024. Our method deploys a multi-scale transformer architecture designed specifically for ultra-high resolution medical image generation, enabling the preservation of both global anatomical context and local image-level details. By leveraging vision-language alignment techniques tailored to medical terminology and imaging modalities, Pixel Perfect MegaMed bridges the gap between textual descriptions and visual representations at unprecedented resolution levels. We apply our model to the CheXpert dataset and demonstrate its ability to generate clinically faithful chest X-rays from text prompts. Beyond visual quality, these high-resolution synthetic images prove valuable for downstream tasks such as classification, showing measurable performance gains when used for data augmentation, particularly in low-data regimes. Our code is accessible through the project website - https://tehraninasab.github.io/pixelperfect-megamed.

  • 4 authors
·
Jul 16, 2025

RoentGen: Vision-Language Foundation Model for Chest X-ray Generation

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

  • 10 authors
·
Nov 23, 2022

A for-loop is all you need. For solving the inverse problem in the case of personalized tumor growth modeling

Solving the inverse problem is the key step in evaluating the capacity of a physical model to describe real phenomena. In medical image computing, it aligns with the classical theme of image-based model personalization. Traditionally, a solution to the problem is obtained by performing either sampling or variational inference based methods. Both approaches aim to identify a set of free physical model parameters that results in a simulation best matching an empirical observation. When applied to brain tumor modeling, one of the instances of image-based model personalization in medical image computing, the overarching drawback of the methods is the time complexity for finding such a set. In a clinical setting with limited time between imaging and diagnosis or even intervention, this time complexity may prove critical. As the history of quantitative science is the history of compression, we align in this paper with the historical tendency and propose a method compressing complex traditional strategies for solving an inverse problem into a simple database query task. We evaluated different ways of performing the database query task assessing the trade-off between accuracy and execution time. On the exemplary task of brain tumor growth modeling, we prove that the proposed method achieves one order speed-up compared to existing approaches for solving the inverse problem. The resulting compute time offers critical means for relying on more complex and, hence, realistic models, for integrating image preprocessing and inverse modeling even deeper, or for implementing the current model into a clinical workflow.

  • 15 authors
·
May 9, 2022

MonetGPT: Solving Puzzles Enhances MLLMs' Image Retouching Skills

Retouching is an essential task in post-manipulation of raw photographs. Generative editing, guided by text or strokes, provides a new tool accessible to users but can easily change the identity of the original objects in unacceptable and unpredictable ways. In contrast, although traditional procedural edits, as commonly supported by photoediting tools (e.g., Gimp, Lightroom), are conservative, they are still preferred by professionals. Unfortunately, professional quality retouching involves many individual procedural editing operations that is challenging to plan for most novices. In this paper, we ask if a multimodal large language model (MLLM) can be taught to critique raw photographs, suggest suitable remedies, and finally realize them with a given set of pre-authored procedural image operations. We demonstrate that MLLMs can be first made aware of the underlying image processing operations, by training them to solve specially designed visual puzzles. Subsequently, such an operation-aware MLLM can both plan and propose edit sequences. To facilitate training, given a set of expert-edited photos, we synthesize a reasoning dataset by procedurally manipulating the expert edits and then grounding a pretrained LLM on the visual adjustments, to synthesize reasoning for finetuning. The proposed retouching operations are, by construction, understandable by the users, preserve object details and resolution, and can be optionally overridden. We evaluate our setup on a variety of test examples and show advantages, in terms of explainability and identity preservation, over existing generative and other procedural alternatives. Code, data, models, and supplementary results can be found via our project website at https://monetgpt.github.io.

  • 3 authors
·
May 9, 2025 2

Preserving Tumor Volumes for Unsupervised Medical Image Registration

Medical image registration is a critical task that estimates the spatial correspondence between pairs of images. However, current traditional and deep-learning-based methods rely on similarity measures to generate a deforming field, which often results in disproportionate volume changes in dissimilar regions, especially in tumor regions. These changes can significantly alter the tumor size and underlying anatomy, which limits the practical use of image registration in clinical diagnosis. To address this issue, we have formulated image registration with tumors as a constraint problem that preserves tumor volumes while maximizing image similarity in other normal regions. Our proposed strategy involves a two-stage process. In the first stage, we use similarity-based registration to identify potential tumor regions by their volume change, generating a soft tumor mask accordingly. In the second stage, we propose a volume-preserving registration with a novel adaptive volume-preserving loss that penalizes the change in size adaptively based on the masks calculated from the previous stage. Our approach balances image similarity and volume preservation in different regions, i.e., normal and tumor regions, by using soft tumor masks to adjust the imposition of volume-preserving loss on each one. This ensures that the tumor volume is preserved during the registration process. We have evaluated our strategy on various datasets and network architectures, demonstrating that our method successfully preserves the tumor volume while achieving comparable registration results with state-of-the-art methods. Our codes is available at: https://dddraxxx.github.io/Volume-Preserving-Registration/.

  • 5 authors
·
Sep 18, 2023

Coupling AI and Citizen Science in Creation of Enhanced Training Dataset for Medical Image Segmentation

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

  • 10 authors
·
Sep 4, 2024

UniTune: Text-Driven Image Editing by Fine Tuning a Diffusion Model on a Single Image

Text-driven image generation methods have shown impressive results recently, allowing casual users to generate high quality images by providing textual descriptions. However, similar capabilities for editing existing images are still out of reach. Text-driven image editing methods usually need edit masks, struggle with edits that require significant visual changes and cannot easily keep specific details of the edited portion. In this paper we make the observation that image-generation models can be converted to image-editing models simply by fine-tuning them on a single image. We also show that initializing the stochastic sampler with a noised version of the base image before the sampling and interpolating relevant details from the base image after sampling further increase the quality of the edit operation. Combining these observations, we propose UniTune, a novel image editing method. UniTune gets as input an arbitrary image and a textual edit description, and carries out the edit while maintaining high fidelity to the input image. UniTune does not require additional inputs, like masks or sketches, and can perform multiple edits on the same image without retraining. We test our method using the Imagen model in a range of different use cases. We demonstrate that it is broadly applicable and can perform a surprisingly wide range of expressive editing operations, including those requiring significant visual changes that were previously impossible.

  • 6 authors
·
Oct 17, 2022

SynthRAD2025 Grand Challenge dataset: generating synthetic CTs for radiotherapy

Medical imaging is essential in modern radiotherapy, supporting diagnosis, treatment planning, and monitoring. Synthetic imaging, particularly synthetic computed tomography (sCT), is gaining traction in radiotherapy. The SynthRAD2025 dataset and Grand Challenge promote advancements in sCT generation by providing a benchmarking platform for algorithms using cone-beam CT (CBCT) and magnetic resonance imaging (MRI). The dataset includes 2362 cases: 890 MRI-CT and 1472 CBCT-CT pairs from head-and-neck, thoracic, and abdominal cancer patients treated at five European university medical centers (UMC Groningen, UMC Utrecht, Radboud UMC, LMU University Hospital Munich, and University Hospital of Cologne). Data were acquired with diverse scanners and protocols. Pre-processing, including rigid and deformable image registration, ensures high-quality, modality-aligned images. Extensive quality assurance validates image consistency and usability. All imaging data is provided in MetaImage (.mha) format, ensuring compatibility with medical image processing tools. Metadata, including acquisition parameters and registration details, is available in structured CSV files. To maintain dataset integrity, SynthRAD2025 is divided into training (65%), validation (10%), and test (25%) sets. The dataset is accessible at https://doi.org/10.5281/zenodo.14918089 under the SynthRAD2025 collection. This dataset supports benchmarking and the development of synthetic imaging techniques for radiotherapy applications. Use cases include sCT generation for MRI-only and MR-guided photon/proton therapy, CBCT-based dose calculations, and adaptive radiotherapy workflows. By integrating diverse acquisition settings, SynthRAD2025 fosters robust, generalizable image synthesis algorithms, advancing personalized cancer care and adaptive radiotherapy.

  • 19 authors
·
Feb 24, 2025

MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

  • 31 authors
·
Oct 9, 2024

MediAug: Exploring Visual Augmentation in Medical Imaging

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

  • 7 authors
·
Apr 26, 2025 1

Exploring the Effect of Dataset Diversity in Self-Supervised Learning for Surgical Computer Vision

Over the past decade, computer vision applications in minimally invasive surgery have rapidly increased. Despite this growth, the impact of surgical computer vision remains limited compared to other medical fields like pathology and radiology, primarily due to the scarcity of representative annotated data. Whereas transfer learning from large annotated datasets such as ImageNet has been conventionally the norm to achieve high-performing models, recent advancements in self-supervised learning (SSL) have demonstrated superior performance. In medical image analysis, in-domain SSL pretraining has already been shown to outperform ImageNet-based initialization. Although unlabeled data in the field of surgical computer vision is abundant, the diversity within this data is limited. This study investigates the role of dataset diversity in SSL for surgical computer vision, comparing procedure-specific datasets against a more heterogeneous general surgical dataset across three different downstream surgical applications. The obtained results show that using solely procedure-specific data can lead to substantial improvements of 13.8%, 9.5%, and 36.8% compared to ImageNet pretraining. However, extending this data with more heterogeneous surgical data further increases performance by an additional 5.0%, 5.2%, and 2.5%, suggesting that increasing diversity within SSL data is beneficial for model performance. The code and pretrained model weights are made publicly available at https://github.com/TimJaspers0801/SurgeNet.

  • 12 authors
·
Jul 25, 2024

Prompt Tuning Inversion for Text-Driven Image Editing Using Diffusion Models

Recently large-scale language-image models (e.g., text-guided diffusion models) have considerably improved the image generation capabilities to generate photorealistic images in various domains. Based on this success, current image editing methods use texts to achieve intuitive and versatile modification of images. To edit a real image using diffusion models, one must first invert the image to a noisy latent from which an edited image is sampled with a target text prompt. However, most methods lack one of the following: user-friendliness (e.g., additional masks or precise descriptions of the input image are required), generalization to larger domains, or high fidelity to the input image. In this paper, we design an accurate and quick inversion technique, Prompt Tuning Inversion, for text-driven image editing. Specifically, our proposed editing method consists of a reconstruction stage and an editing stage. In the first stage, we encode the information of the input image into a learnable conditional embedding via Prompt Tuning Inversion. In the second stage, we apply classifier-free guidance to sample the edited image, where the conditional embedding is calculated by linearly interpolating between the target embedding and the optimized one obtained in the first stage. This technique ensures a superior trade-off between editability and high fidelity to the input image of our method. For example, we can change the color of a specific object while preserving its original shape and background under the guidance of only a target text prompt. Extensive experiments on ImageNet demonstrate the superior editing performance of our method compared to the state-of-the-art baselines.

  • 4 authors
·
May 7, 2023

Medical Image Classification with KAN-Integrated Transformers and Dilated Neighborhood Attention

Convolutional networks, transformers, hybrid models, and Mamba-based architectures have demonstrated strong performance across various medical image classification tasks. However, these methods were primarily designed to classify clean images using labeled data. In contrast, real-world clinical data often involve image corruptions that are unique to multi-center studies and stem from variations in imaging equipment across manufacturers. In this paper, we introduce the Medical Vision Transformer (MedViTV2), a novel architecture incorporating Kolmogorov-Arnold Network (KAN) layers into the transformer architecture for the first time, aiming for generalized medical image classification. We have developed an efficient KAN block to reduce computational load while enhancing the accuracy of the original MedViT. Additionally, to counteract the fragility of our MedViT when scaled up, we propose an enhanced Dilated Neighborhood Attention (DiNA), an adaptation of the efficient fused dot-product attention kernel capable of capturing global context and expanding receptive fields to scale the model effectively and addressing feature collapse issues. Moreover, a hierarchical hybrid strategy is introduced to stack our Local Feature Perception and Global Feature Perception blocks in an efficient manner, which balances local and global feature perceptions to boost performance. Extensive experiments on 17 medical image classification datasets and 12 corrupted medical image datasets demonstrate that MedViTV2 achieved state-of-the-art results in 27 out of 29 experiments with reduced computational complexity. MedViTV2 is 44\% more computationally efficient than the previous version and significantly enhances accuracy, achieving improvements of 4.6\% on MedMNIST, 5.8\% on NonMNIST, and 13.4\% on the MedMNIST-C benchmark.

  • 5 authors
·
Feb 19, 2025 1

LeFusion: Controllable Pathology Synthesis via Lesion-Focused Diffusion Models

Patient data from real-world clinical practice often suffers from data scarcity and long-tail imbalances, leading to biased outcomes or algorithmic unfairness. This study addresses these challenges by generating lesion-containing image-segmentation pairs from lesion-free images. Previous efforts in medical imaging synthesis have struggled with separating lesion information from background, resulting in low-quality backgrounds and limited control over the synthetic output. Inspired by diffusion-based image inpainting, we propose LeFusion, a lesion-focused diffusion model. By redesigning the diffusion learning objectives to focus on lesion areas, we simplify the learning process and improve control over the output while preserving high-fidelity backgrounds by integrating forward-diffused background contexts into the reverse diffusion process. Additionally, we tackle two major challenges in lesion texture synthesis: 1) multi-peak and 2) multi-class lesions. We introduce two effective strategies: histogram-based texture control and multi-channel decomposition, enabling the controlled generation of high-quality lesions in difficult scenarios. Furthermore, we incorporate lesion mask diffusion, allowing control over lesion size, location, and boundary, thus increasing lesion diversity. Validated on 3D cardiac lesion MRI and lung nodule CT datasets, LeFusion-generated data significantly improves the performance of state-of-the-art segmentation models, including nnUNet and SwinUNETR. Code and model are available at https://github.com/M3DV/LeFusion.

  • 7 authors
·
Mar 20, 2024

Unimedvl: Unifying Medical Multimodal Understanding And Generation Through Observation-Knowledge-Analysis

Medical diagnostic applications require models that can process multimodal medical inputs (images, patient histories, lab results) and generate diverse outputs including both textual reports and visual content (annotations, segmentation masks, and images). Despite this need, existing medical AI systems disrupt this unified process: medical image understanding models interpret images but cannot generate visual outputs, while medical image generation models synthesize images but cannot provide textual explanations. This leads to gaps in data representation, feature integration, and task-level multimodal capabilities. To this end, we propose a multi-level framework that draws inspiration from diagnostic workflows through the Observation-Knowledge-Analysis (OKA) paradigm. Specifically, at the observation level, we construct UniMed-5M, a dataset comprising over 5.6M samples that reformat diverse unimodal data into multimodal pairs for foundational observation. At the knowledge level, we propose Progressive Curriculum Learning that systematically introduces medical multimodal knowledge. At the analysis level, we introduce UniMedVL, the first medical unified multimodal model for the simultaneous analysis of image understanding and generation tasks within a single architecture. UniMedVL achieves superior performance on five medical image understanding benchmarks, while matching specialized models in generation quality across eight medical imaging modalities. Crucially, our unified architecture enables bidirectional knowledge sharing: generation tasks enhance visual understanding features, demonstrating that integrating traditionally separate capabilities within a single medical framework unlocks improvements across diverse medical vision-language tasks. Code is available at https://github.com/uni-medical/UniMedVL.

General-Medical-AI General Medical AI
·
Oct 17, 2025 3

IMPACT: A Generic Semantic Loss for Multimodal Medical Image Registration

Image registration is fundamental in medical imaging, enabling precise alignment of anatomical structures for diagnosis, treatment planning, image-guided treatment or longitudinal monitoring. This work introduces IMPACT (Image Metric with Pretrained model-Agnostic Comparison for Transmodality registration), a generic semantic similarity metric designed for seamless integration into diverse image registration frameworks (such as Elastix and Voxelmorph). It compares deep learning-based features extracted from medical images without requiring task-specific training, ensuring broad applicability across various modalities. By leveraging the features of the large-scale pretrained TotalSegmentator models and the ability to integrate Segment Anything Model (SAM) and other large-scale segmentation networks, this approach offers significant advantages. It provides robust, scalable, and efficient solutions for multimodal image registration. The IMPACT loss was evaluated on five challenging registration tasks involving thoracic CT/CBCT, and pelvic MR/CT datasets. Quantitative metrics, such as Target Registration Error and Dice Similarity Coefficient, demonstrated significant improvements in anatomical alignment compared to baseline methods. Qualitative analyses further confirmed the increased robustness of the proposed metric in the face of noise, artifacts, and modality variations. IMPACT's versatility and efficiency make it a valuable tool for advancing registration performance in clinical and research applications, addressing critical challenges in multimodal medical imaging.

  • 8 authors
·
Mar 31, 2025

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

  • 157 authors
·
Aug 30, 2023

FastEdit: Fast Text-Guided Single-Image Editing via Semantic-Aware Diffusion Fine-Tuning

Conventional Text-guided single-image editing approaches require a two-step process, including fine-tuning the target text embedding for over 1K iterations and the generative model for another 1.5K iterations. Although it ensures that the resulting image closely aligns with both the input image and the target text, this process often requires 7 minutes per image, posing a challenge for practical application due to its time-intensive nature. To address this bottleneck, we introduce FastEdit, a fast text-guided single-image editing method with semantic-aware diffusion fine-tuning, dramatically accelerating the editing process to only 17 seconds. FastEdit streamlines the generative model's fine-tuning phase, reducing it from 1.5K to a mere 50 iterations. For diffusion fine-tuning, we adopt certain time step values based on the semantic discrepancy between the input image and target text. Furthermore, FastEdit circumvents the initial fine-tuning step by utilizing an image-to-image model that conditions on the feature space, rather than the text embedding space. It can effectively align the target text prompt and input image within the same feature space and save substantial processing time. Additionally, we apply the parameter-efficient fine-tuning technique LoRA to U-net. With LoRA, FastEdit minimizes the model's trainable parameters to only 0.37\% of the original size. At the same time, we can achieve comparable editing outcomes with significantly reduced computational overhead. We conduct extensive experiments to validate the editing performance of our approach and show promising editing capabilities, including content addition, style transfer, background replacement, and posture manipulation, etc.

  • 4 authors
·
Aug 6, 2024

XrayGPT: Chest Radiographs Summarization using Medical Vision-Language Models

The latest breakthroughs in large vision-language models, such as Bard and GPT-4, have showcased extraordinary abilities in performing a wide range of tasks. Such models are trained on massive datasets comprising billions of public image-text pairs with diverse tasks. However, their performance on task-specific domains, such as radiology, is still under-investigated and potentially limited due to a lack of sophistication in understanding biomedical images. On the other hand, conversational medical models have exhibited remarkable success but have mainly focused on text-based analysis. In this paper, we introduce XrayGPT, a novel conversational medical vision-language model that can analyze and answer open-ended questions about chest radiographs. Specifically, we align both medical visual encoder (MedClip) with a fine-tuned large language model (Vicuna), using a simple linear transformation. This alignment enables our model to possess exceptional visual conversation abilities, grounded in a deep understanding of radiographs and medical domain knowledge. To enhance the performance of LLMs in the medical context, we generate ~217k interactive and high-quality summaries from free-text radiology reports. These summaries serve to enhance the performance of LLMs through the fine-tuning process. Our approach opens up new avenues the research for advancing the automated analysis of chest radiographs. Our open-source demos, models, and instruction sets are available at: https://github.com/mbzuai-oryx/XrayGPT.

  • 8 authors
·
Jun 13, 2023

GIE-Bench: Towards Grounded Evaluation for Text-Guided Image Editing

Editing images using natural language instructions has become a natural and expressive way to modify visual content; yet, evaluating the performance of such models remains challenging. Existing evaluation approaches often rely on image-text similarity metrics like CLIP, which lack precision. In this work, we introduce a new benchmark designed to evaluate text-guided image editing models in a more grounded manner, along two critical dimensions: (i) functional correctness, assessed via automatically generated multiple-choice questions that verify whether the intended change was successfully applied; and (ii) image content preservation, which ensures that non-targeted regions of the image remain visually consistent using an object-aware masking technique and preservation scoring. The benchmark includes over 1000 high-quality editing examples across 20 diverse content categories, each annotated with detailed editing instructions, evaluation questions, and spatial object masks. We conduct a large-scale study comparing GPT-Image-1, the latest flagship in the text-guided image editing space, against several state-of-the-art editing models, and validate our automatic metrics against human ratings. Results show that GPT-Image-1 leads in instruction-following accuracy, but often over-modifies irrelevant image regions, highlighting a key trade-off in the current model behavior. GIE-Bench provides a scalable, reproducible framework for advancing more accurate evaluation of text-guided image editing.

  • 8 authors
·
May 16, 2025 2

Why Registration Quality Matters: Enhancing sCT Synthesis with IMPACT-Based Registration

We participated in the SynthRAD2025 challenge (Tasks 1 and 2) with a unified pipeline for synthetic CT (sCT) generation from MRI and CBCT, implemented using the KonfAI framework. Our model is a 2.5D U-Net++ with a ResNet-34 encoder, trained jointly across anatomical regions and fine-tuned per region. The loss function combined pixel-wise L1 loss with IMPACT-Synth, a perceptual loss derived from SAM and TotalSegmentator to enhance structural fidelity. Training was performed using AdamW (initial learning rate = 0.001, halved every 25k steps) on patch-based, normalized, body-masked inputs (320x320 for MRI, 256x256 for CBCT), with random flipping as the only augmentation. No post-processing was applied. Final predictions leveraged test-time augmentation and five-fold ensembling. The best model was selected based on validation MAE. Two registration strategies were evaluated: (i) Elastix with mutual information, consistent with the challenge pipeline, and (ii) IMPACT, a feature-based similarity metric leveraging pretrained segmentation networks. On the local test sets, IMPACT-based registration achieved more accurate and anatomically consistent alignments than mutual-information-based registration, resulting in improved sCT synthesis with lower MAE and more realistic anatomical structures. On the public validation set, however, models trained with Elastix-aligned data achieved higher scores, reflecting a registration bias favoring alignment strategies consistent with the evaluation pipeline. This highlights how registration errors can propagate into supervised learning, influencing both training and evaluation, and potentially inflating performance metrics at the expense of anatomical fidelity. By promoting anatomically consistent alignment, IMPACT helps mitigate this bias and supports the development of more robust and generalizable sCT synthesis models.

  • 4 authors
·
Oct 24, 2025

Guide-and-Rescale: Self-Guidance Mechanism for Effective Tuning-Free Real Image Editing

Despite recent advances in large-scale text-to-image generative models, manipulating real images with these models remains a challenging problem. The main limitations of existing editing methods are that they either fail to perform with consistent quality on a wide range of image edits or require time-consuming hyperparameter tuning or fine-tuning of the diffusion model to preserve the image-specific appearance of the input image. We propose a novel approach that is built upon a modified diffusion sampling process via the guidance mechanism. In this work, we explore the self-guidance technique to preserve the overall structure of the input image and its local regions appearance that should not be edited. In particular, we explicitly introduce layout-preserving energy functions that are aimed to save local and global structures of the source image. Additionally, we propose a noise rescaling mechanism that allows to preserve noise distribution by balancing the norms of classifier-free guidance and our proposed guiders during generation. Such a guiding approach does not require fine-tuning the diffusion model and exact inversion process. As a result, the proposed method provides a fast and high-quality editing mechanism. In our experiments, we show through human evaluation and quantitative analysis that the proposed method allows to produce desired editing which is more preferable by humans and also achieves a better trade-off between editing quality and preservation of the original image. Our code is available at https://github.com/FusionBrainLab/Guide-and-Rescale.

  • 5 authors
·
Sep 2, 2024 2

ImgEdit: A Unified Image Editing Dataset and Benchmark

Recent advancements in generative models have enabled high-fidelity text-to-image generation. However, open-source image-editing models still lag behind their proprietary counterparts, primarily due to limited high-quality data and insufficient benchmarks. To overcome these limitations, we introduce ImgEdit, a large-scale, high-quality image-editing dataset comprising 1.2 million carefully curated edit pairs, which contain both novel and complex single-turn edits, as well as challenging multi-turn tasks. To ensure the data quality, we employ a multi-stage pipeline that integrates a cutting-edge vision-language model, a detection model, a segmentation model, alongside task-specific in-painting procedures and strict post-processing. ImgEdit surpasses existing datasets in both task novelty and data quality. Using ImgEdit, we train ImgEdit-E1, an editing model using Vision Language Model to process the reference image and editing prompt, which outperforms existing open-source models on multiple tasks, highlighting the value of ImgEdit and model design. For comprehensive evaluation, we introduce ImgEdit-Bench, a benchmark designed to evaluate image editing performance in terms of instruction adherence, editing quality, and detail preservation. It includes a basic testsuite, a challenging single-turn suite, and a dedicated multi-turn suite. We evaluate both open-source and proprietary models, as well as ImgEdit-E1, providing deep analysis and actionable insights into the current behavior of image-editing models. The source data are publicly available on https://github.com/PKU-YuanGroup/ImgEdit.

  • 8 authors
·
May 26, 2025 3

CRISP-SAM2: SAM2 with Cross-Modal Interaction and Semantic Prompting for Multi-Organ Segmentation

Multi-organ medical segmentation is a crucial component of medical image processing, essential for doctors to make accurate diagnoses and develop effective treatment plans. Despite significant progress in this field, current multi-organ segmentation models often suffer from inaccurate details, dependence on geometric prompts and loss of spatial information. Addressing these challenges, we introduce a novel model named CRISP-SAM2 with CRoss-modal Interaction and Semantic Prompting based on SAM2. This model represents a promising approach to multi-organ medical segmentation guided by textual descriptions of organs. Our method begins by converting visual and textual inputs into cross-modal contextualized semantics using a progressive cross-attention interaction mechanism. These semantics are then injected into the image encoder to enhance the detailed understanding of visual information. To eliminate reliance on geometric prompts, we use a semantic prompting strategy, replacing the original prompt encoder to sharpen the perception of challenging targets. In addition, a similarity-sorting self-updating strategy for memory and a mask-refining process is applied to further adapt to medical imaging and enhance localized details. Comparative experiments conducted on seven public datasets indicate that CRISP-SAM2 outperforms existing models. Extensive analysis also demonstrates the effectiveness of our method, thereby confirming its superior performance, especially in addressing the limitations mentioned earlier. Our code is available at: https://github.com/YU-deep/CRISP\_SAM2.git.

  • 8 authors
·
Jun 29, 2025 1

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

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

  • 5 authors
·
Nov 14, 2025

EditVal: Benchmarking Diffusion Based Text-Guided Image Editing Methods

A plethora of text-guided image editing methods have recently been developed by leveraging the impressive capabilities of large-scale diffusion-based generative models such as Imagen and Stable Diffusion. A standardized evaluation protocol, however, does not exist to compare methods across different types of fine-grained edits. To address this gap, we introduce EditVal, a standardized benchmark for quantitatively evaluating text-guided image editing methods. EditVal consists of a curated dataset of images, a set of editable attributes for each image drawn from 13 possible edit types, and an automated evaluation pipeline that uses pre-trained vision-language models to assess the fidelity of generated images for each edit type. We use EditVal to benchmark 8 cutting-edge diffusion-based editing methods including SINE, Imagic and Instruct-Pix2Pix. We complement this with a large-scale human study where we show that EditVall's automated evaluation pipeline is strongly correlated with human-preferences for the edit types we considered. From both the human study and automated evaluation, we find that: (i) Instruct-Pix2Pix, Null-Text and SINE are the top-performing methods averaged across different edit types, however {\it only} Instruct-Pix2Pix and Null-Text are able to preserve original image properties; (ii) Most of the editing methods fail at edits involving spatial operations (e.g., changing the position of an object). (iii) There is no `winner' method which ranks the best individually across a range of different edit types. We hope that our benchmark can pave the way to developing more reliable text-guided image editing tools in the future. We will publicly release EditVal, and all associated code and human-study templates to support these research directions in https://deep-ml-research.github.io/editval/.

  • 8 authors
·
Oct 3, 2023

MICDIR: Multi-scale Inverse-consistent Deformable Image Registration using UNetMSS with Self-Constructing Graph Latent

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

  • 8 authors
·
Mar 8, 2022

Step1X-Edit: A Practical Framework for General Image Editing

In recent years, image editing models have witnessed remarkable and rapid development. The recent unveiling of cutting-edge multimodal models such as GPT-4o and Gemini2 Flash has introduced highly promising image editing capabilities. These models demonstrate an impressive aptitude for fulfilling a vast majority of user-driven editing requirements, marking a significant advancement in the field of image manipulation. However, there is still a large gap between the open-source algorithm with these closed-source models. Thus, in this paper, we aim to release a state-of-the-art image editing model, called Step1X-Edit, which can provide comparable performance against the closed-source models like GPT-4o and Gemini2 Flash. More specifically, we adopt the Multimodal LLM to process the reference image and the user's editing instruction. A latent embedding has been extracted and integrated with a diffusion image decoder to obtain the target image. To train the model, we build a data generation pipeline to produce a high-quality dataset. For evaluation, we develop the GEdit-Bench, a novel benchmark rooted in real-world user instructions. Experimental results on GEdit-Bench demonstrate that Step1X-Edit outperforms existing open-source baselines by a substantial margin and approaches the performance of leading proprietary models, thereby making significant contributions to the field of image editing.

  • 24 authors
·
Apr 24, 2025 3

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

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

  • 5 authors
·
Feb 23, 2025

SAM-Med2D

The Segment Anything Model (SAM) represents a state-of-the-art research advancement in natural image segmentation, achieving impressive results with input prompts such as points and bounding boxes. However, our evaluation and recent research indicate that directly applying the pretrained SAM to medical image segmentation does not yield satisfactory performance. This limitation primarily arises from significant domain gap between natural images and medical images. To bridge this gap, we introduce SAM-Med2D, the most comprehensive studies on applying SAM to medical 2D images. Specifically, we first collect and curate approximately 4.6M images and 19.7M masks from public and private datasets, constructing a large-scale medical image segmentation dataset encompassing various modalities and objects. Then, we comprehensively fine-tune SAM on this dataset and turn it into SAM-Med2D. Unlike previous methods that only adopt bounding box or point prompts as interactive segmentation approach, we adapt SAM to medical image segmentation through more comprehensive prompts involving bounding boxes, points, and masks. We additionally fine-tune the encoder and decoder of the original SAM to obtain a well-performed SAM-Med2D, leading to the most comprehensive fine-tuning strategies to date. Finally, we conducted a comprehensive evaluation and analysis to investigate the performance of SAM-Med2D in medical image segmentation across various modalities, anatomical structures, and organs. Concurrently, we validated the generalization capability of SAM-Med2D on 9 datasets from MICCAI 2023 challenge. Overall, our approach demonstrated significantly superior performance and generalization capability compared to SAM.

  • 15 authors
·
Aug 30, 2023

KorMedMCQA-V: A Multimodal Benchmark for Evaluating Vision-Language Models on the Korean Medical Licensing Examination

We introduce KorMedMCQA-V, a Korean medical licensing-exam-style multimodal multiple-choice question answering benchmark for evaluating vision-language models (VLMs). The dataset consists of 1,534 questions with 2,043 associated images from Korean Medical Licensing Examinations (2012-2023), with about 30% containing multiple images requiring cross-image evidence integration. Images cover clinical modalities including X-ray, computed tomography (CT), electrocardiography (ECG), ultrasound, endoscopy, and other medical visuals. We benchmark over 50 VLMs across proprietary and open-source categories-spanning general-purpose, medical-specialized, and Korean-specialized families-under a unified zero-shot evaluation protocol. The best proprietary model (Gemini-3.0-Pro) achieves 96.9% accuracy, the best open-source model (Qwen3-VL-32B-Thinking) 83.7%, and the best Korean-specialized model (VARCO-VISION-2.0-14B) only 43.2%. We further find that reasoning-oriented model variants gain up to +20 percentage points over instruction-tuned counterparts, medical domain specialization yields inconsistent gains over strong general-purpose baselines, all models degrade on multi-image questions, and performance varies notably across imaging modalities. By complementing the text-only KorMedMCQA benchmark, KorMedMCQA-V forms a unified evaluation suite for Korean medical reasoning across text-only and multimodal conditions. The dataset is available via Hugging Face Datasets: https://huggingface.co/datasets/seongsubae/KorMedMCQA-V.

  • 4 authors
·
Feb 14

Vision-Language Generative Model for View-Specific Chest X-ray Generation

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

  • 8 authors
·
Feb 23, 2023

PIXELS: Progressive Image Xemplar-based Editing with Latent Surgery

Recent advancements in language-guided diffusion models for image editing are often bottle-necked by cumbersome prompt engineering to precisely articulate desired changes. An intuitive alternative calls on guidance from in-the-wild image exemplars to help users bring their imagined edits to life. Contemporary exemplar-based editing methods shy away from leveraging the rich latent space learnt by pre-existing large text-to-image (TTI) models and fall back on training with curated objective functions to achieve the task. Though somewhat effective, this demands significant computational resources and lacks compatibility with diverse base models and arbitrary exemplar count. On further investigation, we also find that these techniques restrict user control to only applying uniform global changes over the entire edited region. In this paper, we introduce a novel framework for progressive exemplar-driven editing with off-the-shelf diffusion models, dubbed PIXELS, to enable customization by providing granular control over edits, allowing adjustments at the pixel or region level. Our method operates solely during inference to facilitate imitative editing, enabling users to draw inspiration from a dynamic number of reference images, or multimodal prompts, and progressively incorporate all the desired changes without retraining or fine-tuning existing TTI models. This capability of fine-grained control opens up a range of new possibilities, including selective modification of individual objects and specifying gradual spatial changes. We demonstrate that PIXELS delivers high-quality edits efficiently, leading to a notable improvement in quantitative metrics as well as human evaluation. By making high-quality image editing more accessible, PIXELS has the potential to enable professional-grade edits to a wider audience with the ease of using any open-source image generation model.

  • 5 authors
·
Jan 16, 2025

CLIP in Medical Imaging: A Survey

Contrastive Language-Image Pre-training (CLIP), a simple yet effective pre-training paradigm, successfully introduces text supervision to vision models. It has shown promising results across various tasks due to its generalizability and interpretability. The use of CLIP has recently gained increasing interest in the medical imaging domain, serving as a pre-training paradigm for image-text alignment, or a critical component in diverse clinical tasks. With the aim of facilitating a deeper understanding of this promising direction, this survey offers an in-depth exploration of the CLIP within the domain of medical imaging, regarding both refined CLIP pre-training and CLIP-driven applications. In this paper, we (1) first start with a brief introduction to the fundamentals of CLIP methodology; (2) then investigate the adaptation of CLIP pre-training in the medical imaging domain, focusing on how to optimize CLIP given characteristics of medical images and reports; (3) further explore practical utilization of CLIP pre-trained models in various tasks, including classification, dense prediction, and cross-modal tasks; and (4) finally discuss existing limitations of CLIP in the context of medical imaging, and propose forward-looking directions to address the demands of medical imaging domain. Studies featuring technical and practical value are both investigated. We expect this survey will provide researchers with a holistic understanding of the CLIP paradigm and its potential implications. The project page of this survey can also be found on https://github.com/zhaozh10/Awesome-CLIP-in-Medical-Imaging.

  • 11 authors
·
Dec 12, 2023

MedSyn: Text-guided Anatomy-aware Synthesis of High-Fidelity 3D CT Images

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

  • 5 authors
·
Oct 5, 2023

Fairness and Robustness of CLIP-Based Models for Chest X-rays

Motivated by the strong performance of CLIP-based models in natural image-text domains, recent efforts have adapted these architectures to medical tasks, particularly in radiology, where large paired datasets of images and reports, such as chest X-rays, are available. While these models have shown encouraging results in terms of accuracy and discriminative performance, their fairness and robustness in the different clinical tasks remain largely underexplored. In this study, we extensively evaluate six widely used CLIP-based models on chest X-ray classification using three publicly available datasets: MIMIC-CXR, NIH-CXR14, and NEATX. We assess the models fairness across six conditions and patient subgroups based on age, sex, and race. Additionally, we assess the robustness to shortcut learning by evaluating performance on pneumothorax cases with and without chest drains. Our results indicate performance gaps between patients of different ages, but more equitable results for the other attributes. Moreover, all models exhibit lower performance on images without chest drains, suggesting reliance on spurious correlations. We further complement the performance analysis with a study of the embeddings generated by the models. While the sensitive attributes could be classified from the embeddings, we do not see such patterns using PCA, showing the limitations of these visualisation techniques when assessing models. Our code is available at https://github.com/TheoSourget/clip_cxr_fairness

  • 6 authors
·
Jul 28, 2025

SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

  • 14 authors
·
Oct 23, 2023

ConceptCLIP: Towards Trustworthy Medical AI via Concept-Enhanced Contrastive Langauge-Image Pre-training

Trustworthiness is essential for the precise and interpretable application of artificial intelligence (AI) in medical imaging. Traditionally, precision and interpretability have been addressed as separate tasks, namely medical image analysis and explainable AI, each developing its own models independently. In this study, for the first time, we investigate the development of a unified medical vision-language pre-training model that can achieve both accurate analysis and interpretable understanding of medical images across various modalities. To build the model, we construct MedConcept-23M, a large-scale dataset comprising 23 million medical image-text pairs extracted from 6.2 million scientific articles, enriched with concepts from the Unified Medical Language System (UMLS). Based on MedConcept-23M, we introduce ConceptCLIP, a medical AI model utilizing concept-enhanced contrastive language-image pre-training. The pre-training of ConceptCLIP involves two primary components: image-text alignment learning (IT-Align) and patch-concept alignment learning (PC-Align). This dual alignment strategy enhances the model's capability to associate specific image regions with relevant concepts, thereby improving both the precision of analysis and the interpretability of the AI system. We conducted extensive experiments on 5 diverse types of medical image analysis tasks, spanning 51 subtasks across 10 image modalities, with the broadest range of downstream tasks. The results demonstrate the effectiveness of the proposed vision-language pre-training model. Further explainability analysis across 6 modalities reveals that ConceptCLIP achieves superior performance, underscoring its robust ability to advance explainable AI in medical imaging. These findings highlight ConceptCLIP's capability in promoting trustworthy AI in the field of medicine.

  • 7 authors
·
Jan 26, 2025

EndoPBR: Material and Lighting Estimation for Photorealistic Surgical Simulations via Physically-based Rendering

The lack of labeled datasets in 3D vision for surgical scenes inhibits the development of robust 3D reconstruction algorithms in the medical domain. Despite the popularity of Neural Radiance Fields and 3D Gaussian Splatting in the general computer vision community, these systems have yet to find consistent success in surgical scenes due to challenges such as non-stationary lighting and non-Lambertian surfaces. As a result, the need for labeled surgical datasets continues to grow. In this work, we introduce a differentiable rendering framework for material and lighting estimation from endoscopic images and known geometry. Compared to previous approaches that model lighting and material jointly as radiance, we explicitly disentangle these scene properties for robust and photorealistic novel view synthesis. To disambiguate the training process, we formulate domain-specific properties inherent in surgical scenes. Specifically, we model the scene lighting as a simple spotlight and material properties as a bidirectional reflectance distribution function, parameterized by a neural network. By grounding color predictions in the rendering equation, we can generate photorealistic images at arbitrary camera poses. We evaluate our method with various sequences from the Colonoscopy 3D Video Dataset and show that our method produces competitive novel view synthesis results compared with other approaches. Furthermore, we demonstrate that synthetic data can be used to develop 3D vision algorithms by finetuning a depth estimation model with our rendered outputs. Overall, we see that the depth estimation performance is on par with fine-tuning with the original real images.

  • 2 authors
·
Feb 27, 2025

seg2med: a segmentation-based medical image generation framework using denoising diffusion probabilistic models

In this study, we present seg2med, an advanced medical image synthesis framework that uses Denoising Diffusion Probabilistic Models (DDPM) to generate high-quality synthetic medical images conditioned on anatomical masks from TotalSegmentator. The framework synthesizes CT and MR images from segmentation masks derived from real patient data and XCAT digital phantoms, achieving a Structural Similarity Index Measure (SSIM) of 0.94 +/- 0.02 for CT and 0.89 +/- 0.04 for MR images compared to ground-truth images of real patients. It also achieves a Feature Similarity Index Measure (FSIM) of 0.78 +/- 0.04 for CT images from XCAT. The generative quality is further supported by a Fr\'echet Inception Distance (FID) of 3.62 for CT image generation. Additionally, seg2med can generate paired CT and MR images with consistent anatomical structures and convert images between CT and MR modalities, achieving SSIM values of 0.91 +/- 0.03 for MR-to-CT and 0.77 +/- 0.04 for CT-to-MR conversion. Despite the limitations of incomplete anatomical details in segmentation masks, the framework shows strong performance in cross-modality synthesis and multimodal imaging. seg2med also demonstrates high anatomical fidelity in CT synthesis, achieving a mean Dice coefficient greater than 0.90 for 11 abdominal organs and greater than 0.80 for 34 organs out of 59 in 58 test cases. The highest Dice of 0.96 +/- 0.01 was recorded for the right scapula. Leveraging the TotalSegmentator toolkit, seg2med enables segmentation mask generation across diverse datasets, supporting applications in clinical imaging, data augmentation, multimodal synthesis, and diagnostic algorithm development.

  • 8 authors
·
Apr 12, 2025

Dynamic Prompt Learning: Addressing Cross-Attention Leakage for Text-Based Image Editing

Large-scale text-to-image generative models have been a ground-breaking development in generative AI, with diffusion models showing their astounding ability to synthesize convincing images following an input text prompt. The goal of image editing research is to give users control over the generated images by modifying the text prompt. Current image editing techniques are susceptible to unintended modifications of regions outside the targeted area, such as on the background or on distractor objects which have some semantic or visual relationship with the targeted object. According to our experimental findings, inaccurate cross-attention maps are at the root of this problem. Based on this observation, we propose Dynamic Prompt Learning (DPL) to force cross-attention maps to focus on correct noun words in the text prompt. By updating the dynamic tokens for nouns in the textual input with the proposed leakage repairment losses, we achieve fine-grained image editing over particular objects while preventing undesired changes to other image regions. Our method DPL, based on the publicly available Stable Diffusion, is extensively evaluated on a wide range of images, and consistently obtains superior results both quantitatively (CLIP score, Structure-Dist) and qualitatively (on user-evaluation). We show improved prompt editing results for Word-Swap, Prompt Refinement, and Attention Re-weighting, especially for complex multi-object scenes.

  • 5 authors
·
Sep 27, 2023

NoHumansRequired: Autonomous High-Quality Image Editing Triplet Mining

Recent advances in generative modeling enable image editing assistants that follow natural language instructions without additional user input. Their supervised training requires millions of triplets: original image, instruction, edited image. Yet mining pixel-accurate examples is hard. Each edit must affect only prompt-specified regions, preserve stylistic coherence, respect physical plausibility, and retain visual appeal. The lack of robust automated edit-quality metrics hinders reliable automation at scale. We present an automated, modular pipeline that mines high-fidelity triplets across domains, resolutions, instruction complexities, and styles. Built on public generative models and running without human intervention, our system uses a task-tuned Gemini validator to score instruction adherence and aesthetics directly, removing any need for segmentation or grounding models. Inversion and compositional bootstrapping enlarge the mined set by approximately 2.2x, enabling large-scale high-fidelity training data. By automating the most repetitive annotation steps, the approach allows a new scale of training without human labeling effort. To democratize research in this resource-intensive area, we release NHR-Edit: an open dataset of 358k high-quality triplets. In the largest cross-dataset evaluation, it surpasses all public alternatives. We also release Bagel-NHR-Edit, an open-source fine-tuned Bagel model, which achieves state-of-the-art metrics in our experiments.

  • 7 authors
·
Jul 18, 2025 1

medigan: a Python library of pretrained generative models for medical image synthesis

Synthetic data generated by generative models can enhance the performance and capabilities of data-hungry deep learning models in medical imaging. However, there is (1) limited availability of (synthetic) datasets and (2) generative models are complex to train, which hinders their adoption in research and clinical applications. To reduce this entry barrier, we propose medigan, a one-stop shop for pretrained generative models implemented as an open-source framework-agnostic Python library. medigan allows researchers and developers to create, increase, and domain-adapt their training data in just a few lines of code. Guided by design decisions based on gathered end-user requirements, we implement medigan based on modular components for generative model (i) execution, (ii) visualisation, (iii) search & ranking, and (iv) contribution. The library's scalability and design is demonstrated by its growing number of integrated and readily-usable pretrained generative models consisting of 21 models utilising 9 different Generative Adversarial Network architectures trained on 11 datasets from 4 domains, namely, mammography, endoscopy, x-ray, and MRI. Furthermore, 3 applications of medigan are analysed in this work, which include (a) enabling community-wide sharing of restricted data, (b) investigating generative model evaluation metrics, and (c) improving clinical downstream tasks. In (b), extending on common medical image synthesis assessment and reporting standards, we show Fréchet Inception Distance variability based on image normalisation and radiology-specific feature extraction.

  • 12 authors
·
Sep 28, 2022

Augmentation-Driven Metric for Balancing Preservation and Modification in Text-Guided Image Editing

The development of vision-language and generative models has significantly advanced text-guided image editing, which seeks preservation of core elements in the source image while implementing modifications based on the target text. However, in the absence of evaluation metrics specifically tailored for text-guided image editing, existing metrics are limited in balancing the consideration of preservation and modification. Especially, our analysis reveals that CLIPScore, the most commonly used metric, tends to favor modification and ignore core attributes to be preserved, resulting in inaccurate evaluations. To address this problem, we propose AugCLIP, which balances preservation and modification by estimating the representation of an ideal edited image that aligns with the target text with minimum alteration on the source image. We augment detailed textual descriptions on the source image and the target text using a multi-modal large language model, to model a hyperplane that separates CLIP space into source or target. The representation of the ideal edited image is an orthogonal projection of the source image into the hyperplane, which encapsulates the relative importance of each attribute considering the interdependent relationships. Our extensive experiments on five benchmark datasets, encompassing a diverse range of editing scenarios, demonstrate that AugCLIP aligns remarkably well with human evaluation standards compared to existing metrics. The code for evaluation will be open-sourced to contribute to the community.

  • 8 authors
·
Oct 15, 2024

Imagic: Text-Based Real Image Editing with Diffusion Models

Text-conditioned image editing has recently attracted considerable interest. However, most methods are currently either limited to specific editing types (e.g., object overlay, style transfer), or apply to synthetically generated images, or require multiple input images of a common object. In this paper we demonstrate, for the very first time, the ability to apply complex (e.g., non-rigid) text-guided semantic edits to a single real image. For example, we can change the posture and composition of one or multiple objects inside an image, while preserving its original characteristics. Our method can make a standing dog sit down or jump, cause a bird to spread its wings, etc. -- each within its single high-resolution natural image provided by the user. Contrary to previous work, our proposed method requires only a single input image and a target text (the desired edit). It operates on real images, and does not require any additional inputs (such as image masks or additional views of the object). Our method, which we call "Imagic", leverages a pre-trained text-to-image diffusion model for this task. It produces a text embedding that aligns with both the input image and the target text, while fine-tuning the diffusion model to capture the image-specific appearance. We demonstrate the quality and versatility of our method on numerous inputs from various domains, showcasing a plethora of high quality complex semantic image edits, all within a single unified framework.

  • 8 authors
·
Oct 17, 2022 1

Generative Enhancement for 3D Medical Images

The limited availability of 3D medical image datasets, due to privacy concerns and high collection or annotation costs, poses significant challenges in the field of medical imaging. While a promising alternative is the use of synthesized medical data, there are few solutions for realistic 3D medical image synthesis due to difficulties in backbone design and fewer 3D training samples compared to 2D counterparts. In this paper, we propose GEM-3D, a novel generative approach to the synthesis of 3D medical images and the enhancement of existing datasets using conditional diffusion models. Our method begins with a 2D slice, noted as the informed slice to serve the patient prior, and propagates the generation process using a 3D segmentation mask. By decomposing the 3D medical images into masks and patient prior information, GEM-3D offers a flexible yet effective solution for generating versatile 3D images from existing datasets. GEM-3D can enable dataset enhancement by combining informed slice selection and generation at random positions, along with editable mask volumes to introduce large variations in diffusion sampling. Moreover, as the informed slice contains patient-wise information, GEM-3D can also facilitate counterfactual image synthesis and dataset-level de-enhancement with desired control. Experiments on brain MRI and abdomen CT images demonstrate that GEM-3D is capable of synthesizing high-quality 3D medical images with volumetric consistency, offering a straightforward solution for dataset enhancement during inference. The code is available at https://github.com/HKU-MedAI/GEM-3D.

  • 6 authors
·
Mar 19, 2024

Fréchet Radiomic Distance (FRD): A Versatile Metric for Comparing Medical Imaging Datasets

Determining whether two sets of images belong to the same or different distributions or domains is a crucial task in modern medical image analysis and deep learning; for example, to evaluate the output quality of image generative models. Currently, metrics used for this task either rely on the (potentially biased) choice of some downstream task, such as segmentation, or adopt task-independent perceptual metrics (e.g., Fréchet Inception Distance/FID) from natural imaging, which we show insufficiently capture anatomical features. To this end, we introduce a new perceptual metric tailored for medical images, FRD (Fréchet Radiomic Distance), which utilizes standardized, clinically meaningful, and interpretable image features. We show that FRD is superior to other image distribution metrics for a range of medical imaging applications, including out-of-domain (OOD) detection, the evaluation of image-to-image translation (by correlating more with downstream task performance as well as anatomical consistency and realism), and the evaluation of unconditional image generation. Moreover, FRD offers additional benefits such as stability and computational efficiency at low sample sizes, sensitivity to image corruptions and adversarial attacks, feature interpretability, and correlation with radiologist-perceived image quality. Additionally, we address key gaps in the literature by presenting an extensive framework for the multifaceted evaluation of image similarity metrics in medical imaging -- including the first large-scale comparative study of generative models for medical image translation -- and release an accessible codebase to facilitate future research. Our results are supported by thorough experiments spanning a variety of datasets, modalities, and downstream tasks, highlighting the broad potential of FRD for medical image analysis.

  • 19 authors
·
Dec 2, 2024

MCP-MedSAM: A Powerful Lightweight Medical Segment Anything Model Trained with a Single GPU in Just One Day

Medical image segmentation involves partitioning medical images into meaningful regions, with a focus on identifying anatomical structures and lesions. It has broad applications in healthcare, and deep learning methods have enabled significant advancements in automating this process. Recently, the introduction of the Segmentation Anything Model (SAM), the first foundation model for segmentation task, has prompted researchers to adapt it for the medical domain to improve performance across various tasks. However, SAM's large model size and high GPU requirements hinder its scalability and development in the medical domain. In this work, we propose MCP-MedSAM, a powerful and lightweight medical SAM model designed to be trainable on a single A100 GPU with 40GB of memory within one day while delivering superior segmentation performance. Recognizing the significant internal differences between modalities and the need for direct segmentation target information within bounding boxes, we introduce two kinds of prompts: the modality prompt and the content prompt. After passing through the prompt encoder, their embedding representations can further improve the segmentation performance by incorporating more relevant information without adding significant training overhead. Additionally, we adopt an effective modality-based data sampling strategy to address data imbalance between modalities, ensuring more balanced performance across all modalities. Our method was trained and evaluated using a large-scale challenge dataset, compared to top-ranking methods on the challenge leaderboard, MCP-MedSAM achieved superior performance while requiring only one day of training on a single GPU. The code is publicly available at blue{https://github.com/dong845/MCP-MedSAM}.}

  • 3 authors
·
Dec 8, 2024

Pivotal Tuning for Latent-based Editing of Real Images

Recently, a surge of advanced facial editing techniques have been proposed that leverage the generative power of a pre-trained StyleGAN. To successfully edit an image this way, one must first project (or invert) the image into the pre-trained generator's domain. As it turns out, however, StyleGAN's latent space induces an inherent tradeoff between distortion and editability, i.e. between maintaining the original appearance and convincingly altering some of its attributes. Practically, this means it is still challenging to apply ID-preserving facial latent-space editing to faces which are out of the generator's domain. In this paper, we present an approach to bridge this gap. Our technique slightly alters the generator, so that an out-of-domain image is faithfully mapped into an in-domain latent code. The key idea is pivotal tuning - a brief training process that preserves the editing quality of an in-domain latent region, while changing its portrayed identity and appearance. In Pivotal Tuning Inversion (PTI), an initial inverted latent code serves as a pivot, around which the generator is fined-tuned. At the same time, a regularization term keeps nearby identities intact, to locally contain the effect. This surgical training process ends up altering appearance features that represent mostly identity, without affecting editing capabilities. We validate our technique through inversion and editing metrics, and show preferable scores to state-of-the-art methods. We further qualitatively demonstrate our technique by applying advanced edits (such as pose, age, or expression) to numerous images of well-known and recognizable identities. Finally, we demonstrate resilience to harder cases, including heavy make-up, elaborate hairstyles and/or headwear, which otherwise could not have been successfully inverted and edited by state-of-the-art methods.

  • 4 authors
·
Jun 10, 2021

MedMNIST-C: Comprehensive benchmark and improved classifier robustness by simulating realistic image corruptions

The integration of neural-network-based systems into clinical practice is limited by challenges related to domain generalization and robustness. The computer vision community established benchmarks such as ImageNet-C as a fundamental prerequisite to measure progress towards those challenges. Similar datasets are largely absent in the medical imaging community which lacks a comprehensive benchmark that spans across imaging modalities and applications. To address this gap, we create and open-source MedMNIST-C, a benchmark dataset based on the MedMNIST+ collection covering 12 datasets and 9 imaging modalities. We simulate task and modality-specific image corruptions of varying severity to comprehensively evaluate the robustness of established algorithms against real-world artifacts and distribution shifts. We further provide quantitative evidence that our simple-to-use artificial corruptions allow for highly performant, lightweight data augmentation to enhance model robustness. Unlike traditional, generic augmentation strategies, our approach leverages domain knowledge, exhibiting significantly higher robustness when compared to widely adopted methods. By introducing MedMNIST-C and open-sourcing the corresponding library allowing for targeted data augmentations, we contribute to the development of increasingly robust methods tailored to the challenges of medical imaging. The code is available at https://github.com/francescodisalvo05/medmnistc-api .

  • 3 authors
·
Jun 25, 2024

Preference Fine-Tuning for Factuality in Chest X-Ray Interpretation Models Without Human Feedback

Radiologists play a crucial role by translating medical images into medical reports. However, the field faces staffing shortages and increasing workloads. While automated approaches using vision-language models (VLMs) show promise as assistants, they require exceptionally high accuracy. Most current VLMs in radiology rely solely on supervised fine-tuning (SFT). Meanwhile, in the general domain, additional preference fine-tuning has become standard practice. The challenge in radiology lies in the prohibitive cost of obtaining radiologist feedback. We propose a scalable automated preference alignment technique for VLMs in radiology, focusing on chest X-ray (CXR) report generation. Our method leverages publicly available datasets with an LLM-as-a-Judge mechanism, eliminating the need for additional expert radiologist feedback. We evaluate and benchmark five direct alignment algorithms (DAAs). Our results show up to a 57.4% improvement in average GREEN scores, a LLM-based metric for evaluating CXR reports, and a 9.2% increase in an average across six metrics (domain specific and general), compared to the SFT baseline. We study reward overoptimization via length exploitation, with reports lengthening by up to 3.2x. To assess a potential alignment tax, we benchmark on six additional diverse tasks, finding no significant degradations. A reader study involving four board-certified radiologists indicates win rates of up to 0.62 over the SFT baseline, while significantly penalizing verbosity. Our analysis provides actionable insights for the development of VLMs in high-stakes fields like radiology.

  • 11 authors
·
Oct 9, 2024

DVPT: Dynamic Visual Prompt Tuning of Large Pre-trained Models for Medical Image Analysis

Limited labeled data makes it hard to train models from scratch in medical domain, and an important paradigm is pre-training and then fine-tuning. Large pre-trained models contain rich representations, which can be adapted to downstream medical tasks. However, existing methods either tune all the parameters or the task-specific layers of the pre-trained models, ignoring the input variations of medical images, and thus they are not efficient or effective. In this work, we aim to study parameter-efficient fine-tuning (PEFT) for medical image analysis, and propose a dynamic visual prompt tuning method, named DVPT. It can extract knowledge beneficial to downstream tasks from large models with a few trainable parameters. Firstly, the frozen features are transformed by an lightweight bottleneck layer to learn the domain-specific distribution of downstream medical tasks, and then a few learnable visual prompts are used as dynamic queries and then conduct cross-attention with the transformed features, attempting to acquire sample-specific knowledge that are suitable for each sample. Finally, the features are projected to original feature dimension and aggregated with the frozen features. This DVPT module can be shared between different Transformer layers, further reducing the trainable parameters. To validate DVPT, we conduct extensive experiments with different pre-trained models on medical classification and segmentation tasks. We find such PEFT method can not only efficiently adapt the pre-trained models to the medical domain, but also brings data efficiency with partial labeled data. For example, with 0.5\% extra trainable parameters, our method not only outperforms state-of-the-art PEFT methods, even surpasses the full fine-tuning by more than 2.20\% Kappa score on medical classification task. It can saves up to 60\% labeled data and 99\% storage cost of ViT-B/16.

  • 5 authors
·
Jul 19, 2023

HiFi Tuner: High-Fidelity Subject-Driven Fine-Tuning for Diffusion Models

This paper explores advancements in high-fidelity personalized image generation through the utilization of pre-trained text-to-image diffusion models. While previous approaches have made significant strides in generating versatile scenes based on text descriptions and a few input images, challenges persist in maintaining the subject fidelity within the generated images. In this work, we introduce an innovative algorithm named HiFi Tuner to enhance the appearance preservation of objects during personalized image generation. Our proposed method employs a parameter-efficient fine-tuning framework, comprising a denoising process and a pivotal inversion process. Key enhancements include the utilization of mask guidance, a novel parameter regularization technique, and the incorporation of step-wise subject representations to elevate the sample fidelity. Additionally, we propose a reference-guided generation approach that leverages the pivotal inversion of a reference image to mitigate unwanted subject variations and artifacts. We further extend our method to a novel image editing task: substituting the subject in an image through textual manipulations. Experimental evaluations conducted on the DreamBooth dataset using the Stable Diffusion model showcase promising results. Fine-tuning solely on textual embeddings improves CLIP-T score by 3.6 points and improves DINO score by 9.6 points over Textual Inversion. When fine-tuning all parameters, HiFi Tuner improves CLIP-T score by 1.2 points and improves DINO score by 1.2 points over DreamBooth, establishing a new state of the art.

  • 7 authors
·
Nov 29, 2023 2

Rapid patient-specific neural networks for intraoperative X-ray to volume registration

The integration of artificial intelligence in image-guided interventions holds transformative potential, promising to extract 3D geometric and quantitative information from conventional 2D imaging modalities during complex procedures. Achieving this requires the rapid and precise alignment of 2D intraoperative images (e.g., X-ray) with 3D preoperative volumes (e.g., CT, MRI). However, current 2D/3D registration methods fail across the broad spectrum of procedures dependent on X-ray guidance: traditional optimization techniques require custom parameter tuning for each subject, whereas neural networks trained on small datasets do not generalize to new patients or require labor-intensive manual annotations, increasing clinical burden and precluding application to new anatomical targets. To address these challenges, we present xvr, a fully automated framework for training patient-specific neural networks for 2D/3D registration. xvr uses physics-based simulation to generate abundant high-quality training data from a patient's own preoperative volumetric imaging, thereby overcoming the inherently limited ability of supervised models to generalize to new patients and procedures. Furthermore, xvr requires only 5 minutes of training per patient, making it suitable for emergency interventions as well as planned procedures. We perform the largest evaluation of a 2D/3D registration algorithm on real X-ray data to date and find that xvr robustly generalizes across a diverse dataset comprising multiple anatomical structures, imaging modalities, and hospitals. Across surgical tasks, xvr achieves submillimeter-accurate registration at intraoperative speeds, improving upon existing methods by an order of magnitude. xvr is released as open-source software freely available at https://github.com/eigenvivek/xvr.

  • 8 authors
·
Mar 20, 2025

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data-features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

  • 22 authors
·
Nov 19, 2024

MedCLIP-SAM: Bridging Text and Image Towards Universal Medical Image Segmentation

Medical image segmentation of anatomical structures and pathology is crucial in modern clinical diagnosis, disease study, and treatment planning. To date, great progress has been made in deep learning-based segmentation techniques, but most methods still lack data efficiency, generalizability, and interactability. Consequently, the development of new, precise segmentation methods that demand fewer labeled datasets is of utmost importance in medical image analysis. Recently, the emergence of foundation models, such as CLIP and Segment-Anything-Model (SAM), with comprehensive cross-domain representation opened the door for interactive and universal image segmentation. However, exploration of these models for data-efficient medical image segmentation is still limited, but is highly necessary. In this paper, we propose a novel framework, called MedCLIP-SAM that combines CLIP and SAM models to generate segmentation of clinical scans using text prompts in both zero-shot and weakly supervised settings. To achieve this, we employed a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss to fine-tune the BiomedCLIP model and the recent gScoreCAM to generate prompts to obtain segmentation masks from SAM in a zero-shot setting. Additionally, we explored the use of zero-shot segmentation labels in a weakly supervised paradigm to improve the segmentation quality further. By extensively testing three diverse segmentation tasks and medical image modalities (breast tumor ultrasound, brain tumor MRI, and lung X-ray), our proposed framework has demonstrated excellent accuracy. Code is available at https://github.com/HealthX-Lab/MedCLIP-SAM.

  • 4 authors
·
Mar 29, 2024

Barlow-Swin: Toward a novel siamese-based segmentation architecture using Swin-Transformers

Medical image segmentation is a critical task in clinical workflows, particularly for the detection and delineation of pathological regions. While convolutional architectures like U-Net have become standard for such tasks, their limited receptive field restricts global context modeling. Recent efforts integrating transformers have addressed this, but often result in deep, computationally expensive models unsuitable for real-time use. In this work, we present a novel end-to-end lightweight architecture designed specifically for real-time binary medical image segmentation. Our model combines a Swin Transformer-like encoder with a U-Net-like decoder, connected via skip pathways to preserve spatial detail while capturing contextual information. Unlike existing designs such as Swin Transformer or U-Net, our architecture is significantly shallower and competitively efficient. To improve the encoder's ability to learn meaningful features without relying on large amounts of labeled data, we first train it using Barlow Twins, a self-supervised learning method that helps the model focus on important patterns by reducing unnecessary repetition in the learned features. After this pretraining, we fine-tune the entire model for our specific task. Experiments on benchmark binary segmentation tasks demonstrate that our model achieves competitive accuracy with substantially reduced parameter count and faster inference, positioning it as a practical alternative for deployment in real-time and resource-limited clinical environments. The code for our method is available at Github repository: https://github.com/mkianih/Barlow-Swin.

  • 5 authors
·
Sep 8, 2025

LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

  • 12 authors
·
Jun 20, 2023

Bora: Biomedical Generalist Video Generation Model

Generative models hold promise for revolutionizing medical education, robot-assisted surgery, and data augmentation for medical AI development. Diffusion models can now generate realistic images from text prompts, while recent advancements have demonstrated their ability to create diverse, high-quality videos. However, these models often struggle with generating accurate representations of medical procedures and detailed anatomical structures. This paper introduces Bora, the first spatio-temporal diffusion probabilistic model designed for text-guided biomedical video generation. Bora leverages Transformer architecture and is pre-trained on general-purpose video generation tasks. It is fine-tuned through model alignment and instruction tuning using a newly established medical video corpus, which includes paired text-video data from various biomedical fields. To the best of our knowledge, this is the first attempt to establish such a comprehensive annotated biomedical video dataset. Bora is capable of generating high-quality video data across four distinct biomedical domains, adhering to medical expert standards and demonstrating consistency and diversity. This generalist video generative model holds significant potential for enhancing medical consultation and decision-making, particularly in resource-limited settings. Additionally, Bora could pave the way for immersive medical training and procedure planning. Extensive experiments on distinct medical modalities such as endoscopy, ultrasound, MRI, and cell tracking validate the effectiveness of our model in understanding biomedical instructions and its superior performance across subjects compared to state-of-the-art generation models.

  • 8 authors
·
Jul 11, 2024

MedCLIP-SAMv2: Towards Universal Text-Driven Medical Image Segmentation

Segmentation of anatomical structures and pathological regions in medical images is essential for modern clinical diagnosis, disease research, and treatment planning. While significant advancements have been made in deep learning-based segmentation techniques, many of these methods still suffer from limitations in data efficiency, generalizability, and interactivity. As a result, developing precise segmentation methods that require fewer labeled datasets remains a critical challenge in medical image analysis. Recently, the introduction of foundation models like CLIP and Segment-Anything-Model (SAM), with robust cross-domain representations, has paved the way for interactive and universal image segmentation. However, further exploration of these models for data-efficient segmentation in medical imaging is still needed and highly relevant. In this paper, we introduce MedCLIP-SAMv2, a novel framework that integrates the CLIP and SAM models to perform segmentation on clinical scans using text prompts, in both zero-shot and weakly supervised settings. Our approach includes fine-tuning the BiomedCLIP model with a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss, and leveraging the Multi-modal Information Bottleneck (M2IB) to create visual prompts for generating segmentation masks from SAM in the zero-shot setting. We also investigate using zero-shot segmentation labels within a weakly supervised paradigm to enhance segmentation quality further. Extensive testing across four diverse segmentation tasks and medical imaging modalities (breast tumor ultrasound, brain tumor MRI, lung X-ray, and lung CT) demonstrates the high accuracy of our proposed framework. Our code is available at https://github.com/HealthX-Lab/MedCLIP-SAMv2.

  • 4 authors
·
Sep 28, 2024

GPT-IMAGE-EDIT-1.5M: A Million-Scale, GPT-Generated Image Dataset

Recent advancements in large multimodal models like GPT-4o have set a new standard for high-fidelity, instruction-guided image editing. However, the proprietary nature of these models and their training data creates a significant barrier for open-source research. To bridge this gap, we introduce GPT-IMAGE-EDIT-1.5M, a publicly available, large-scale image-editing corpus containing more than 1.5 million high-quality triplets (instruction, source image, edited image). We systematically construct this dataset by leveraging the versatile capabilities of GPT-4o to unify and refine three popular image-editing datasets: OmniEdit, HQ-Edit, and UltraEdit. Specifically, our methodology involves 1) regenerating output images to enhance visual quality and instruction alignment, and 2) selectively rewriting prompts to improve semantic clarity. To validate the efficacy of our dataset, we fine-tune advanced open-source models on GPT-IMAGE-EDIT-1.5M. The empirical results are exciting, e.g., the fine-tuned FluxKontext achieves highly competitive performance across a comprehensive suite of benchmarks, including 7.24 on GEdit-EN, 3.80 on ImgEdit-Full, and 8.78 on Complex-Edit, showing stronger instruction following and higher perceptual quality while maintaining identity. These scores markedly exceed all previously published open-source methods and substantially narrow the gap to leading proprietary models. We hope the full release of GPT-IMAGE-EDIT-1.5M can help to catalyze further open research in instruction-guided image editing.

  • 7 authors
·
Jul 28, 2025 2

LORE: Latent Optimization for Precise Semantic Control in Rectified Flow-based Image Editing

Text-driven image editing enables users to flexibly modify visual content through natural language instructions, and is widely applied to tasks such as semantic object replacement, insertion, and removal. While recent inversion-based editing methods using rectified flow models have achieved promising results in image quality, we identify a structural limitation in their editing behavior: the semantic bias toward the source concept encoded in the inverted noise tends to suppress attention to the target concept. This issue becomes particularly critical when the source and target semantics are dissimilar, where the attention mechanism inherently leads to editing failure or unintended modifications in non-target regions. In this paper, we systematically analyze and validate this structural flaw, and introduce LORE, a training-free and efficient image editing method. LORE directly optimizes the inverted noise, addressing the core limitations in generalization and controllability of existing approaches, enabling stable, controllable, and general-purpose concept replacement, without requiring architectural modification or model fine-tuning. We conduct comprehensive evaluations on three challenging benchmarks: PIEBench, SmartEdit, and GapEdit. Experimental results show that LORE significantly outperforms strong baselines in terms of semantic alignment, image quality, and background fidelity, demonstrating the effectiveness and scalability of latent-space optimization for general-purpose image editing.

  • 2 authors
·
Aug 5, 2025

MedSegFactory: Text-Guided Generation of Medical Image-Mask Pairs

This paper presents MedSegFactory, a versatile medical synthesis framework that generates high-quality paired medical images and segmentation masks across modalities and tasks. It aims to serve as an unlimited data repository, supplying image-mask pairs to enhance existing segmentation tools. The core of MedSegFactory is a dual-stream diffusion model, where one stream synthesizes medical images and the other generates corresponding segmentation masks. To ensure precise alignment between image-mask pairs, we introduce Joint Cross-Attention (JCA), enabling a collaborative denoising paradigm by dynamic cross-conditioning between streams. This bidirectional interaction allows both representations to guide each other's generation, enhancing consistency between generated pairs. MedSegFactory unlocks on-demand generation of paired medical images and segmentation masks through user-defined prompts that specify the target labels, imaging modalities, anatomical regions, and pathological conditions, facilitating scalable and high-quality data generation. This new paradigm of medical image synthesis enables seamless integration into diverse medical imaging workflows, enhancing both efficiency and accuracy. Extensive experiments show that MedSegFactory generates data of superior quality and usability, achieving competitive or state-of-the-art performance in 2D and 3D segmentation tasks while addressing data scarcity and regulatory constraints.

  • 8 authors
·
Apr 9, 2025

Large-Scale Domain-Specific Pretraining for Biomedical Vision-Language Processing

Contrastive pretraining on parallel image-text data has attained great success in vision-language processing (VLP), as exemplified by CLIP and related methods. However, prior explorations tend to focus on general domains in the web. Biomedical images and text are rather different, but publicly available datasets are small and skew toward chest X-ray, thus severely limiting progress. In this paper, we conducted by far the largest study on biomedical VLP, using 15 million figure-caption pairs extracted from biomedical research articles in PubMed Central. Our dataset (PMC-15M) is two orders of magnitude larger than existing biomedical image-text datasets such as MIMIC-CXR, and spans a diverse range of biomedical images. The standard CLIP method is suboptimal for the biomedical domain. We propose BiomedCLIP with domain-specific adaptations tailored to biomedical VLP. We conducted extensive experiments and ablation studies on standard biomedical imaging tasks from retrieval to classification to visual question-answering (VQA). BiomedCLIP established new state of the art in a wide range of standard datasets, substantially outperformed prior VLP approaches. Surprisingly, BiomedCLIP even outperformed radiology-specific state-of-the-art models such as BioViL on radiology-specific tasks such as RSNA pneumonia detection, thus highlighting the utility in large-scale pretraining across all biomedical image types. We will release our models at https://aka.ms/biomedclip to facilitate future research in biomedical VLP.

  • 13 authors
·
Mar 1, 2023