Daily Papers

In semantic segmentation, the accuracy of models heavily depends on the high-quality annotations. However, in many practical scenarios such as medical imaging and remote sensing, obtaining true annotations is not straightforward and usually requires significant human labor. Relying on human labor often introduces annotation errors, including mislabeling, omissions, and inconsistency between annotators. In the case of remote sensing, differences in procurement time can lead to misaligned ground truth annotations. These label errors are not independently distributed, and instead usually appear in spatially connected regions where adjacent pixels are more likely to share the same errors. To address these issues, we propose an approximate Bayesian estimation based on a probabilistic model that assumes training data includes label errors, incorporating the tendency for these errors to occur with spatial correlations between adjacent pixels. Bayesian inference requires computing the posterior distribution of label errors, which becomes intractable when spatial correlations are present. We represent the correlation of label errors between adjacent pixels through a Gaussian distribution whose covariance is structured by a Kac-Murdock-Szeg\"{o} (KMS) matrix, solving the computational challenges. Through experiments on multiple segmentation tasks, we confirm that leveraging the spatial correlation of label errors significantly improves performance. Notably, in specific tasks such as lung segmentation, the proposed method achieves performance comparable to training with clean labels under moderate noise levels. Code is available at https://github.com/pfnet-research/Bayesian_SpatialCorr.

Deep-learning models have been successful in biomedical image segmentation. To generalize for real-world deployment, test-time augmentation (TTA) methods are often used to transform the test image into different versions that are hopefully closer to the training domain. Unfortunately, due to the vast diversity of instance scale and image styles, many augmented test images produce undesirable results, thus lowering the overall performance. This work proposes a new TTA framework, S^3-TTA, which selects the suitable image scale and style for each test image based on a transformation consistency metric. In addition, S^3-TTA constructs an end-to-end augmentation-segmentation joint-training pipeline to ensure a task-oriented augmentation. On public benchmarks for cell and lung segmentation, S^3-TTA demonstrates improvements over the prior art by 3.4% and 1.3%, respectively, by simply augmenting the input data in testing phase.

Accurately segmenting different organs from medical images is a critical prerequisite for computer-assisted diagnosis and intervention planning. This study proposes a deep learning-based approach for segmenting various organs from CT and MRI scans and classifying diseases. Our study introduces a novel technique integrating momentum within residual blocks for enhanced training dynamics in medical image analysis. We applied our method in two distinct tasks: segmenting liver, lung, & colon data and classifying abdominal pelvic CT and MRI scans. The proposed approach has shown promising results, outperforming state-of-the-art methods on publicly available benchmarking datasets. For instance, in the lung segmentation dataset, our approach yielded significant enhancements over the TransNetR model, including a 5.72% increase in dice score, a 5.04% improvement in mean Intersection over Union (mIoU), an 8.02% improvement in recall, and a 4.42% improvement in precision. Hence, incorporating momentum led to state-of-the-art performance in both segmentation and classification tasks, representing a significant advancement in the field of medical imaging.

Chest X-Ray (CXR) imaging for pulmonary diagnosis raises significant challenges, primarily because bone structures can obscure critical details necessary for accurate diagnosis. Recent advances in deep learning, particularly with diffusion models, offer significant promise for effectively minimizing the visibility of bone structures in CXR images, thereby improving clarity and diagnostic accuracy. Nevertheless, existing diffusion-based methods for bone suppression in CXR imaging struggle to balance the complete suppression of bones with preserving local texture details. Additionally, their high computational demand and extended processing time hinder their practical use in clinical settings. To address these limitations, we introduce a Global-Local Latent Consistency Model (GL-LCM) architecture. This model combines lung segmentation, dual-path sampling, and global-local fusion, enabling fast high-resolution bone suppression in CXR images. To tackle potential boundary artifacts and detail blurring in local-path sampling, we further propose Local-Enhanced Guidance, which addresses these issues without additional training. Comprehensive experiments on a self-collected dataset SZCH-X-Rays, and the public dataset JSRT, reveal that our GL-LCM delivers superior bone suppression and remarkable computational efficiency, significantly outperforming several competitive methods. Our code is available at https://github.com/diaoquesang/GL-LCM.

The performance on deep learning is significantly affected by volume of training data. Models pre-trained from massive dataset such as ImageNet become a powerful weapon for speeding up training convergence and improving accuracy. Similarly, models based on large dataset are important for the development of deep learning in 3D medical images. However, it is extremely challenging to build a sufficiently large dataset due to difficulty of data acquisition and annotation in 3D medical imaging. We aggregate the dataset from several medical challenges to build 3DSeg-8 dataset with diverse modalities, target organs, and pathologies. To extract general medical three-dimension (3D) features, we design a heterogeneous 3D network called Med3D to co-train multi-domain 3DSeg-8 so as to make a series of pre-trained models. We transfer Med3D pre-trained models to lung segmentation in LIDC dataset, pulmonary nodule classification in LIDC dataset and liver segmentation on LiTS challenge. Experiments show that the Med3D can accelerate the training convergence speed of target 3D medical tasks 2 times compared with model pre-trained on Kinetics dataset, and 10 times compared with training from scratch as well as improve accuracy ranging from 3% to 20%. Transferring our Med3D model on state-the-of-art DenseASPP segmentation network, in case of single model, we achieve 94.6\% Dice coefficient which approaches the result of top-ranged algorithms on the LiTS challenge.

Image registration is important for medical imaging, the estimation of the spatial transformation between different images. Many previous studies have used learning-based methods for coarse-to-fine registration to efficiently perform 3D image registration. The coarse-to-fine approach, however, is limited when dealing with the different motions of nearby objects. Here we propose a novel Motion-Aware (MA) structure that captures the different motions in a region. The MA structure incorporates a novel Residual Aligner (RA) module which predicts the multi-head displacement field used to disentangle the different motions of multiple neighbouring objects. Compared with other deep learning methods, the network based on the MA structure and RA module achieve one of the most accurate unsupervised inter-subject registration on the 9 organs of assorted sizes in abdominal CT scans, with the highest-ranked registration of the veins (Dice Similarity Coefficient / Average surface distance: 62\%/4.9mm for the vena cava and 34\%/7.9mm for the portal and splenic vein), with a half-sized structure and more efficient computation. Applied to the segmentation of lungs in chest CT scans, the new network achieves results which were indistinguishable from the best-ranked networks (94\%/3.0mm). Additionally, the theorem on predicted motion pattern and the design of MA structure are validated by further analysis.

Considering the increased workload in pathology laboratories today, automated tools such as artificial intelligence models can help pathologists with their tasks and ease the workload. In this paper, we are proposing a segmentation model (DRU-Net) that can provide a delineation of human non-small cell lung carcinomas and an augmentation method that can improve classification results. The proposed model is a fused combination of truncated pre-trained DenseNet201 and ResNet101V2 as a patch-wise classifier followed by a lightweight U-Net as a refinement model. We have used two datasets (Norwegian Lung Cancer Biobank and Haukeland University Hospital lung cancer cohort) to create our proposed model. The DRU-Net model achieves an average of 0.91 Dice similarity coefficient. The proposed spatial augmentation method (multi-lens distortion) improved the network performance by 3%. Our findings show that choosing image patches that specifically include regions of interest leads to better results for the patch-wise classifier compared to other sampling methods. The qualitative analysis showed that the DRU-Net model is generally successful in detecting the tumor. On the test set, some of the cases showed areas of false positive and false negative segmentation in the periphery, particularly in tumors with inflammatory and reactive changes.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

Purpose: Automating tasks such as lung tumor localization and segmentation in radiological images can free valuable time for radiologists and other clinical personnel. Convolutional neural networks may be suited for such tasks, but require substantial amounts of labeled data to train. Obtaining labeled data is a challenge, especially in the medical domain. Methods: This paper investigates the use of a teacher-student design to utilize datasets with different types of supervision to train an automatic model performing pulmonary tumor segmentation on computed tomography images. The framework consists of two models: the student that performs end-to-end automatic tumor segmentation and the teacher that supplies the student additional pseudo-annotated data during training. Results: Using only a small proportion of semantically labeled data and a large number of bounding box annotated data, we achieved competitive performance using a teacher-student design. Models trained on larger amounts of semantic annotations did not perform better than those trained on teacher-annotated data. Conclusions: Our results demonstrate the potential of utilizing teacher-student designs to reduce the annotation load, as less supervised annotation schemes may be performed, without any real degradation in segmentation accuracy.

The coronavirus disease (COVID-19) has resulted in a pandemic crippling the a breadth of services critical to daily life. Segmentation of lung infections in computerized tomography (CT) slices could be be used to improve diagnosis and understanding of COVID-19 in patients. Deep learning systems lack interpretability because of their black box nature. Inspired by human communication of complex ideas through language, we propose a symbolic framework based on emergent languages for the segmentation of COVID-19 infections in CT scans of lungs. We model the cooperation between two artificial agents - a Sender and a Receiver. These agents synergistically cooperate using emergent symbolic language to solve the task of semantic segmentation. Our game theoretic approach is to model the cooperation between agents unlike Generative Adversarial Networks (GANs). The Sender retrieves information from one of the higher layers of the deep network and generates a symbolic sentence sampled from a categorical distribution of vocabularies. The Receiver ingests the stream of symbols and cogenerates the segmentation mask. A private emergent language is developed that forms the communication channel used to describe the task of segmentation of COVID infections. We augment existing state of the art semantic segmentation architectures with our symbolic generator to form symbolic segmentation models. Our symbolic segmentation framework achieves state of the art performance for segmentation of lung infections caused by COVID-19. Our results show direct interpretation of symbolic sentences to discriminate between normal and infected regions, infection morphology and image characteristics. We show state of the art results for segmentation of COVID-19 lung infections in CT.

As lung cancer evolves, the presence of enlarged and potentially malignant lymph nodes must be assessed to properly estimate disease progression and select the best treatment strategy. Following the clinical guidelines, estimation of short-axis diameter and mediastinum station are paramount for correct diagnosis. A method for accurate and automatic segmentation is hence decisive for quantitatively describing lymph nodes. In this study, the use of 3D convolutional neural networks, either through slab-wise schemes or the leveraging of downsampled entire volumes, is investigated. Furthermore, the potential impact from simple ensemble strategies is considered. As lymph nodes have similar attenuation values to nearby anatomical structures, we suggest using the knowledge of other organs as prior information to guide the segmentation task. To assess the segmentation and instance detection performances, a 5-fold cross-validation strategy was followed over a dataset of 120 contrast-enhanced CT volumes. For the 1178 lymph nodes with a short-axis diameter geq10 mm, our best performing approach reached a patient-wise recall of 92%, a false positive per patient ratio of 5, and a segmentation overlap of 80.5%. The method performs similarly well across all stations. Fusing a slab-wise and a full volume approach within an ensemble scheme generated the best performances. The anatomical priors guiding strategy is promising, yet a larger set than four organs appears needed to generate an optimal benefit. A larger dataset is also mandatory, given the wide range of expressions a lymph node can exhibit (i.e., shape, location, and attenuation), and contrast uptake variations.

Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly integrated to retain relative priority of activated regions, which benefits the subsequent channel-wise recalibration. Then, attention distillation module is introduced to reinforce representation learning of tubular objects. Fine-grained details in high-resolution attention maps are passing down from one layer to its previous layer recursively to enrich context. Anatomy prior of lung context map and distance transform map is designed and incorporated for better artery-vein differentiation capacity. Extensive experiments demonstrated considerable performance gains brought by these components. Compared with state-of-the-art methods, our method extracted much more branches while maintaining competitive overall segmentation performance. Codes and models are available at http://www.pami.sjtu.edu.cn/News/56

Tuberculosis (TB) is a chronic lung disease that occurs due to bacterial infection and is one of the top 10 leading causes of death. Accurate and early detection of TB is very important, otherwise, it could be life-threatening. In this work, we have detected TB reliably from the chest X-ray images using image pre-processing, data augmentation, image segmentation, and deep-learning classification techniques. Several public databases were used to create a database of 700 TB infected and 3500 normal chest X-ray images for this study. Nine different deep CNNs (ResNet18, ResNet50, ResNet101, ChexNet, InceptionV3, Vgg19, DenseNet201, SqueezeNet, and MobileNet), which were used for transfer learning from their pre-trained initial weights and trained, validated and tested for classifying TB and non-TB normal cases. Three different experiments were carried out in this work: segmentation of X-ray images using two different U-net models, classification using X-ray images, and segmented lung images. The accuracy, precision, sensitivity, F1-score, specificity in the detection of tuberculosis using X-ray images were 97.07 %, 97.34 %, 97.07 %, 97.14 % and 97.36 % respectively. However, segmented lungs for the classification outperformed than whole X-ray image-based classification and accuracy, precision, sensitivity, F1-score, specificity were 99.9 %, 99.91 %, 99.9 %, 99.9 %, and 99.52 % respectively. The paper also used a visualization technique to confirm that CNN learns dominantly from the segmented lung regions results in higher detection accuracy. The proposed method with state-of-the-art performance can be useful in the computer-aided faster diagnosis of tuberculosis.

To improve the prognosis of patients suffering from pulmonary diseases, such as lung cancer, early diagnosis and treatment are crucial. The analysis of CT images is invaluable for diagnosis, whereas high quality segmentation of the airway tree are required for intervention planning and live guidance during bronchoscopy. Recently, the Multi-domain Airway Tree Modeling (ATM'22) challenge released a large dataset, both enabling training of deep-learning based models and bringing substantial improvement of the state-of-the-art for the airway segmentation task. However, the ATM'22 dataset includes few patients with severe pathologies affecting the airway tree anatomy. In this study, we introduce a new public benchmark dataset (AeroPath), consisting of 27 CT images from patients with pathologies ranging from emphysema to large tumors, with corresponding trachea and bronchi annotations. Second, we present a multiscale fusion design for automatic airway segmentation. Models were trained on the ATM'22 dataset, tested on the AeroPath dataset, and further evaluated against competitive open-source methods. The same performance metrics as used in the ATM'22 challenge were used to benchmark the different considered approaches. Lastly, an open web application is developed, to easily test the proposed model on new data. The results demonstrated that our proposed architecture predicted topologically correct segmentations for all the patients included in the AeroPath dataset. The proposed method is robust and able to handle various anomalies, down to at least the fifth airway generation. In addition, the AeroPath dataset, featuring patients with challenging pathologies, will contribute to development of new state-of-the-art methods. The AeroPath dataset and the web application are made openly available.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

We present ReXGroundingCT, the first publicly available dataset to link free-text radiology findings with pixel-level segmentations in 3D chest CT scans that is manually annotated. While prior datasets have relied on structured labels or predefined categories, ReXGroundingCT captures the full expressiveness of clinical language represented in free text and grounds it to spatially localized 3D segmentation annotations in volumetric imaging. This addresses a critical gap in medical AI: the ability to connect complex, descriptive text, such as "3 mm nodule in the left lower lobe", to its precise anatomical location in three-dimensional space, a capability essential for grounded radiology report generation systems. The dataset comprises 3,142 non-contrast chest CT scans paired with standardized radiology reports from the CT-RATE dataset. Using a systematic three-stage pipeline, GPT-4 was used to extract positive lung and pleural findings, which were then manually segmented by expert annotators. A total of 8,028 findings across 16,301 entities were annotated, with quality control performed by board-certified radiologists. Approximately 79% of findings are focal abnormalities, while 21% are non-focal. The training set includes up to three representative segmentations per finding, while the validation and test sets contain exhaustive labels for each finding entity. ReXGroundingCT establishes a new benchmark for developing and evaluating sentence-level grounding and free-text medical segmentation models in chest CT. The dataset can be accessed at https://huggingface.co/datasets/rajpurkarlab/ReXGroundingCT.

Instance level detection and segmentation of thoracic diseases or abnormalities are crucial for automatic diagnosis in chest X-ray images. Leveraging on constant structure and disease relations extracted from domain knowledge, we propose a structure-aware relation network (SAR-Net) extending Mask R-CNN. The SAR-Net consists of three relation modules: 1. the anatomical structure relation module encoding spatial relations between diseases and anatomical parts. 2. the contextual relation module aggregating clues based on query-key pair of disease RoI and lung fields. 3. the disease relation module propagating co-occurrence and causal relations into disease proposals. Towards making a practical system, we also provide ChestX-Det, a chest X-Ray dataset with instance-level annotations (boxes and masks). ChestX-Det is a subset of the public dataset NIH ChestX-ray14. It contains ~3500 images of 13 common disease categories labeled by three board-certified radiologists. We evaluate our SAR-Net on it and another dataset DR-Private. Experimental results show that it can enhance the strong baseline of Mask R-CNN with significant improvements. The ChestX-Det is released at https://github.com/Deepwise-AILab/ChestX-Det-Dataset.

Airway segmentation on CT scans is critical for pulmonary disease diagnosis and endobronchial navigation. Manual extraction of airway requires strenuous efforts due to the complicated structure and various appearance of airway. For automatic airway extraction, convolutional neural networks (CNNs) based methods have recently become the state-of-the-art approach. However, there still remains a challenge for CNNs to perceive the tree-like pattern and comprehend the connectivity of airway. To address this, we propose a voxel-connectivity aware approach named AirwayNet for accurate airway segmentation. By connectivity modeling, conventional binary segmentation task is transformed into 26 tasks of connectivity prediction. Thus, our AirwayNet learns both airway structure and relationship between neighboring voxels. To take advantage of context knowledge, lung distance map and voxel coordinates are fed into AirwayNet as additional semantic information. Compared to existing approaches, AirwayNet achieved superior performance, demonstrating the effectiveness of the network's awareness of voxel connectivity.

Despite that deep learning has achieved state-of-the-art performance for medical image segmentation, its success relies on a large set of manually annotated images for training that are expensive to acquire. In this paper, we propose an annotation-efficient learning framework for segmentation tasks that avoids annotations of training images, where we use an improved Cycle-Consistent Generative Adversarial Network (GAN) to learn from a set of unpaired medical images and auxiliary masks obtained either from a shape model or public datasets. We first use the GAN to generate pseudo labels for our training images under the implicit high-level shape constraint represented by a Variational Auto-encoder (VAE)-based discriminator with the help of the auxiliary masks, and build a Discriminator-guided Generator Channel Calibration (DGCC) module which employs our discriminator's feedback to calibrate the generator for better pseudo labels. To learn from the pseudo labels that are noisy, we further introduce a noise-robust iterative learning method using noise-weighted Dice loss. We validated our framework with two situations: objects with a simple shape model like optic disc in fundus images and fetal head in ultrasound images, and complex structures like lung in X-Ray images and liver in CT images. Experimental results demonstrated that 1) Our VAE-based discriminator and DGCC module help to obtain high-quality pseudo labels. 2) Our proposed noise-robust learning method can effectively overcome the effect of noisy pseudo labels. 3) The segmentation performance of our method without using annotations of training images is close or even comparable to that of learning from human annotations.

To investigate whether the pleurae, airways and vessels surrounding a nodule on non-contrast computed tomography (CT) can discriminate benign and malignant pulmonary nodules. The LIDC-IDRI dataset, one of the largest publicly available CT database, was exploited for study. A total of 1556 nodules from 694 patients were involved in statistical analysis, where nodules with average scorings <3 and >3 were respectively denoted as benign and malignant. Besides, 339 nodules from 113 patients with diagnosis ground-truth were independently evaluated. Computer algorithms were developed to segment pulmonary structures and quantify the distances to pleural surface, airways and vessels, as well as the counting number and normalized volume of airways and vessels near a nodule. Odds ratio (OR) and Chi-square (\chi^2) testing were performed to demonstrate the correlation between features of surrounding structures and nodule malignancy. A non-parametric receiver operating characteristic (ROC) analysis was conducted in logistic regression to evaluate discrimination ability of each structure. For benign and malignant groups, the average distances from nodules to pleural surface, airways and vessels are respectively (6.56, 5.19), (37.08, 26.43) and (1.42, 1.07) mm. The correlation between nodules and the counting number of airways and vessels that contact or project towards nodules are respectively (OR=22.96, \chi^2=105.04) and (OR=7.06, \chi^2=290.11). The correlation between nodules and the volume of airways and vessels are (OR=9.19, \chi^2=159.02) and (OR=2.29, \chi^2=55.89). The areas-under-curves (AUCs) for pleurae, airways and vessels are respectively 0.5202, 0.6943 and 0.6529. Our results show that malignant nodules are often surrounded by more pulmonary structures compared with benign ones, suggesting that features of these structures could be viewed as lung cancer biomarkers.

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.

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.

Collecting large-scale medical datasets with fully annotated samples for training of deep networks is prohibitively expensive, especially for 3D volume data. Recent breakthroughs in self-supervised learning (SSL) offer the ability to overcome the lack of labeled training samples by learning feature representations from unlabeled data. However, most current SSL techniques in the medical field have been designed for either 2D images or 3D volumes. In practice, this restricts the capability to fully leverage unlabeled data from numerous sources, which may include both 2D and 3D data. Additionally, the use of these pre-trained networks is constrained to downstream tasks with compatible data dimensions. In this paper, we propose a novel framework for unsupervised joint learning on 2D and 3D data modalities. Given a set of 2D images or 2D slices extracted from 3D volumes, we construct an SSL task based on a 2D contrastive clustering problem for distinct classes. The 3D volumes are exploited by computing vectored embedding at each slice and then assembling a holistic feature through deformable self-attention mechanisms in Transformer, allowing incorporating long-range dependencies between slices inside 3D volumes. These holistic features are further utilized to define a novel 3D clustering agreement-based SSL task and masking embedding prediction inspired by pre-trained language models. Experiments on downstream tasks, such as 3D brain segmentation, lung nodule detection, 3D heart structures segmentation, and abnormal chest X-ray detection, demonstrate the effectiveness of our joint 2D and 3D SSL approach. We improve plain 2D Deep-ClusterV2 and SwAV by a significant margin and also surpass various modern 2D and 3D SSL approaches.

The development of successful artificial intelligence models for chest X-ray analysis relies on large, diverse datasets with high-quality annotations. While several databases of chest X-ray images have been released, most include disease diagnosis labels but lack detailed pixel-level anatomical segmentation labels. To address this gap, we introduce an extensive chest X-ray multi-center segmentation dataset with uniform and fine-grain anatomical annotations for images coming from six well-known publicly available databases: CANDID-PTX, ChestX-ray8, Chexpert, MIMIC-CXR-JPG, Padchest, and VinDr-CXR, resulting in 676,803 segmentation masks. Our methodology utilizes the HybridGNet model to ensure consistent and high-quality segmentations across all datasets. Rigorous validation, including expert physician evaluation and automatic quality control, was conducted to validate the resulting masks. Additionally, we provide individualized quality indices per mask and an overall quality estimation per dataset. This dataset serves as a valuable resource for the broader scientific community, streamlining the development and assessment of innovative methodologies in chest X-ray analysis. The CheXmask dataset is publicly available at: https://physionet.org/content/chexmask-cxr-segmentation-data/.

Reading and interpreting chest X-ray images is one of the most radiologist's routines. However, it still can be challenging, even for the most experienced ones. Therefore, we proposed a multi-model deep learning-based automated chest X-ray report generator system designed to assist radiologists in their work. The basic idea of the proposed system is by utilizing multi binary-classification models for detecting multi abnormalities, with each model responsible for detecting one abnormality, in a single image. In this study, we limited the radiology abnormalities detection to only cardiomegaly, lung effusion, and consolidation. The system generates a radiology report by performing the following three steps: image pre-processing, utilizing deep learning models to detect abnormalities, and producing a report. The aim of the image pre-processing step is to standardize the input by scaling it to 128x128 pixels and slicing it into three segments, which covers the upper, lower, and middle parts of the lung. After pre-processing, each corresponding model classifies the image, resulting in a 0 (zero) for no abnormality detected and a 1 (one) for the presence of an abnormality. The prediction outputs of each model are then concatenated to form a 'result code'. The 'result code' is used to construct a report by selecting the appropriate pre-determined sentence for each detected abnormality in the report generation step. The proposed system is expected to reduce the workload of radiologists and increase the accuracy of chest X-ray diagnosis.

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

Precise image segmentation provides clinical study with meaningful and well-structured information. Despite the remarkable progress achieved in medical image segmentation, there is still an absence of foundation segmentation model that can segment a wide range of anatomical categories with easy user interaction. In this paper, we propose a universal and interactive volumetric medical image segmentation model, named SegVol. By training on 90k unlabeled Computed Tomography (CT) volumes and 6k labeled CTs, this foundation model supports the segmentation of over 200 anatomical categories using semantic and spatial prompts. Extensive experiments verify that SegVol outperforms the state of the art by a large margin on multiple segmentation benchmarks. Notably, on three challenging lesion datasets, our method achieves around 20% higher Dice score than nnU-Net. The model and data are publicly available at: https://github.com/BAAI-DCAI/SegVol.

Recently, intelligent analysis of lung nodules with the assistant of computer aided detection (CAD) techniques can improve the accuracy rate of lung cancer diagnosis. However, existing CAD systems and pulmonary datasets mainly focus on Computed Tomography (CT) images from one single period, while ignoring the cross spatio-temporal features associated with the progression of nodules contained in imaging data from various captured periods of lung cancer. If the evolution patterns of nodules across various periods in the patients' CT sequences can be explored, it will play a crucial role in guiding the precise screening identification of lung cancer. Therefore, a cross spatio-temporal lung nodule dataset with pathological information for nodule identification and diagnosis is constructed, which contains 328 CT sequences and 362 annotated nodules from 109 patients. This comprehensive database is intended to drive research in the field of CAD towards more practical and robust methods, and also contribute to the further exploration of precision medicine related field. To ensure patient confidentiality, we have removed sensitive information from the dataset.

In the diverse field of medical imaging, automatic segmentation has numerous applications and must handle a wide variety of input domains, such as different types of Computed Tomography (CT) scans and Magnetic Resonance (MR) images. This heterogeneity challenges automatic segmentation algorithms to maintain consistent performance across different modalities due to the requirement for spatially aligned and paired images. Typically, segmentation models are trained using a single modality, which limits their ability to generalize to other types of input data without employing transfer learning techniques. Additionally, leveraging complementary information from different modalities to enhance segmentation precision often necessitates substantial modifications to popular encoder-decoder designs, such as introducing multiple branched encoding or decoding paths for each modality. In this work, we propose a simple Multi-Modal Segmentation (MulModSeg) strategy to enhance medical image segmentation across multiple modalities, specifically CT and MR. It incorporates two key designs: a modality-conditioned text embedding framework via a frozen text encoder that adds modality awareness to existing segmentation frameworks without significant structural modifications or computational overhead, and an alternating training procedure that facilitates the integration of essential features from unpaired CT and MR inputs. Through extensive experiments with both Fully Convolutional Network and Transformer-based backbones, MulModSeg consistently outperforms previous methods in segmenting abdominal multi-organ and cardiac substructures for both CT and MR modalities. The code is available in this {https://github.com/ChengyinLee/MulModSeg_2024{link}}.

Lung nodules can be an alarming precursor to potential lung cancer. Missed nodule detections during chest radiograph analysis remains a common challenge among thoracic radiologists. In this work, we present a multi-task lung nodule detection algorithm for chest radiograph analysis. Unlike past approaches, our algorithm predicts a global-level label indicating nodule presence along with local-level labels predicting nodule locations using a Dual Head Network (DHN). We demonstrate the favorable nodule detection performance that our multi-task formulation yields in comparison to conventional methods. In addition, we introduce a novel Dual Head Augmentation (DHA) strategy tailored for DHN, and we demonstrate its significance in further enhancing global and local nodule predictions.

Segmentation of biomedical images can assist radiologists to make a better diagnosis and take decisions faster by helping in the detection of abnormalities, such as tumors. Manual or semi-automated segmentation, however, can be a time-consuming task. Most deep learning based automated segmentation methods are supervised and rely on manually segmented ground-truth. A possible solution for the problem would be an unsupervised deep learning based approach for automated segmentation, which this research work tries to address. We use a W-Net architecture and modified it, such that it can be applied to 3D volumes. In addition, to suppress noise in the segmentation we added attention gates to the skip connections. The loss for the segmentation output was calculated using soft N-Cuts and for the reconstruction output using SSIM. Conditional Random Fields were used as a post-processing step to fine-tune the results. The proposed method has shown promising results, with a dice coefficient of 0.88 for the liver segmentation compared against manual segmentation.

Lung diseases represent a significant global health challenge, with Chest X-Ray (CXR) being a key diagnostic tool due to their accessibility and affordability. Nonetheless, the detection of pulmonary lesions is often hindered by overlapping bone structures in CXR images, leading to potential misdiagnoses. To address this issue, we developed an end-to-end framework called BS-LDM, designed to effectively suppress bone in high-resolution CXR images. This framework is based on conditional latent diffusion models and incorporates a multi-level hybrid loss-constrained vector-quantized generative adversarial network which is crafted for perceptual compression, ensuring the preservation of details. To further enhance the framework's performance, we introduce offset noise and a temporal adaptive thresholding strategy. These additions help minimize discrepancies in generating low-frequency information, thereby improving the clarity of the generated soft tissue images. Additionally, we have compiled a high-quality bone suppression dataset named SZCH-X-Rays. This dataset includes 818 pairs of high-resolution CXR and dual-energy subtraction soft tissue images collected from a partner hospital. Moreover, we processed 241 data pairs from the JSRT dataset into negative images, which are more commonly used in clinical practice. Our comprehensive experimental and clinical evaluations reveal that BS-LDM excels in bone suppression, underscoring its significant clinical value.

Lung cancer stands as the preeminent cause of cancer-related mortality globally. Prompt and precise diagnosis, coupled with effective treatment, is imperative to reduce the fatality rates associated with this formidable disease. This study introduces a cutting-edge deep learning framework for the classification of lung cancer from CT scan imagery. The research encompasses a suite of image pre-processing strategies, notably Canny edge detection, and wavelet transformations, which precede the extraction of salient features and subsequent classification via a Multi-Layer Perceptron (MLP). The optimization process is further refined using the Dragonfly Algorithm (DA). The methodology put forth has attained an impressive training and testing accuracy of 99.82\%, underscoring its efficacy and reliability in the accurate diagnosis of lung cancer.

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.

With an estimated 160,000 deaths in 2018, lung cancer is the most common cause of cancer death in the United States. Lung cancer CT screening has been shown to reduce mortality by up to 40% and is now included in US screening guidelines. Reducing the high error rates in lung cancer screening is imperative because of the high clinical and financial costs caused by diagnosis mistakes. Despite the use of standards for radiological diagnosis, persistent inter-grader variability and incomplete characterization of comprehensive imaging findings remain as limitations of current methods. These limitations suggest opportunities for more sophisticated systems to improve performance and inter-reader consistency. In this report, we reproduce a state-of-the-art deep learning algorithm for lung cancer risk prediction. Our model predicts malignancy probability and risk bucket classification from lung CT studies. This allows for risk categorization of patients being screened and suggests the most appropriate surveillance and management. Combining our solution high accuracy, consistency and fully automated nature, our approach may enable highly efficient screening procedures and accelerate the adoption of lung cancer screening.

Lung diseases remain a critical global health concern, and it's crucial to have accurate and quick ways to diagnose them. This work focuses on classifying different lung diseases into five groups: viral pneumonia, bacterial pneumonia, COVID, tuberculosis, and normal lungs. Employing advanced deep learning techniques, we explore a diverse range of models including CNN, hybrid models, ensembles, transformers, and Big Transfer. The research encompasses comprehensive methodologies such as hyperparameter tuning, stratified k-fold cross-validation, and transfer learning with fine-tuning.Remarkably, our findings reveal that the Xception model, fine-tuned through 5-fold cross-validation, achieves the highest accuracy of 96.21\%. This success shows that our methods work well in accurately identifying different lung diseases. The exploration of explainable artificial intelligence (XAI) methodologies further enhances our understanding of the decision-making processes employed by these models, contributing to increased trust in their clinical applications.

Learning anatomical segmentation from heterogeneous labels in multi-center datasets is a common situation encountered in clinical scenarios, where certain anatomical structures are only annotated in images coming from particular medical centers, but not in the full database. Here we first show how state-of-the-art pixel-level segmentation models fail in naively learning this task due to domain memorization issues and conflicting labels. We then propose to adopt HybridGNet, a landmark-based segmentation model which learns the available anatomical structures using graph-based representations. By analyzing the latent space learned by both models, we show that HybridGNet naturally learns more domain-invariant feature representations, and provide empirical evidence in the context of chest X-ray multiclass segmentation. We hope these insights will shed light on the training of deep learning models with heterogeneous labels from public and multi-center datasets.

With the development of Deep Neural Networks (DNNs), many efforts have been made to handle medical image segmentation. Traditional methods such as nnUNet train specific segmentation models on the individual datasets. Plenty of recent methods have been proposed to adapt the foundational Segment Anything Model (SAM) to medical image segmentation. However, they still focus on discrete representations to generate pixel-wise predictions, which are spatially inflexible and scale poorly to higher resolution. In contrast, implicit methods learn continuous representations for segmentation, which is crucial for medical image segmentation. In this paper, we propose I-MedSAM, which leverages the benefits of both continuous representations and SAM, to obtain better cross-domain ability and accurate boundary delineation. Since medical image segmentation needs to predict detailed segmentation boundaries, we designed a novel adapter to enhance the SAM features with high-frequency information during Parameter-Efficient Fine-Tuning (PEFT). To convert the SAM features and coordinates into continuous segmentation output, we utilize Implicit Neural Representation (INR) to learn an implicit segmentation decoder. We also propose an uncertainty-guided sampling strategy for efficient learning of INR. Extensive evaluations on 2D medical image segmentation tasks have shown that our proposed method with only 1.6M trainable parameters outperforms existing methods including discrete and implicit methods. The code will be available at: https://github.com/ucwxb/I-MedSAM.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

Recently, Computer-Aided Diagnosis (CAD) systems have emerged as indispensable tools in clinical diagnostic workflows, significantly alleviating the burden on radiologists. Nevertheless, despite their integration into clinical settings, CAD systems encounter limitations. Specifically, while CAD systems can achieve high performance in the detection of lung nodules, they face challenges in accurately predicting multiple cancer types. This limitation can be attributed to the scarcity of publicly available datasets annotated with expert-level cancer type information. This research aims to bridge this gap by providing publicly accessible datasets and reliable tools for medical diagnosis, facilitating a finer categorization of different types of lung diseases so as to offer precise treatment recommendations. To achieve this objective, we curated a diverse dataset of lung Computed Tomography (CT) images, comprising 330 annotated nodules (nodules are labeled as bounding boxes) from 95 distinct patients. The quality of the dataset was evaluated using a variety of classical classification and detection models, and these promising results demonstrate that the dataset has a feasible application and further facilitate intelligent auxiliary diagnosis.

Leveraging the powerful capabilities of diffusion models has yielded quite effective results in medical image segmentation tasks. However, existing methods typically transfer the original training process directly without specific adjustments for segmentation tasks. Furthermore, the commonly used pre-trained diffusion models still have deficiencies in feature extraction. Based on these considerations, we propose LEAF, a medical image segmentation model grounded in latent diffusion models. During the fine-tuning process, we replace the original noise prediction pattern with a direct prediction of the segmentation map, thereby reducing the variance of segmentation results. We also employ a feature distillation method to align the hidden states of the convolutional layers with the features from a transformer-based vision encoder. Experimental results demonstrate that our method enhances the performance of the original diffusion model across multiple segmentation datasets for different disease types. Notably, our approach does not alter the model architecture, nor does it increase the number of parameters or computation during the inference phase, making it highly efficient.

This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.

Chest X-rays (CXRs) are commonly utilized as a low-dose modality for lung screening. Nonetheless, the efficacy of CXRs is somewhat impeded, given that approximately 75% of the lung area overlaps with bone, which in turn hampers the detection and diagnosis of diseases. As a remedial measure, bone suppression techniques have been introduced. The current dual-energy subtraction imaging technique in the clinic requires costly equipment and subjects being exposed to high radiation. To circumvent these issues, deep learning-based image generation algorithms have been proposed. However, existing methods fall short in terms of producing high-quality images and capturing texture details, particularly with pulmonary vessels. To address these issues, this paper proposes a new bone suppression framework, termed BS-Diff, that comprises a conditional diffusion model equipped with a U-Net architecture and a simple enhancement module to incorporate an autoencoder. Our proposed network cannot only generate soft tissue images with a high bone suppression rate but also possesses the capability to capture fine image details. Additionally, we compiled the largest dataset since 2010, including data from 120 patients with high-definition, high-resolution paired CXRs and soft tissue images collected by our affiliated hospital. Extensive experiments, comparative analyses, ablation studies, and clinical evaluations indicate that the proposed BS-Diff outperforms several bone-suppression models across multiple metrics. Our code can be accessed at https://github.com/Benny0323/BS-Diff.

Medical image segmentation allows quantifying target structure size and shape, aiding in disease diagnosis, prognosis, surgery planning, and comprehension.Building upon recent advancements in foundation Vision-Language Models (VLMs) from natural image-text pairs, several studies have proposed adapting them to Vision-Language Segmentation Models (VLSMs) that allow using language text as an additional input to segmentation models. Introducing auxiliary information via text with human-in-the-loop prompting during inference opens up unique opportunities, such as open vocabulary segmentation and potentially more robust segmentation models against out-of-distribution data. Although transfer learning from natural to medical images has been explored for image-only segmentation models, the joint representation of vision-language in segmentation problems remains underexplored. This study introduces the first systematic study on transferring VLSMs to 2D medical images, using carefully curated 11 datasets encompassing diverse modalities and insightful language prompts and experiments. Our findings demonstrate that although VLSMs show competitive performance compared to image-only models for segmentation after finetuning in limited medical image datasets, not all VLSMs utilize the additional information from language prompts, with image features playing a dominant role. While VLSMs exhibit enhanced performance in handling pooled datasets with diverse modalities and show potential robustness to domain shifts compared to conventional segmentation models, our results suggest that novel approaches are required to enable VLSMs to leverage the various auxiliary information available through language prompts. The code and datasets are available at https://github.com/naamiinepal/medvlsm.

The field of medical image segmentation is hindered by the scarcity of large, publicly available annotated datasets. Not all datasets are made public for privacy reasons, and creating annotations for a large dataset is time-consuming and expensive, as it requires specialized expertise to accurately identify regions of interest (ROIs) within the images. To address these challenges, we evaluate the performance of the Segment Anything Model (SAM) as an annotation tool for medical data by using it to produce so-called "pseudo labels" on the Medical Segmentation Decathlon (MSD) computed tomography (CT) tasks. The pseudo labels are then used in place of ground truth labels to train a UNet model in a weakly-supervised manner. We experiment with different prompt types on SAM and find that the bounding box prompt is a simple yet effective method for generating pseudo labels. This method allows us to develop a weakly-supervised model that performs comparably to a fully supervised model.

Medical image segmentation aims to delineate the anatomical or pathological structures of interest, playing a crucial role in clinical diagnosis. A substantial amount of high-quality annotated data is crucial for constructing high-precision deep segmentation models. However, medical annotation is highly cumbersome and time-consuming, especially for medical videos or 3D volumes, due to the huge labeling space and poor inter-frame consistency. Recently, a fundamental task named Moving Object Segmentation (MOS) has made significant advancements in natural images. Its objective is to delineate moving objects from the background within image sequences, requiring only minimal annotations. In this paper, we propose the first foundation model, named iMOS, for MOS in medical images. Extensive experiments on a large multi-modal medical dataset validate the effectiveness of the proposed iMOS. Specifically, with the annotation of only a small number of images in the sequence, iMOS can achieve satisfactory tracking and segmentation performance of moving objects throughout the entire sequence in bi-directions. We hope that the proposed iMOS can help accelerate the annotation speed of experts, and boost the development of medical foundation models.

Real-world medical image segmentation has tremendous long-tailed complexity of objects, among which tail conditions correlate with relatively rare diseases and are clinically significant. A trustworthy medical AI algorithm should demonstrate its effectiveness on tail conditions to avoid clinically dangerous damage in these out-of-distribution (OOD) cases. In this paper, we adopt the concept of object queries in Mask Transformers to formulate semantic segmentation as a soft cluster assignment. The queries fit the feature-level cluster centers of inliers during training. Therefore, when performing inference on a medical image in real-world scenarios, the similarity between pixels and the queries detects and localizes OOD regions. We term this OOD localization as MaxQuery. Furthermore, the foregrounds of real-world medical images, whether OOD objects or inliers, are lesions. The difference between them is less than that between the foreground and background, possibly misleading the object queries to focus redundantly on the background. Thus, we propose a query-distribution (QD) loss to enforce clear boundaries between segmentation targets and other regions at the query level, improving the inlier segmentation and OOD indication. Our proposed framework is tested on two real-world segmentation tasks, i.e., segmentation of pancreatic and liver tumors, outperforming previous state-of-the-art algorithms by an average of 7.39% on AUROC, 14.69% on AUPR, and 13.79% on FPR95 for OOD localization. On the other hand, our framework improves the performance of inlier segmentation by an average of 5.27% DSC when compared with the leading baseline nnUNet.

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

Medical image segmentation is an important analysis task in clinical practice and research. Deep learning has massively advanced the field, but current approaches are mostly based on models trained for a specific task. Training such models or adapting them to a new condition is costly due to the need for (manually) labeled data. The emergence of vision foundation models, especially Segment Anything, offers a path to universal segmentation for medical images, overcoming these issues. Here, we study how to improve Segment Anything for medical images by comparing different finetuning strategies on a large and diverse dataset. We evaluate the finetuned models on a wide range of interactive and (automatic) semantic segmentation tasks. We find that the performance can be clearly improved for interactive segmentation. However, semantic segmentation does not benefit from pretraining on medical images. Our best model, MedicoSAM, is publicly available at https://github.com/computational-cell-analytics/medico-sam. We show that it is compatible with existing tools for data annotation and believe that it will be of great practical value.

Rapid advancements in medical image segmentation performance have been significantly driven by the development of Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs). These models follow the discriminative pixel-wise classification learning paradigm and often have limited ability to generalize across diverse medical imaging datasets. In this manuscript, we introduce Generative Medical Segmentation (GMS), a novel approach leveraging a generative model to perform image segmentation. Concretely, GMS employs a robust pre-trained vision foundation model to extract latent representations for images and corresponding ground truth masks, followed by a model that learns a mapping function from the image to the mask in the latent space. Once trained, the model generates an estimated segmentation mask using the pre-trained vision foundation model to decode the predicted latent representation back into the image space. The design of GMS leads to fewer trainable parameters in the model which reduces the risk of overfitting and enhances its generalization capability. Our experimental analysis across five public datasets in different medical imaging domains demonstrates GMS outperforms existing discriminative and generative segmentation models. Furthermore, GMS is able to generalize well across datasets from different centers within the same imaging modality. Our experiments suggest GMS offers a scalable and effective solution for medical image segmentation. GMS implementation and trained model weights are available at https://github.com/King-HAW/GMS.

In this paper, a 3D-RegNet-based neural network is proposed for diagnosing the physical condition of patients with coronavirus (Covid-19) infection. In the application of clinical medicine, lung CT images are utilized by practitioners to determine whether a patient is infected with coronavirus. However, there are some laybacks can be considered regarding to this diagnostic method, such as time consuming and low accuracy. As a relatively large organ of human body, important spatial features would be lost if the lungs were diagnosed utilizing two dimensional slice image. Therefore, in this paper, a deep learning model with 3D image was designed. The 3D image as input data was comprised of two-dimensional pulmonary image sequence and from which relevant coronavirus infection 3D features were extracted and classified. The results show that the test set of the 3D model, the result: f1 score of 0.8379 and AUC value of 0.8807 have been achieved.

Accurate medical image segmentation is crucial for precise anatomical delineation. Deep learning models like U-Net have shown great success but depend heavily on large datasets and struggle with domain shifts, complex structures, and limited training samples. Recent studies have explored diffusion models for segmentation by iteratively refining masks. However, these methods still retain the conventional image-to-mask mapping, making them highly sensitive to input data, which hampers stability and generalization. In contrast, we introduce DiffAtlas, a novel generative framework that models both images and masks through diffusion during training, effectively ``GenAI-fying'' atlas-based segmentation. During testing, the model is guided to generate a specific target image-mask pair, from which the corresponding mask is obtained. DiffAtlas retains the robustness of the atlas paradigm while overcoming its scalability and domain-specific limitations. Extensive experiments on CT and MRI across same-domain, cross-modality, varying-domain, and different data-scale settings using the MMWHS and TotalSegmentator datasets demonstrate that our approach outperforms existing methods, particularly in limited-data and zero-shot modality segmentation. Code is available at https://github.com/M3DV/DiffAtlas.

Deep learning (DL) has become the dominant approach for medical image segmentation, yet ensuring the reliability and clinical applicability of these models requires addressing key challenges such as annotation variability, calibration, and uncertainty estimation. This is why we created the Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS), which highlights the critical role of multiple annotators in establishing a more comprehensive ground truth, emphasizing that segmentation is inherently subjective and that leveraging inter-annotator variability is essential for robust model evaluation. Seven teams participated in the challenge, submitting a variety of DL models evaluated using metrics such as Dice Similarity Coefficient (DSC), Expected Calibration Error (ECE), and Continuous Ranked Probability Score (CRPS). By incorporating consensus and dissensus ground truth, we assess how DL models handle uncertainty and whether their confidence estimates align with true segmentation performance. Our findings reinforce the importance of well-calibrated models, as better calibration is strongly correlated with the quality of the results. Furthermore, we demonstrate that segmentation models trained on diverse datasets and enriched with pre-trained knowledge exhibit greater robustness, particularly in cases deviating from standard anatomical structures. Notably, the best-performing models achieved high DSC and well-calibrated uncertainty estimates. This work underscores the need for multi-annotator ground truth, thorough calibration assessments, and uncertainty-aware evaluations to develop trustworthy and clinically reliable DL-based medical image segmentation models.

Most of the existing chest X-ray datasets include labels from a list of findings without specifying their locations on the radiographs. This limits the development of machine learning algorithms for the detection and localization of chest abnormalities. In this work, we describe a dataset of more than 100,000 chest X-ray scans that were retrospectively collected from two major hospitals in Vietnam. Out of this raw data, we release 18,000 images that were manually annotated by a total of 17 experienced radiologists with 22 local labels of rectangles surrounding abnormalities and 6 global labels of suspected diseases. The released dataset is divided into a training set of 15,000 and a test set of 3,000. Each scan in the training set was independently labeled by 3 radiologists, while each scan in the test set was labeled by the consensus of 5 radiologists. We designed and built a labeling platform for DICOM images to facilitate these annotation procedures. All images are made publicly available (https://www.physionet.org/content/vindr-cxr/1.0.0/) in DICOM format along with the labels of both the training set and the test set.

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%.

Tissue segmentation is a routine preprocessing step to reduce the computational cost of whole slide image (WSI) analysis by excluding background regions. Traditional image processing techniques are commonly used for tissue segmentation, but often require manual adjustments to parameter values for atypical cases, fail to exclude all slide and scanning artifacts from the background, and are unable to segment adipose tissue. Pen marking artifacts in particular can be a potential source of bias for subsequent analyses if not removed. In addition, several applications require the separation of individual cross-sections, which can be challenging due to tissue fragmentation and adjacent positioning. To address these problems, we develop a convolutional neural network for tissue and pen marking segmentation using a dataset of 200 H&E stained WSIs. For separating tissue cross-sections, we propose a novel post-processing method based on clustering predicted centroid locations of the cross-sections in a 2D histogram. On an independent test set, the model achieved a mean Dice score of 0.981pm0.033 for tissue segmentation and a mean Dice score of 0.912pm0.090 for pen marking segmentation. The mean absolute difference between the number of annotated and separated cross-sections was 0.075pm0.350. Our results demonstrate that the proposed model can accurately segment H&E stained tissue cross-sections and pen markings in WSIs while being robust to many common slide and scanning artifacts. The model with trained model parameters and post-processing method are made publicly available as a Python package called SlideSegmenter.

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}.}

In the domain of medical imaging, many supervised learning based methods for segmentation face several challenges such as high variability in annotations from multiple experts, paucity of labelled data and class imbalanced datasets. These issues may result in segmentations that lack the requisite precision for clinical analysis and can be misleadingly overconfident without associated uncertainty quantification. We propose the PULASki for biomedical image segmentation that accurately captures variability in expert annotations, even in small datasets. Our approach makes use of an improved loss function based on statistical distances in a conditional variational autoencoder structure (Probabilistic UNet), which improves learning of the conditional decoder compared to the standard cross-entropy particularly in class imbalanced problems. We analyse our method for two structurally different segmentation tasks (intracranial vessel and multiple sclerosis (MS) lesion) and compare our results to four well-established baselines in terms of quantitative metrics and qualitative output. Empirical results demonstrate the PULASKi method outperforms all baselines at the 5\% significance level. The generated segmentations are shown to be much more anatomically plausible than in the 2D case, particularly for the vessel task. Our method can also be applied to a wide range of multi-label segmentation tasks and and is useful for downstream tasks such as hemodynamic modelling (computational fluid dynamics and data assimilation), clinical decision making, and treatment planning.

Semi-supervised learning relaxes the need of large pixel-wise labeled datasets for image segmentation by leveraging unlabeled data. A prominent way to exploit unlabeled data is to regularize model predictions. Since the predictions of unlabeled data can be unreliable, uncertainty-aware schemes are typically employed to gradually learn from meaningful and reliable predictions. Uncertainty estimation methods, however, rely on multiple inferences from the model predictions that must be computed for each training step, which is computationally expensive. Moreover, these uncertainty maps capture pixel-wise disparities and do not consider global information. This work proposes a novel method to estimate segmentation uncertainty by leveraging global information from the segmentation masks. More precisely, an anatomically-aware representation is first learnt to model the available segmentation masks. The learnt representation thereupon maps the prediction of a new segmentation into an anatomically-plausible segmentation. The deviation from the plausible segmentation aids in estimating the underlying pixel-level uncertainty in order to further guide the segmentation network. The proposed method consequently estimates the uncertainty using a single inference from our representation, thereby reducing the total computation. We evaluate our method on two publicly available segmentation datasets of left atria in cardiac MRIs and of multiple organs in abdominal CTs. Our anatomically-aware method improves the segmentation accuracy over the state-of-the-art semi-supervised methods in terms of two commonly used evaluation metrics.

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model. Our code is available at: https://github.com/levayz/ProtoSAM

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

Image segmentation remains a pivotal component in medical image analysis, aiding in the extraction of critical information for precise diagnostic practices. With the advent of deep learning, automated image segmentation methods have risen to prominence, showcasing exceptional proficiency in processing medical imagery. Motivated by the Segment Anything Model (SAM)-a foundational model renowned for its remarkable precision and robust generalization capabilities in segmenting 2D natural images-we introduce SAM3D, an innovative adaptation tailored for 3D volumetric medical image analysis. Unlike current SAM-based methods that segment volumetric data by converting the volume into separate 2D slices for individual analysis, our SAM3D model processes the entire 3D volume image in a unified approach. Extensive experiments are conducted on multiple medical image datasets to demonstrate that our network attains competitive results compared with other state-of-the-art methods in 3D medical segmentation tasks while being significantly efficient in terms of parameters. Code and checkpoints are available at https://github.com/UARK-AICV/SAM3D.

Active contour models have achieved prominent success in the area of image segmentation, allowing complex objects to be segmented from the background for further analysis. Existing models can be divided into region-based active contour models and edge-based active contour models. However, both models use direct image data to achieve segmentation and face many challenging problems in terms of the initial contour position, noise sensitivity, local minima and inefficiency owing to the in-homogeneity of image intensities. The saliency map of an image changes the image representation, making it more visual and meaningful. In this study, we propose a novel model that uses the advantages of a saliency map with local image information (LIF) and overcomes the drawbacks of previous models. The proposed model is driven by a saliency map of an image and the local image information to enhance the progress of the active contour models. In this model, the saliency map of an image is first computed to find the saliency driven local fitting energy. Then, the saliency-driven local fitting energy is combined with the LIF model, resulting in a final novel energy functional. This final energy functional is formulated through a level set formulation, and regulation terms are added to evolve the contour more precisely across the object boundaries. The quality of the proposed method was verified on different synthetic images, real images and publicly available datasets, including medical images. The image segmentation results, and quantitative comparisons confirmed the contour initialization independence, noise insensitivity, and superior segmentation accuracy of the proposed model in comparison to the other segmentation models.

Medical researchers and clinicians often need to perform novel segmentation tasks on a set of related images. Existing methods for segmenting a new dataset are either interactive, requiring substantial human effort for each image, or require an existing set of previously labeled images. We introduce a system, MultiverSeg, that enables practitioners to rapidly segment an entire new dataset without requiring access to any existing labeled data from that task or domain. Along with the image to segment, the model takes user interactions such as clicks, bounding boxes or scribbles as input, and predicts a segmentation. As the user segments more images, those images and segmentations become additional inputs to the model, providing context. As the context set of labeled images grows, the number of interactions required to segment each new image decreases. We demonstrate that MultiverSeg enables users to interactively segment new datasets efficiently, by amortizing the number of interactions per image to achieve an accurate segmentation. Compared to using a state-of-the-art interactive segmentation method, MultiverSeg reduced the total number of clicks by 36% and scribble steps by 25% to achieve 90% Dice on sets of images from unseen tasks. We release code and model weights at https://multiverseg.csail.mit.edu

Efficient, reliable and reproducible target volume delineation is a key step in the effective planning of breast radiotherapy. However, post-operative breast target delineation is challenging as the contrast between the tumor bed volume (TBV) and normal breast tissue is relatively low in CT images. In this study, we propose to mimic the marker-guidance procedure in manual target delineation. We developed a saliency-based deep learning segmentation (SDL-Seg) algorithm for accurate TBV segmentation in post-operative breast irradiation. The SDL-Seg algorithm incorporates saliency information in the form of markers' location cues into a U-Net model. The design forces the model to encode the location-related features, which underscores regions with high saliency levels and suppresses low saliency regions. The saliency maps were generated by identifying markers on CT images. Markers' locations were then converted to probability maps using a distance-transformation coupled with a Gaussian filter. Subsequently, the CT images and the corresponding saliency maps formed a multi-channel input for the SDL-Seg network. Our in-house dataset was comprised of 145 prone CT images from 29 post-operative breast cancer patients, who received 5-fraction partial breast irradiation (PBI) regimen on GammaPod. The performance of the proposed method was compared against basic U-Net. Our model achieved mean (standard deviation) of 76.4 %, 6.76 mm, and 1.9 mm for DSC, HD95, and ASD respectively on the test set with computation time of below 11 seconds per one CT volume. SDL-Seg showed superior performance relative to basic U-Net for all the evaluation metrics while preserving low computation cost. The findings demonstrate that SDL-Seg is a promising approach for improving the efficiency and accuracy of the on-line treatment planning procedure of PBI, such as GammaPod based PBI.

Medical imaging analysis plays a critical role in the diagnosis and treatment of various medical conditions. This paper focuses on chest X-ray images and their corresponding radiological reports. It presents a new model that learns a joint X-ray image & report representation. The model is based on a novel alignment scheme between the visual data and the text, which takes into account both local and global information. Furthermore, the model integrates domain-specific information of two types -- lateral images and the consistent visual structure of chest images. Our representation is shown to benefit three types of retrieval tasks: text-image retrieval, class-based retrieval, and phrase-grounding.

Recent advances in segmentation foundation models have enabled accurate and efficient segmentation across a wide range of natural images and videos, but their utility to medical data remains unclear. In this work, we first present a comprehensive benchmarking of the Segment Anything Model 2 (SAM2) across 11 medical image modalities and videos and point out its strengths and weaknesses by comparing it to SAM1 and MedSAM. Then, we develop a transfer learning pipeline and demonstrate SAM2 can be quickly adapted to medical domain by fine-tuning. Furthermore, we implement SAM2 as a 3D slicer plugin and Gradio API for efficient 3D image and video segmentation. The code has been made publicly available at https://github.com/bowang-lab/MedSAM.

Deep learning models have emerged as the cornerstone of medical image segmentation, but their efficacy hinges on the availability of extensive manually labeled datasets and their adaptability to unforeseen categories remains a challenge. Few-shot segmentation (FSS) offers a promising solution by endowing models with the capacity to learn novel classes from limited labeled examples. A leading method for FSS is ALPNet, which compares features between the query image and the few available support segmented images. A key question about using ALPNet is how to design its features. In this work, we delve into the potential of using features from DINOv2, which is a foundational self-supervised learning model in computer vision. Leveraging the strengths of ALPNet and harnessing the feature extraction capabilities of DINOv2, we present a novel approach to few-shot segmentation that not only enhances performance but also paves the way for more robust and adaptable medical image analysis.

Medical image and video segmentation is a critical task for precision medicine, which has witnessed considerable progress in developing task or modality-specific and generalist models for 2D images. However, there have been limited studies on building general-purpose models for 3D images and videos with comprehensive user studies. Here, we present MedSAM2, a promptable segmentation foundation model for 3D image and video segmentation. The model is developed by fine-tuning the Segment Anything Model 2 on a large medical dataset with over 455,000 3D image-mask pairs and 76,000 frames, outperforming previous models across a wide range of organs, lesions, and imaging modalities. Furthermore, we implement a human-in-the-loop pipeline to facilitate the creation of large-scale datasets resulting in, to the best of our knowledge, the most extensive user study to date, involving the annotation of 5,000 CT lesions, 3,984 liver MRI lesions, and 251,550 echocardiogram video frames, demonstrating that MedSAM2 can reduce manual costs by more than 85%. MedSAM2 is also integrated into widely used platforms with user-friendly interfaces for local and cloud deployment, making it a practical tool for supporting efficient, scalable, and high-quality segmentation in both research and healthcare environments.

We propose a minimal path method to simultaneously compute segmentation masks and extract centerlines of tubular structures with line-topology. Minimal path methods are commonly used for the segmentation of tubular structures in a wide variety of applications. Recent methods use features extracted by CNNs, and often outperform methods using hand-tuned features. However, for CNN-based methods, the samples used for training may be generated inappropriately, so that they can be very different from samples encountered during inference. We approach this discrepancy by introducing a novel iterative training scheme, which enables generating better training samples specifically tailored for the minimal path methods without changing existing annotations. In our method, segmentation masks and centerlines are not determined after one another by post-processing, but obtained using the same steps. Our method requires only very few annotated training images. Comparison with seven previous approaches on three public datasets, including satellite images and medical images, shows that our method achieves state-of-the-art results both for segmentation masks and centerlines.

Chest radiography is an extremely powerful imaging modality, allowing for a detailed inspection of a patient's thorax, but requiring specialized training for proper interpretation. With the advent of high performance general purpose computer vision algorithms, the accurate automated analysis of chest radiographs is becoming increasingly of interest to researchers. However, a key challenge in the development of these techniques is the lack of sufficient data. Here we describe MIMIC-CXR-JPG v2.0.0, a large dataset of 377,110 chest x-rays associated with 227,827 imaging studies sourced from the Beth Israel Deaconess Medical Center between 2011 - 2016. Images are provided with 14 labels derived from two natural language processing tools applied to the corresponding free-text radiology reports. MIMIC-CXR-JPG is derived entirely from the MIMIC-CXR database, and aims to provide a convenient processed version of MIMIC-CXR, as well as to provide a standard reference for data splits and image labels. All images have been de-identified to protect patient privacy. The dataset is made freely available to facilitate and encourage a wide range of research in medical computer vision.

The high cure rate of cancer is inextricably linked to physicians' accuracy in diagnosis and treatment, therefore a model that can accomplish high-precision tumor segmentation has become a necessity in many applications of the medical industry. It can effectively lower the rate of misdiagnosis while considerably lessening the burden on clinicians. However, fully automated target organ segmentation is problematic due to the irregular stereo structure of 3D volume organs. As a basic model for this class of real applications, U-Net excels. It can learn certain global and local features, but still lacks the capacity to grasp spatial long-range relationships and contextual information at multiple scales. This paper proposes a tumor segmentation model MPU-Net for patient volume CT images, which is inspired by Transformer with a global attention mechanism. By combining image serialization with the Position Attention Module, the model attempts to comprehend deeper contextual dependencies and accomplish precise positioning. Each layer of the decoder is also equipped with a multi-scale module and a cross-attention mechanism. The capability of feature extraction and integration at different levels has been enhanced, and the hybrid loss function developed in this study can better exploit high-resolution characteristic information. Moreover, the suggested architecture is tested and evaluated on the Liver Tumor Segmentation Challenge 2017 (LiTS 2017) dataset. Compared with the benchmark model U-Net, MPU-Net shows excellent segmentation results. The dice, accuracy, precision, specificity, IOU, and MCC metrics for the best model segmentation results are 92.17%, 99.08%, 91.91%, 99.52%, 85.91%, and 91.74%, respectively. Outstanding indicators in various aspects illustrate the exceptional performance of this framework in automatic medical image segmentation.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Bronchopulmonary dysplasia (BPD) is a chronic lung disease affecting 35% of extremely low birth weight infants. Defined by oxygen dependence at 36 weeks postmenstrual age, it causes lifelong respiratory complications. However, preventive interventions carry severe risks, including neurodevelopmental impairment, ventilator-induced lung injury, and systemic complications. Therefore, early BPD prognosis and prediction of BPD outcome is crucial to avoid unnecessary toxicity in low risk infants. Admission radiographs of extremely preterm infants are routinely acquired within 24h of life and could serve as a non-invasive prognostic tool. In this work, we developed and investigated a deep learning approach using chest X-rays from 163 extremely low-birth-weight infants (leq32 weeks gestation, 401-999g) obtained within 24 hours of birth. We fine-tuned a ResNet-50 pretrained specifically on adult chest radiographs, employing progressive layer freezing with discriminative learning rates to prevent overfitting and evaluated a CutMix augmentation and linear probing. For moderate/severe BPD outcome prediction, our best performing model with progressive freezing, linear probing and CutMix achieved an AUROC of 0.78 pm 0.10, balanced accuracy of 0.69 pm 0.10, and an F1-score of 0.67 pm 0.11. In-domain pre-training significantly outperformed ImageNet initialization (p = 0.031) which confirms domain-specific pretraining to be important for BPD outcome prediction. Routine IRDS grades showed limited prognostic value (AUROC 0.57 pm 0.11), confirming the need of learned markers. Our approach demonstrates that domain-specific pretraining enables accurate BPD prediction from routine day-1 radiographs. Through progressive freezing and linear probing, the method remains computationally feasible for site-level implementation and future federated learning deployments.

The availability of large public datasets and the increased amount of computing power have shifted the interest of the medical community to high-performance algorithms. However, little attention is paid to the quality of the data and their annotations. High performance on benchmark datasets may be reported without considering possible shortcuts or artifacts in the data, besides, models are not tested on subpopulation groups. With this work, we aim to raise awareness about shortcuts problems. We validate previous findings, and present a case study on chest X-rays using two publicly available datasets. We share annotations for a subset of pneumothorax images with drains. We conclude with general recommendations for medical image classification.

Segmenting biomarkers in medical images is crucial for various biotech applications. Despite advances, Transformer and CNN based methods often struggle with variations in staining and morphology, limiting feature extraction. In medical image segmentation, where datasets often have limited sample availability, recent state-of-the-art (SOTA) methods achieve higher accuracy by leveraging pre-trained encoders, whereas end-to-end methods tend to underperform. This is due to challenges in effectively transferring rich multiscale features from encoders to decoders, as well as limitations in decoder efficiency. To address these issues, we propose an architecture that captures multi-scale local and global contextual information and a novel decoder design, which effectively integrates features from the encoder, emphasizes important channels and regions, and reconstructs spatial dimensions to enhance segmentation accuracy. Our method, compatible with various encoders, outperforms SOTA methods, as demonstrated by experiments on four datasets and ablation studies. Specifically, our method achieves absolute performance gains of 2.76% on MoNuSeg, 3.12% on DSB, 2.87% on Electron Microscopy, and 4.03% on TNBC datasets compared to existing SOTA methods. Code: https://github.com/saadwazir/MCADS-Decoder

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

Lung cancer is responsible for 21% of cancer deaths in the UK and five-year survival rates are heavily influenced by the stage the cancer was identified at. Recent studies have demonstrated the capability of AI methods for accurate and early diagnosis of lung cancer from routine scans. However, this evidence has not translated into clinical practice with one barrier being a lack of interpretable models. This study investigates the application Variational Autoencoders (VAEs), a type of generative AI model, to lung cancer lesions. Proposed models were trained on lesions extracted from 3D CT scans in the LIDC-IDRI public dataset. Latent vector representations of 2D slices produced by the VAEs were explored through clustering to justify their quality and used in an MLP classifier model for lung cancer diagnosis, the best model achieved state-of-the-art metrics of AUC 0.98 and 93.1% accuracy. Cluster analysis shows the VAE latent space separates the dataset of malignant and benign lesions based on meaningful feature components including tumour size, shape, patient and malignancy class. We also include a comparative analysis of the standard Gaussian VAE (GVAE) and the more recent Dirichlet VAE (DirVAE), which replaces the prior with a Dirichlet distribution to encourage a more explainable latent space with disentangled feature representation. Finally, we demonstrate the potential for latent space traversals corresponding to clinically meaningful feature changes.

The development of larger models for medical image analysis has led to increased performance. However, it also affected our ability to explain and validate model decisions. Models can use non-relevant parts of images, also called spurious correlations or shortcuts, to obtain high performance on benchmark datasets but fail in real-world scenarios. In this work, we challenge the capacity of convolutional neural networks (CNN) to classify chest X-rays and eye fundus images while masking out clinically relevant parts of the image. We show that all models trained on the PadChest dataset, irrespective of the masking strategy, are able to obtain an Area Under the Curve (AUC) above random. Moreover, the models trained on full images obtain good performance on images without the region of interest (ROI), even superior to the one obtained on images only containing the ROI. We also reveal a possible spurious correlation in the Chaksu dataset while the performances are more aligned with the expectation of an unbiased model. We go beyond the performance analysis with the usage of the explainability method SHAP and the analysis of embeddings. We asked a radiology resident to interpret chest X-rays under different masking to complement our findings with clinical knowledge. Our code is available at https://github.com/TheoSourget/MMC_Masking and https://github.com/TheoSourget/MMC_Masking_EyeFundus

We present a labeled large-scale, high resolution chest x-ray dataset for the automated exploration of medical images along with their associated reports. This dataset includes more than 160,000 images obtained from 67,000 patients that were interpreted and reported by radiologists at Hospital San Juan Hospital (Spain) from 2009 to 2017, covering six different position views and additional information on image acquisition and patient demography. The reports were labeled with 174 different radiographic findings, 19 differential diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and mapped onto standard Unified Medical Language System (UMLS) terminology. Of these reports, 27% were manually annotated by trained physicians and the remaining set was labeled using a supervised method based on a recurrent neural network with attention mechanisms. The labels generated were then validated in an independent test set achieving a 0.93 Micro-F1 score. To the best of our knowledge, this is one of the largest public chest x-ray database suitable for training supervised models concerning radiographs, and the first to contain radiographic reports in Spanish. The PadChest dataset can be downloaded from http://bimcv.cipf.es/bimcv-projects/padchest/.

Automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical, coarse-to-fine classification on image patches and regions, i.e. superpixels. We first present a dense labeling of local image patches via P{-}ConvNet and nearest neighbor fusion. Then we describe a regional ConvNet (R_1{-}ConvNet) that samples a set of bounding boxes around each image superpixel at different scales of contexts in a "zoom-out" fashion. Our ConvNets learn to assign class probabilities for each superpixel region of being pancreas. Last, we study a stacked R_2{-}ConvNet leveraging the joint space of CT intensities and the P{-}ConvNet dense probability maps. Both 3D Gaussian smoothing and 2D conditional random fields are exploited as structured predictions for post-processing. We evaluate on CT images of 82 patients in 4-fold cross-validation. We achieve a Dice Similarity Coefficient of 83.6pm6.3% in training and 71.8pm10.7% in testing.

Segment Anything Model (SAM) has achieved impressive results for natural image segmentation with input prompts such as points and bounding boxes. Its success largely owes to massive labeled training data. However, directly applying SAM to medical image segmentation cannot perform well because SAM lacks medical knowledge -- it does not use medical images for training. To incorporate medical knowledge into SAM, we introduce SA-Med2D-20M, a large-scale segmentation dataset of 2D medical images built upon numerous public and private datasets. It consists of 4.6 million 2D medical images and 19.7 million corresponding masks, covering almost the whole body and showing significant diversity. This paper describes all the datasets collected in SA-Med2D-20M and details how to process these datasets. Furthermore, comprehensive statistics of SA-Med2D-20M are presented to facilitate the better use of our dataset, which can help the researchers build medical vision foundation models or apply their models to downstream medical applications. We hope that the large scale and diversity of SA-Med2D-20M can be leveraged to develop medical artificial intelligence for enhancing diagnosis, medical image analysis, knowledge sharing, and education. The data with the redistribution license is publicly available at https://github.com/OpenGVLab/SAM-Med2D.

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

In this work we address the problem of landmark-based segmentation for anatomical structures. We propose HybridGNet, an encoder-decoder neural architecture which combines standard convolutions for image feature encoding, with graph convolutional neural networks to decode plausible representations of anatomical structures. We benchmark the proposed architecture considering other standard landmark and pixel-based models for anatomical segmentation in chest x-ray images, and found that HybridGNet is more robust to image occlusions. We also show that it can be used to construct landmark-based segmentations from pixel level annotations. Our experimental results suggest that HybridGNet produces accurate and anatomically plausible landmark-based segmentations, by naturally incorporating shape constraints within the decoding process via spectral convolutions.

Curating datasets for object segmentation is a difficult task. With the advent of large-scale pre-trained generative models, conditional image generation has been given a significant boost in result quality and ease of use. In this paper, we present a novel method that enables the generation of general foreground-background segmentation models from simple textual descriptions, without requiring segmentation labels. We leverage and explore pre-trained latent diffusion models, to automatically generate weak segmentation masks for concepts and objects. The masks are then used to fine-tune the diffusion model on an inpainting task, which enables fine-grained removal of the object, while at the same time providing a synthetic foreground and background dataset. We demonstrate that using this method beats previous methods in both discriminative and generative performance and closes the gap with fully supervised training while requiring no pixel-wise object labels. We show results on the task of segmenting four different objects (humans, dogs, cars, birds) and a use case scenario in medical image analysis. The code is available at https://github.com/MischaD/fobadiffusion.

Modern studies in radiograph representation learning rely on either self-supervision to encode invariant semantics or associated radiology reports to incorporate medical expertise, while the complementarity between them is barely noticed. To explore this, we formulate the self- and report-completion as two complementary objectives and present a unified framework based on masked record modeling (MRM). In practice, MRM reconstructs masked image patches and masked report tokens following a multi-task scheme to learn knowledge-enhanced semantic representations. With MRM pre-training, we obtain pre-trained models that can be well transferred to various radiography tasks. Specifically, we find that MRM offers superior performance in label-efficient fine-tuning. For instance, MRM achieves 88.5% mean AUC on CheXpert using 1% labeled data, outperforming previous R^2L methods with 100% labels. On NIH ChestX-ray, MRM outperforms the best performing counterpart by about 3% under small labeling ratios. Besides, MRM surpasses self- and report-supervised pre-training in identifying the pneumonia type and the pneumothorax area, sometimes by large margins.

The Segment Anything Model (SAM) has recently gained popularity in the field of image segmentation due to its impressive capabilities in various segmentation tasks and its prompt-based interface. However, recent studies and individual experiments have shown that SAM underperforms in medical image segmentation, since the lack of the medical specific knowledge. This raises the question of how to enhance SAM's segmentation capability for medical images. In this paper, instead of fine-tuning the SAM model, we propose the Medical SAM Adapter (Med-SA), which incorporates domain-specific medical knowledge into the segmentation model using a light yet effective adaptation technique. In Med-SA, we propose Space-Depth Transpose (SD-Trans) to adapt 2D SAM to 3D medical images and Hyper-Prompting Adapter (HyP-Adpt) to achieve prompt-conditioned adaptation. We conduct comprehensive evaluation experiments on 17 medical image segmentation tasks across various image modalities. Med-SA outperforms several state-of-the-art (SOTA) medical image segmentation methods, while updating only 2\% of the parameters. Our code is released at https://github.com/KidsWithTokens/Medical-SAM-Adapter.

The success of Deep Neural Network (DNN) models significantly depends on the quality of provided annotations. In medical image segmentation, for example, having multiple expert annotations for each data point is common to minimize subjective annotation bias. Then, the goal of estimation is to filter out the label noise and recover the ground-truth masks, which are not explicitly given. This paper proposes a probabilistic model for noisy observations that allows us to build a confident classification and segmentation models. To accomplish it, we explicitly model label noise and introduce a new information-based regularization that pushes the network to recover the ground-truth labels. In addition, for segmentation task we adjust the loss function by prioritizing learning in high-confidence regions where all the annotators agree on labeling. We evaluate the proposed method on a series of classification tasks such as noisy versions of MNIST, CIFAR-10, Fashion-MNIST datasets as well as CIFAR-10N, which is real-world dataset with noisy human annotations. Additionally, for segmentation task, we consider several medical imaging datasets, such as, LIDC and RIGA that reflect real-world inter-variability among multiple annotators. Our experiments show that our algorithm outperforms state-of-the-art solutions for the considered classification and segmentation problems.

In this study, we evaluate the performance of the Segment Anything Model (SAM) in clinical radiotherapy. Our results indicate that SAM's 'segment anything' mode can achieve clinically acceptable segmentation results in most organs-at-risk (OARs) with Dice scores higher than 0.7. SAM's 'box prompt' mode further improves the Dice scores by 0.1 to 0.5. Considering the size of the organ and the clarity of its boundary, SAM displays better performance for large organs with clear boundaries but performs worse for smaller organs with unclear boundaries. Given that SAM, a model pre-trained purely on natural images, can handle the delineation of OARs from medical images with clinically acceptable accuracy, these results highlight SAM's robust generalization capabilities with consistent accuracy in automatic segmentation for radiotherapy. In other words, SAM can achieve delineation of different OARs at different sites using a generic automatic segmentation model. SAM's generalization capabilities across different disease sites suggest that it is technically feasible to develop a generic model for automatic segmentation in radiotherapy.

Medical image segmentation is a key task in the imaging workflow, influencing many image-based decisions. Traditional, fully-supervised segmentation models rely on large amounts of labeled training data, typically obtained through manual annotation, which can be an expensive, time-consuming, and error-prone process. This signals a need for accurate, automatic, and annotation-efficient methods of training these models. We propose ADA-SAM (automated, domain-specific, and adaptive segment anything model), a novel multitask learning framework for medical image segmentation that leverages class activation maps from an auxiliary classifier to guide the predictions of the semi-supervised segmentation branch, which is based on the Segment Anything (SAM) framework. Additionally, our ADA-SAM model employs a novel gradient feedback mechanism to create a learnable connection between the segmentation and classification branches by using the segmentation gradients to guide and improve the classification predictions. We validate ADA-SAM on real-world clinical data collected during rehabilitation trials, and demonstrate that our proposed method outperforms both fully-supervised and semi-supervised baselines by double digits in limited label settings. Our code is available at: https://github.com/tbwa233/ADA-SAM.

Current 3D scene segmentation methods are heavily dependent on manually annotated 3D training datasets. Such manual annotations are labor-intensive, and often lack fine-grained details. Importantly, models trained on this data typically struggle to recognize object classes beyond the annotated classes, i.e., they do not generalize well to unseen domains and require additional domain-specific annotations. In contrast, 2D foundation models demonstrate strong generalization and impressive zero-shot abilities, inspiring us to incorporate these characteristics from 2D models into 3D models. Therefore, we explore the use of image segmentation foundation models to automatically generate training labels for 3D segmentation. We propose Segment3D, a method for class-agnostic 3D scene segmentation that produces high-quality 3D segmentation masks. It improves over existing 3D segmentation models (especially on fine-grained masks), and enables easily adding new training data to further boost the segmentation performance -- all without the need for manual training labels.

The detailed images produced by Magnetic Resonance Imaging (MRI) provide life-critical information for the diagnosis and treatment of prostate cancer. To provide standardized acquisition, interpretation and usage of the complex MRI images, the PI-RADS v2 guideline was proposed. An automated segmentation following the guideline facilitates consistent and precise lesion detection, staging and treatment. The guideline recommends a division of the prostate into four zones, PZ (peripheral zone), TZ (transition zone), DPU (distal prostatic urethra) and AFS (anterior fibromuscular stroma). Not every zone shares a boundary with the others and is present in every slice. Further, the representations captured by a single model might not suffice for all zones. This motivated us to design a dual-branch convolutional neural network (CNN), where each branch captures the representations of the connected zones separately. Further, the representations from different branches act complementary to each other at the second stage of training, where they are fine-tuned through an unsupervised loss. The loss penalises the difference in predictions from the two branches for the same class. We also incorporate multi-task learning in our framework to further improve the segmentation accuracy. The proposed approach improves the segmentation accuracy of the baseline (mean absolute symmetric distance) by 7.56%, 11.00%, 58.43% and 19.67% for PZ, TZ, DPU and AFS zones respectively.

The emergence of large models, also known as foundation models, has brought significant advancements to AI research. One such model is Segment Anything (SAM), which is designed for image segmentation tasks. However, as with other foundation models, our experimental findings suggest that SAM may fail or perform poorly in certain segmentation tasks, such as shadow detection and camouflaged object detection (concealed object detection). This study first paves the way for applying the large pre-trained image segmentation model SAM to these downstream tasks, even in situations where SAM performs poorly. Rather than fine-tuning the SAM network, we propose SAM-Adapter, which incorporates domain-specific information or visual prompts into the segmentation network by using simple yet effective adapters. By integrating task-specific knowledge with general knowledge learnt by the large model, SAM-Adapter can significantly elevate the performance of SAM in challenging tasks as shown in extensive experiments. We can even outperform task-specific network models and achieve state-of-the-art performance in the task we tested: camouflaged object detection, shadow detection. We also tested polyp segmentation (medical image segmentation) and achieves better results. We believe our work opens up opportunities for utilizing SAM in downstream tasks, with potential applications in various fields, including medical image processing, agriculture, remote sensing, and more.

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.

Whole-heart segmentation from CT and MRI scans is crucial for cardiovascular disease analysis, yet existing methods struggle with modality-specific biases and the need for extensive labeled datasets. To address these challenges, we propose a foundation model for whole-heart segmentation using a self-supervised learning (SSL) framework based on a student-teacher architecture. Our model is pretrained on a large, unlabeled dataset of CT and MRI scans, leveraging the xLSTM backbone to capture long-range spatial dependencies and complex anatomical structures in 3D medical images. By incorporating multi-modal pretraining, our approach ensures strong generalization across both CT and MRI modalities, mitigating modality-specific variations and improving segmentation accuracy in diverse clinical settings. The use of large-scale unlabeled data significantly reduces the dependency on manual annotations, enabling robust performance even with limited labeled data. We further introduce an xLSTM-UNet-based architecture for downstream whole-heart segmentation tasks, demonstrating its effectiveness on few-label CT and MRI datasets. Our results validate the robustness and adaptability of the proposed model, highlighting its potential for advancing automated whole-heart segmentation in medical imaging.

Quantitative tools are increasingly appealing for decision support in healthcare, driven by the growing capabilities of advanced AI systems. However, understanding the predictive uncertainties surrounding a tool's output is crucial for decision-makers to ensure reliable and transparent decisions. In this paper, we present a case study on pulmonary nodule detection for lung cancer screening, enhancing an advanced detection model with an uncertainty quantification technique called conformal risk control (CRC). We demonstrate that prediction sets with conformal guarantees are attractive measures of predictive uncertainty in the safety-critical healthcare domain, allowing end-users to achieve arbitrary validity by trading off false positives and providing formal statistical guarantees on model performance. Among ground-truth nodules annotated by at least three radiologists, our model achieves a sensitivity that is competitive with that generally achieved by individual radiologists, with a slight increase in false positives. Furthermore, we illustrate the risks of using off-the-shelve prediction models when faced with ontological uncertainty, such as when radiologists disagree on what constitutes the ground truth on pulmonary nodules.

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

Segment Anything Model (SAM) has demonstrated impressive performance on a wide range of natural image segmentation tasks. However, its performance significantly deteriorates when directly applied to medical domain, due to the remarkable differences between natural images and medical images. Some researchers have attempted to train SAM on large scale medical datasets. However, poor zero-shot performance is observed from the experimental results. In this context, inspired by the superior performance of U-Net-like models in medical image segmentation, we propose SAMUNet, a new foundation model which incorporates U-Net to the original SAM, to fully leverage the powerful contextual modeling ability of convolutions. To be specific, we parallel a convolutional branch in the image encoder, which is trained independently with the vision Transformer branch frozen. Additionally, we employ multi-scale fusion in the mask decoder, to facilitate accurate segmentation of objects with different scales. We train SAM-UNet on SA-Med2D-16M, the largest 2-dimensional medical image segmentation dataset to date, yielding a universal pretrained model for medical images. Extensive experiments are conducted to evaluate the performance of the model, and state-of-the-art result is achieved, with a dice similarity coefficient score of 0.883 on SA-Med2D-16M dataset. Specifically, in zero-shot segmentation experiments, our model not only significantly outperforms previous large medical SAM models across all modalities, but also substantially mitigates the performance degradation seen on unseen modalities. It should be highlighted that SAM-UNet is an efficient and extensible foundation model, which can be further fine-tuned for other downstream tasks in medical community. The code is available at https://github.com/Hhankyangg/sam-unet.

The performance of image segmentation models has historically been constrained by the high cost of collecting large-scale annotated data. The Segment Anything Model (SAM) alleviates this original problem through a promptable, semantics-agnostic, segmentation paradigm and yet still requires manual visual-prompts or complex domain-dependent prompt-generation rules to process a new image. Towards reducing this new burden, our work investigates the task of object segmentation when provided with, alternatively, only a small set of reference images. Our key insight is to leverage strong semantic priors, as learned by foundation models, to identify corresponding regions between a reference and a target image. We find that correspondences enable automatic generation of instance-level segmentation masks for downstream tasks and instantiate our ideas via a multi-stage, training-free method incorporating (1) memory bank construction; (2) representation aggregation and (3) semantic-aware feature matching. Our experiments show significant improvements on segmentation metrics, leading to state-of-the-art performance on COCO FSOD (36.8% nAP), PASCAL VOC Few-Shot (71.2% nAP50) and outperforming existing training-free approaches on the Cross-Domain FSOD benchmark (22.4% nAP).

The recently introduced Segment Anything Model (SAM) combines a clever architecture and large quantities of training data to obtain remarkable image segmentation capabilities. However, it fails to reproduce such results for Out-Of-Distribution (OOD) domains such as medical images. Moreover, while SAM is conditioned on either a mask or a set of points, it may be desirable to have a fully automatic solution. In this work, we replace SAM's conditioning with an encoder that operates on the same input image. By adding this encoder and without further fine-tuning SAM, we obtain state-of-the-art results on multiple medical images and video benchmarks. This new encoder is trained via gradients provided by a frozen SAM. For inspecting the knowledge within it, and providing a lightweight segmentation solution, we also learn to decode it into a mask by a shallow deconvolution network.

Accurate segmentation is essential for echocardiography-based assessment of cardiovascular diseases (CVDs). However, the variability among sonographers and the inherent challenges of ultrasound images hinder precise segmentation. By leveraging the joint representation of image and text modalities, Vision-Language Segmentation Models (VLSMs) can incorporate rich contextual information, potentially aiding in accurate and explainable segmentation. However, the lack of readily available data in echocardiography hampers the training of VLSMs. In this study, we explore using synthetic datasets from Semantic Diffusion Models (SDMs) to enhance VLSMs for echocardiography segmentation. We evaluate results for two popular VLSMs (CLIPSeg and CRIS) using seven different kinds of language prompts derived from several attributes, automatically extracted from echocardiography images, segmentation masks, and their metadata. Our results show improved metrics and faster convergence when pretraining VLSMs on SDM-generated synthetic images before finetuning on real images. The code, configs, and prompts are available at https://github.com/naamiinepal/synthetic-boost.

The pandemic resulted in vast repositories of unstructured data, including radiology reports, due to increased medical examinations. Previous research on automated diagnosis of COVID-19 primarily focuses on X-ray images, despite their lower precision compared to computed tomography (CT) scans. In this work, we leverage unstructured data from a hospital and harness the fine-grained details offered by CT scans to perform zero-shot multi-label classification based on contrastive visual language learning. In collaboration with human experts, we investigate the effectiveness of multiple zero-shot models that aid radiologists in detecting pulmonary embolisms and identifying intricate lung details like ground glass opacities and consolidations. Our empirical analysis provides an overview of the possible solutions to target such fine-grained tasks, so far overlooked in the medical multimodal pretraining literature. Our investigation promises future advancements in the medical image analysis community by addressing some challenges associated with unstructured data and fine-grained multi-label classification.

Collective insights from a group of experts have always proven to outperform an individual's best diagnostic for clinical tasks. For the task of medical image segmentation, existing research on AI-based alternatives focuses more on developing models that can imitate the best individual rather than harnessing the power of expert groups. In this paper, we introduce a single diffusion model-based approach that produces multiple plausible outputs by learning a distribution over group insights. Our proposed model generates a distribution of segmentation masks by leveraging the inherent stochastic sampling process of diffusion using only minimal additional learning. We demonstrate on three different medical image modalities- CT, ultrasound, and MRI that our model is capable of producing several possible variants while capturing the frequencies of their occurrences. Comprehensive results show that our proposed approach outperforms existing state-of-the-art ambiguous segmentation networks in terms of accuracy while preserving naturally occurring variation. We also propose a new metric to evaluate the diversity as well as the accuracy of segmentation predictions that aligns with the interest of clinical practice of collective insights.

In some medical imaging tasks and other settings where only small parts of the image are informative for the classification task, traditional CNNs can sometimes struggle to generalise. Manually annotated Regions of Interest (ROI) are sometimes used to isolate the most informative parts of the image. However, these are expensive to collect and may vary significantly across annotators. To overcome these issues, we propose a framework that employs saliency maps to obtain soft spatial attention masks that modulate the image features at different scales. We refer to our method as Adversarial Counterfactual Attention (ACAT). ACAT increases the baseline classification accuracy of lesions in brain CT scans from 71.39% to 72.55% and of COVID-19 related findings in lung CT scans from 67.71% to 70.84% and exceeds the performance of competing methods. We investigate the best way to generate the saliency maps employed in our architecture and propose a way to obtain them from adversarially generated counterfactual images. They are able to isolate the area of interest in brain and lung CT scans without using any manual annotations. In the task of localising the lesion location out of 6 possible regions, they obtain a score of 65.05% on brain CT scans, improving the score of 61.29% obtained with the best competing method.

Segment anything model (SAM) has revolutionized natural image segmentation, but its performance on medical images is limited. This work presents MedSAM, the first attempt at extending the success of SAM to medical images, with the goal of creating a universal tool for the segmentation of various medical targets. Specifically, we first curate a large-scale medical image dataset, encompassing over 200,000 masks across 11 different modalities. Then, we develop a simple fine-tuning method to adapt SAM to general medical image segmentation. Comprehensive experiments on 21 3D segmentation tasks and 9 2D segmentation tasks demonstrate that MedSAM outperforms the default SAM model with an average Dice Similarity Coefficient (DSC) of 22.5% and 17.6% on 3D and 2D segmentation tasks, respectively. The code and trained model are publicly available at https://github.com/bowang-lab/MedSAM.

Conventional medical image segmentation methods have been found inadequate in facilitating physicians with the identification of specific lesions for diagnosis and treatment. Given the utility of text as an instructional format, we introduce a novel task termed Medical Image Referring Segmentation (MIRS), which requires segmenting specified lesions in images based on the given language expressions. Due to the varying object scales in medical images, MIRS demands robust vision-language modeling and comprehensive multi-scale interaction for precise localization and segmentation under linguistic guidance. However, existing medical image segmentation methods fall short in meeting these demands, resulting in insufficient segmentation accuracy. In response, we propose an approach named Language-guided Scale-aware MedSegmentor (LSMS), incorporating two appealing designs: (1)~a Scale-aware Vision-Language Attention module that leverages diverse convolutional kernels to acquire rich visual knowledge and interact closely with linguistic features, thereby enhancing lesion localization capability; (2)~a Full-Scale Decoder that globally models multi-modal features across various scales, capturing complementary information between scales to accurately outline lesion boundaries. Addressing the lack of suitable datasets for MIRS, we constructed a vision-language medical dataset called Reference Hepatic Lesion Segmentation (RefHL-Seg). This dataset comprises 2,283 abdominal CT slices from 231 cases, with corresponding textual annotations and segmentation masks for various liver lesions in images. We validated the performance of LSMS for MIRS and conventional medical image segmentation tasks across various datasets. Our LSMS consistently outperforms on all datasets with lower computational costs. The code and datasets will be released.

While deep learning models have become the predominant method for medical image segmentation, they are typically not capable of generalizing to unseen segmentation tasks involving new anatomies, image modalities, or labels. Given a new segmentation task, researchers generally have to train or fine-tune models, which is time-consuming and poses a substantial barrier for clinical researchers, who often lack the resources and expertise to train neural networks. We present UniverSeg, a method for solving unseen medical segmentation tasks without additional training. Given a query image and example set of image-label pairs that define a new segmentation task, UniverSeg employs a new Cross-Block mechanism to produce accurate segmentation maps without the need for additional training. To achieve generalization to new tasks, we have gathered and standardized a collection of 53 open-access medical segmentation datasets with over 22,000 scans, which we refer to as MegaMedical. We used this collection to train UniverSeg on a diverse set of anatomies and imaging modalities. We demonstrate that UniverSeg substantially outperforms several related methods on unseen tasks, and thoroughly analyze and draw insights about important aspects of the proposed system. The UniverSeg source code and model weights are freely available at https://universeg.csail.mit.edu

Achieving robust performance and fairness across diverse patient populations remains a challenge in developing clinically deployable deep learning models for diagnostic imaging. Synthetic data generation has emerged as a promising strategy to address limitations in dataset scale and diversity. We introduce RoentGen-v2, a text-to-image diffusion model for chest radiographs that enables fine-grained control over both radiographic findings and patient demographic attributes, including sex, age, and race/ethnicity. RoentGen-v2 is the first model to generate clinically plausible images with demographic conditioning, facilitating the creation of a large, demographically balanced synthetic dataset comprising over 565,000 images. We use this large synthetic dataset to evaluate optimal training pipelines for downstream disease classification models. In contrast to prior work that combines real and synthetic data naively, we propose an improved training strategy that leverages synthetic data for supervised pretraining, followed by fine-tuning on real data. Through extensive evaluation on over 137,000 chest radiographs from five institutions, we demonstrate that synthetic pretraining consistently improves model performance, generalization to out-of-distribution settings, and fairness across demographic subgroups. Across datasets, synthetic pretraining led to a 6.5% accuracy increase in the performance of downstream classification models, compared to a modest 2.7% increase when naively combining real and synthetic data. We observe this performance improvement simultaneously with the reduction of the underdiagnosis fairness gap by 19.3%. These results highlight the potential of synthetic imaging to advance equitable and generalizable medical deep learning under real-world data constraints. We open source our code, trained models, and synthetic dataset at https://github.com/StanfordMIMI/RoentGen-v2 .

Idiopathic pulmonary fibrosis (IPF) is a progressive disease that irreversibly transforms lung tissue into rigid fibrotic structures, leading to debilitating symptoms such as shortness of breath and chronic fatigue. The heterogeneity and complexity of this disease, particularly regarding its severity and progression rate, have made predicting its future course a complex and challenging task. Besides, traditional diagnostic methods based on clinical evaluations and imaging have limitations in capturing the disease's complexity. Using the Kaggle Pulmonary Fibrosis Progression dataset, which includes computed tomography images, and clinical information, the model predicts changes in forced vital capacity (FVC), a key progression indicator. Our method uses a proposed context-aware sequential-parallel hybrid transformer model and clinical information enrichment for its prediction. The proposed method achieved a Laplace Log-Likelihood score of -6.508, outperforming prior methods and demonstrating superior predictive capabilities. These results highlight the potential of advanced deep learning techniques to provide more accurate and timely predictions, offering a transformative approach to the diagnosis and management of IPF, with implications for improved patient outcomes and therapeutic advancements.

Accurate segmentation of regions of interest in biomedical images holds substantial value in image analysis. Although several foundation models for biomedical segmentation have currently achieved excellent performance on certain datasets, they typically demonstrate sub-optimal performance on unseen domain data. We owe the deficiency to lack of vision-language knowledge before segmentation. Multimodal Large Language Models (MLLMs) bring outstanding understanding and reasoning capabilities to multimodal tasks, which inspires us to leverage MLLMs to inject Vision-Language Knowledge (VLK), thereby enabling vision models to demonstrate superior generalization capabilities on cross-domain datasets. In this paper, we propose using MLLMs to guide SAM in learning microscopy crose-domain data, unifying Segment Anything in Microscopy, named uLLSAM. Specifically, we propose the Vision-Language Semantic Alignment (VLSA) module, which injects VLK into Segment Anything Model (SAM). We find that after SAM receives global VLK prompts, its performance improves significantly, but there are deficiencies in boundary contour perception. Therefore, we further propose Semantic Boundary Regularization (SBR) to prompt SAM. Our method achieves performance improvements of 7.71% in Dice and 12.10% in SA across 9 in-domain microscopy datasets, achieving state-of-the-art performance. Our method also demonstrates improvements of 6.79% in Dice and 10.08% in SA across 10 out-ofdomain datasets, exhibiting strong generalization capabilities. Code is available at https://github.com/ieellee/uLLSAM.

State Space Models (SSMs), especially Mamba, have shown great promise in medical image segmentation due to their ability to model long-range dependencies with linear computational complexity. However, accurate medical image segmentation requires the effective learning of both multi-scale detailed feature representations and global contextual dependencies. Although existing works have attempted to address this issue by integrating CNNs and SSMs to leverage their respective strengths, they have not designed specialized modules to effectively capture multi-scale feature representations, nor have they adequately addressed the directional sensitivity problem when applying Mamba to 2D image data. To overcome these limitations, we propose a Multi-Scale Vision Mamba UNet model for medical image segmentation, termed MSVM-UNet. Specifically, by introducing multi-scale convolutions in the VSS blocks, we can more effectively capture and aggregate multi-scale feature representations from the hierarchical features of the VMamba encoder and better handle 2D visual data. Additionally, the large kernel patch expanding (LKPE) layers achieve more efficient upsampling of feature maps by simultaneously integrating spatial and channel information. Extensive experiments on the Synapse and ACDC datasets demonstrate that our approach is more effective than some state-of-the-art methods in capturing and aggregating multi-scale feature representations and modeling long-range dependencies between pixels.

This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.

Diffusion models have been used extensively for high quality image and video generation tasks. In this paper, we propose a novel conditional diffusion model with spatial attention and latent embedding (cDAL) for medical image segmentation. In cDAL, a convolutional neural network (CNN) based discriminator is used at every time-step of the diffusion process to distinguish between the generated labels and the real ones. A spatial attention map is computed based on the features learned by the discriminator to help cDAL generate more accurate segmentation of discriminative regions in an input image. Additionally, we incorporated a random latent embedding into each layer of our model to significantly reduce the number of training and sampling time-steps, thereby making it much faster than other diffusion models for image segmentation. We applied cDAL on 3 publicly available medical image segmentation datasets (MoNuSeg, Chest X-ray and Hippocampus) and observed significant qualitative and quantitative improvements with higher Dice scores and mIoU over the state-of-the-art algorithms. The source code is publicly available at https://github.com/Hejrati/cDAL/.

When developing deep neural networks for segmenting intraoperative ultrasound images, several practical issues are encountered frequently, such as the presence of ultrasound frames that do not contain regions of interest and the high variance in ground-truth labels. In this study, we evaluate the utility of a pre-screening classification network prior to the segmentation network. Experimental results demonstrate that such a classifier, minimising frame classification errors, was able to directly impact the number of false positive and false negative frames. Importantly, the segmentation accuracy on the classifier-selected frames, that would be segmented, remains comparable to or better than those from standalone segmentation networks. Interestingly, the efficacy of the pre-screening classifier was affected by the sampling methods for training labels from multiple observers, a seemingly independent problem. We show experimentally that a previously proposed approach, combining random sampling and consensus labels, may need to be adapted to perform well in our application. Furthermore, this work aims to share practical experience in developing a machine learning application that assists highly variable interventional imaging for prostate cancer patients, to present robust and reproducible open-source implementations, and to report a set of comprehensive results and analysis comparing these practical, yet important, options in a real-world clinical application.

Medical image segmentation methods downsample images for feature extraction and then upsample them to restore resolution for pixel-level predictions. In such a schema, upsample technique is vital in restoring information for better performance. However, existing upsample techniques leverage little information from downsampling paths. The local and detailed feature from the shallower layer such as boundary and tissue texture is particularly more important in medical segmentation compared with natural image segmentation. To this end, we propose a novel upsample approach for medical image segmentation, Window Attention Upsample (WAU), which upsamples features conditioned on local and detailed features from downsampling path in local windows by introducing attention decoders of Transformer. WAU could serve as a general upsample method and be incorporated into any segmentation model that possesses lateral connections. We first propose the Attention Upsample which consists of Attention Decoder (AD) and bilinear upsample. AD leverages pixel-level attention to model long-range dependency and global information for a better upsample. Bilinear upsample is introduced as the residual connection to complement the upsampled features. Moreover, considering the extensive memory and computation cost of pixel-level attention, we further design a window attention scheme to restrict attention computation in local windows instead of the global range. We evaluate our method (WAU) on classic U-Net structure with lateral connections and achieve state-of-the-art performance on Synapse multi-organ segmentation, Medical Segmentation Decathlon (MSD) Brain, and Automatic Cardiac Diagnosis Challenge (ACDC) datasets. We also validate the effectiveness of our method on multiple classic architectures and achieve consistent improvement.

The convolutional neural network-based methods have become more and more popular for medical image segmentation due to their outstanding performance. However, they struggle with capturing long-range dependencies, which are essential for accurately modeling global contextual correlations. Thanks to the ability to model long-range dependencies by expanding the receptive field, the transformer-based methods have gained prominence. Inspired by this, we propose an advanced 2D feature extraction method by combining the convolutional neural network and Transformer architectures. More specifically, we introduce a parallelized encoder structure, where one branch uses ResNet to extract local information from images, while the other branch uses Transformer to extract global information. Furthermore, we integrate pyramid structures into the Transformer to extract global information at varying resolutions, especially in intensive prediction tasks. To efficiently utilize the different information in the parallelized encoder at the decoder stage, we use a channel attention module to merge the features of the encoder and propagate them through skip connections and bottlenecks. Intensive numerical experiments are performed on both aortic vessel tree, cardiac, and multi-organ datasets. By comparing with state-of-the-art medical image segmentation methods, our method is shown with better segmentation accuracy, especially on small organs. The code is publicly available on https://github.com/HongkunSun/ParaTransCNN.