Cardiac image segmentation is essential for automated cardiac function assessment and monitoring of changes in cardiac structures over time. Inspired by coarse-to-fine approaches in image analysis, we propose a novel multitask compositional segmentation approach that can simultaneously localize the heart in a cardiac image and perform part-based segmentation of different regions of interest. We demonstrate that this compositional approach achieves better results than direct segmentation of the anatomies. Further, we propose a novel Cross-Modal Feature Integration (CMFI) module to leverage the metadata related to cardiac imaging collected during image acquisition. We perform experiments on two different modalities, MRI and ultrasound, using public datasets, Multi-disease, Multi-View, and Multi-Centre (M&Ms-2) and Multi-structure Ultrasound Segmentation (CAMUS) data, to showcase the efficiency of the proposed compositional segmentation method and Cross-Modal Feature Integration module incorporating metadata within the proposed compositional segmentation network. The source code is available: https://github.com/kabbas570/CompSeg-MetaData.
Self-Supervised Learning (SSL) presents an exciting opportunity to unlock the potential of vast, untapped clinical datasets, for various downstream applications that suffer from the scarcity of labeled data. While SSL has revolutionized fields like natural language processing and computer vision, its adoption in 3D medical image computing has been limited by three key pitfalls: Small pre-training dataset sizes, architectures inadequate for 3D medical image analysis, and insufficient evaluation practices. In this paper, we address these issues by i) leveraging a large-scale dataset of 39k 3D brain MRI volumes and ii) using a Residual Encoder U-Net architecture within the state-of-the-art nnU-Net framework. iii) A robust development framework, incorporating 5 development and 8 testing brain MRI segmentation datasets, allowed performance-driven design decisions to optimize the simple concept of Masked Auto Encoders (MAEs) for 3D CNNs. The resulting model not only surpasses previous SSL methods but also outperforms the strong nnU-Net baseline by an average of approximately 3 Dice points setting a new state-of-the-art. Our code and models are made available here.
Medical image segmentation is pivotal in healthcare, enhancing diagnostic accuracy, informing treatment strategies, and tracking disease progression. This process allows clinicians to extract critical information from visual data, enabling personalized patient care. However, developing neural networks for segmentation remains challenging, especially when preserving image resolution, which is essential in detecting subtle details that influence diagnoses. Moreover, the lack of transparency in these deep learning models has slowed their adoption in clinical practice. Efforts in model interpretability are increasingly focused on making these models' decision-making processes more transparent. In this paper, we introduce MAPUNetR, a novel architecture that synergizes the strengths of transformer models with the proven U-Net framework for medical image segmentation. Our model addresses the resolution preservation challenge and incorporates attention maps highlighting segmented regions, increasing accuracy and interpretability. Evaluated on the BraTS 2020 dataset, MAPUNetR achieved a dice score of 0.88 and a dice coefficient of 0.92 on the ISIC 2018 dataset. Our experiments show that the model maintains stable performance and potential as a powerful tool for medical image segmentation in clinical practice.
The remarkable capabilities of the Segment Anything Model (SAM) for tackling image segmentation tasks in an intuitive and interactive manner has sparked interest in the design of effective visual prompts. Such interest has led to the creation of automated point prompt selection strategies, typically motivated from a feature extraction perspective. However, there is still very little understanding of how appropriate these automated visual prompting strategies are, particularly when compared to humans, across diverse image domains. Additionally, the performance benefits of including such automated visual prompting strategies within the finetuning process of SAM also remains unexplored, as does the effect of interpretable factors like distance between the prompt points on segmentation performance. To bridge these gaps, we leverage a recently released visual prompting dataset, PointPrompt, and introduce a number of benchmarking tasks that provide an array of opportunities to improve the understanding of the way human prompts differ from automated ones and what underlying factors make for effective visual prompts. We demonstrate that the resulting segmentation scores obtained by humans are approximately 29% higher than those given by automated strategies and identify potential features that are indicative of prompting performance with $R^2$ scores over 0.5. Additionally, we demonstrate that performance when using automated methods can be improved by up to 68% via a finetuning approach. Overall, our experiments not only showcase the existing gap between human prompts and automated methods, but also highlight potential avenues through which this gap can be leveraged to improve effective visual prompt design. Further details along with the dataset links and codes are available at https://github.com/olivesgatech/PointPrompt
In this paper, we propose a new approach to perform supervised texture classification/segmentation. The proposed idea is to feed a Fully Convolutional Network with specific texture descriptors. These texture features are extracted from images by using an empirical curvelet transform. We propose a method to build a unique empirical curvelet filter bank adapted to a given dictionary of textures. We then show that the output of these filters can be used to build efficient texture descriptors utilized to finally feed deep learning networks. Our approach is finally evaluated on several datasets and compare the results to various state-of-the-art algorithms and show that the proposed method dramatically outperform all existing ones.
Flare stacks play an important role in the treatment of waste gas and waste materials in petroleum fossil energy plants. Monitoring the efficiency of flame combustion is of great significance for environmental protection. The traditional method of monitoring with sensors is not only expensive, but also easily damaged in harsh combustion environments. In this paper, we propose to monitor the quality of flames using only visual features, including the area ratio of flame to smoke, RGB information of flames, angle of flames and other features. Comprehensive use of image segmentation, target detection, target tracking, principal component analysis, GPT-4 and other methods or tools to complete this task. In the end, real-time monitoring of the picture can be achieved, and when the combustion efficiency is low, measures such as adjusting the ratio of air and waste can be taken in time. As far as we know, the method of this paper is relatively innovative and has industrial production value.
The advancement of artificial intelligence (AI) in food and nutrition research is hindered by a critical bottleneck: the lack of annotated food data. Despite the rise of highly efficient AI models designed for tasks such as food segmentation and classification, their practical application might necessitate proficiency in AI and machine learning principles, which can act as a challenge for non-AI experts in the field of nutritional sciences. Alternatively, it highlights the need to translate AI models into user-friendly tools that are accessible to all. To address this, we present a demo of a semi-automatic food image annotation tool leveraging the Segment Anything Model (SAM). The tool enables prompt-based food segmentation via user interactions, promoting user engagement and allowing them to further categorise food items within meal images and specify weight/volume if necessary. Additionally, we release a fine-tuned version of SAM's mask decoder, dubbed MealSAM, with the ViT-B backbone tailored specifically for food image segmentation. Our objective is not only to contribute to the field by encouraging participation, collaboration, and the gathering of more annotated food data but also to make AI technology available for a broader audience by translating AI into practical tools.
Improving the fairness of federated learning (FL) benefits healthy and sustainable collaboration, especially for medical applications. However, existing fair FL methods ignore the specific characteristics of medical FL applications, i.e., domain shift among the datasets from different hospitals. In this work, we propose Fed-LWR to improve performance fairness from the perspective of feature shift, a key issue influencing the performance of medical FL systems caused by domain shift. Specifically, we dynamically perceive the bias of the global model across all hospitals by estimating the layer-wise difference in feature representations between local and global models. To minimize global divergence, we assign higher weights to hospitals with larger differences. The estimated client weights help us to re-aggregate the local models per layer to obtain a fairer global model. We evaluate our method on two widely used federated medical image segmentation benchmarks. The results demonstrate that our method achieves better and fairer performance compared with several state-of-the-art fair FL methods.
Deep learning has proven to be a highly effective tool for a wide range of applications, significantly when leveraging the power of multi-loss functions to optimize performance on multiple criteria simultaneously. However, optimal selection and weighting loss functions in deep learning tasks can significantly influence model performance, yet manual tuning of these functions is often inefficient and inflexible. We propose a novel framework called dynamic memory fusion for adaptive multi-loss function penalizing in real-time to address this. This framework leverages historical loss values data to dynamically adjust the weighting of multiple loss functions throughout the training process. Additionally, this framework integrates an auxiliary loss function to enhance model performance in the early stages. To further research horizons, we introduce the class-balanced dice loss function, designed to address class imbalance by prioritizing underrepresented classes. Experiments on breast ultrasound datasets demonstrate that the framework improves segmentation performance across various metrics. These results demonstrate the effectiveness of our proposed framework in ensuring that the model dynamically adjusts its focus to prioritize the most relevant criteria, leading to improved performance in evolving environments. The source code for our proposed methodology is publicly available on GitHub.
Recently, many foundation models for medical image analysis such as MedSAM, SwinUNETR have been released and proven to be useful in multiple tasks. However, considering the inherent heterogeneity and inhomogeneity of real-world medical data, directly applying these models to specific medical image segmentation tasks often leads to negative domain shift effects, which can severely weaken the model's segmentation capabilities. To this end, we propose an adaptive amalgamation knowledge framework that aims to train a versatile foundation model to handle the joint goals of multiple expert models, each specialized for a distinct task. Specifically, we first train an nnUNet-based expert model for each task, and reuse the pre-trained SwinUNTER as the target foundation model. Then, the input data for all challenging tasks are encoded in the foundation model and the expert models, respectively, and their backbone features are jointly projected into the adaptive amalgamation layer. Within the hidden layer, the hierarchical attention mechanisms are designed to achieve adaptive merging of the target model to the hidden layer feature knowledge of all experts, which significantly reduces the domain shift arising from the inter-task differences. Finally, the gold amalgamated features and the prompt features are fed into the mask decoder to obtain the segmentation results. Extensive experiments conducted in these challenging tasks demonstrate the effectiveness and adaptability of our foundation model for real-world medical image segmentation.
Current methods for microplastic identification in water samples are costly and require expert analysis. Here, we propose a deep learning segmentation model to automatically identify microplastics in microscopic images. We labeled images of microplastic from the Moore Institute for Plastic Pollution Research and employ a Generative Adversarial Network (GAN) to supplement and generate diverse training data. To verify the validity of the generated data, we conducted a reader study where an expert was able to discern the generated microplastic from real microplastic at a rate of 68 percent. Our segmentation model trained on the combined data achieved an F1-Score of 0.91 on a diverse dataset, compared to the model without generated data's 0.82. With our findings we aim to enhance the ability of both experts and citizens to detect microplastic across diverse ecological contexts, thereby improving the cost and accessibility of microplastic analysis.
In this work, we examine the effectiveness of an uncertainty quantification framework known as Evidential Deep Learning applied in the context of biomedical image segmentation. This class of models involves assigning Dirichlet distributions as priors for segmentation labels, and enables a few distinct definitions of model uncertainties. Using the cardiac and prostate MRI images available in the Medical Segmentation Decathlon for validation, we found that Evidential Deep Learning models with U-Net backbones generally yielded superior correlations between prediction errors and uncertainties relative to the conventional baseline equipped with Shannon entropy measure, Monte-Carlo Dropout and Deep Ensemble methods. We also examined these models' effectiveness in active learning, finding that relative to the standard Shannon entropy-based sampling, they yielded higher point-biserial uncertainty-error correlations while attaining similar performances in Dice-Sorensen coefficients. These superior features of EDL models render them well-suited for segmentation tasks that warrant a critical sensitivity in detecting large model errors.
In medical image segmentation tasks, the scarcity of labeled training data poses a significant challenge when training deep neural networks. When using U-Net-style architectures, it is common practice to address this problem by pretraining the encoder part on a large general-purpose dataset like ImageNet. However, these methods are resource-intensive and do not guarantee improved performance on the downstream task. In this paper we investigate a variety of training setups on medical image segmentation datasets, using ImageNet-pretrained models. By examining over 300 combinations of models, datasets, and training methods, we find that shorter pretraining often leads to better results on the downstream task, providing additional proof to the well-known fact that the accuracy of the model on ImageNet is a poor indicator for downstream performance. As our main contribution, we introduce a novel transferability metric, based on contrastive learning, that measures how robustly a pretrained model is able to represent the target data. In contrast to other transferability scores, our method is applicable to the case of transferring from ImageNet classification to medical image segmentation. We apply our robustness score by measuring it throughout the pretraining phase to indicate when the model weights are optimal for downstream transfer. This reduces pretraining time and improves results on the target task.
In the past few years, deep learning algorithms have been widely used for cardiac image segmentation. However, most of these architectures rely on convolutions that hardly model long-range dependencies, limiting their ability to extract contextual information. In order to tackle this issue, this article introduces the Swin Filtering Block network (SFB-net) which takes advantage of both conventional and swin transformer layers. The former are used to introduce spatial attention at the bottom of the network, while the latter are applied to focus on high level semantically rich features between the encoder and decoder. An average Dice score of 92.4 was achieved on the ACDC dataset. To the best of our knowledge, this result outperforms any other work on this dataset. The average Dice score of 87.99 obtained on the M\&M's dataset demonstrates that the proposed method generalizes well to data from different vendors and centres.
Continuous and accurate segmentation of airways in chest CT images is essential for preoperative planning and real-time bronchoscopy navigation. Despite advances in deep learning for medical image segmentation, maintaining airway continuity remains a challenge, particularly due to intra-class imbalance between large and small branches and blurred CT scan details. To address these challenges, we propose a progressive curriculum learning pipeline and a Scale-Enhanced U-Net (SE-UNet) to enhance segmentation continuity. Specifically, our progressive curriculum learning pipeline consists of three stages: extracting main airways, identifying small airways, and repairing discontinuities. The cropping sampling strategy in each stage reduces feature interference between airways of different scales, effectively addressing the challenge of intra-class imbalance. In the third training stage, we present an Adaptive Topology-Responsive Loss (ATRL) to guide the network to focus on airway continuity. The progressive training pipeline shares the same SE-UNet, integrating multi-scale inputs and Detail Information Enhancers (DIEs) to enhance information flow and effectively capture the intricate details of small airways. Additionally, we propose a robust airway tree parsing method and hierarchical evaluation metrics to provide more clinically relevant and precise analysis. Experiments on both in-house and public datasets demonstrate that our method outperforms existing approaches, significantly improving the accuracy of small airways and the completeness of the airway tree. The code will be released upon publication.
Advanced image segmentation and processing tools present an opportunity to study cell processes and their dynamics. However, image analysis is often routine and time-consuming. Nowadays, alternative data-driven approaches using deep learning are potentially offering automatized, accurate, and fast image analysis. In this paper, we extend the applications of Cellpose, a state-of-the-art cell segmentation framework, with feature extraction capabilities to assess morphological characteristics. We also introduce a dataset of DAPI and FITC stained cells to which our new method is applied.
The annotation of patient organs is a crucial part of various diagnostic and treatment procedures, such as radiotherapy planning. Manual annotation is extremely time-consuming, while its automation using modern image analysis techniques has not yet reached levels sufficient for clinical adoption. This paper investigates the idea of semi-supervised medical image segmentation using human gaze as interactive input for segmentation correction. In particular, we fine-tuned the Segment Anything Model in Medical Images (MedSAM), a public solution that uses various prompt types as additional input for semi-automated segmentation correction. We used human gaze data from reading abdominal images as a prompt for fine-tuning MedSAM. The model was validated on a public WORD database, which consists of 120 CT scans of 16 abdominal organs. The results of the gaze-assisted MedSAM were shown to be superior to the results of the state-of-the-art segmentation models. In particular, the average Dice coefficient for 16 abdominal organs was 85.8%, 86.7%, 81.7%, and 90.5% for nnUNetV2, ResUNet, original MedSAM, and our gaze-assisted MedSAM model, respectively.
Multi-modality (MM) semi-supervised learning (SSL) based medical image segmentation has recently gained increasing attention for its ability to utilize MM data and reduce reliance on labeled images. However, current methods face several challenges: (1) Complex network designs hinder scalability to scenarios with more than two modalities. (2) Focusing solely on modality-invariant representation while neglecting modality-specific features, leads to incomplete MM learning. (3) Leveraging unlabeled data with generative methods can be unreliable for SSL. To address these problems, we propose Double Bank Dual Consistency (DBDC), a novel MM-SSL approach for medical image segmentation. To address challenge (1), we propose a modality all-in-one segmentation network that accommodates data from any number of modalities, removing the limitation on modality count. To address challenge (2), we design two learnable plug-in banks, Modality-Level Modulation bank (MLMB) and Modality-Level Prototype (MLPB) bank, to capture both modality-invariant and modality-specific knowledge. These banks are updated using our proposed Modality Prototype Contrastive Learning (MPCL). Additionally, we design Modality Adaptive Weighting (MAW) to dynamically adjust learning weights for each modality, ensuring balanced MM learning as different modalities learn at different rates. Finally, to address challenge (3), we introduce a Dual Consistency (DC) strategy that enforces consistency at both the image and feature levels without relying on generative methods. We evaluate our method on a 2-to-4 modality segmentation task using three open-source datasets, and extensive experiments show that our method outperforms state-of-the-art approaches.
Early detection through imaging and accurate diagnosis is crucial in mitigating the high mortality rate associated with breast cancer. However, locating tumors from low-resolution and high-noise medical images is extremely challenging. Therefore, this paper proposes a novel PGDiffSeg (Prior-Guided Diffusion Denoising Model with Parameter-Shared Attention) that applies diffusion denoising methods to breast cancer medical image segmentation, accurately recovering the affected areas from Gaussian noise. Firstly, we design a parallel pipeline for noise processing and semantic information processing and propose a parameter-shared attention module (PSA) in multi-layer that seamlessly integrates these two pipelines. This integration empowers PGDiffSeg to incorporate semantic details at multiple levels during the denoising process, producing highly accurate segmentation maps. Secondly, we introduce a guided strategy that leverages prior knowledge to simulate the decision-making process of medical professionals, thereby enhancing the model's ability to locate tumor positions precisely. Finally, we provide the first-ever discussion on the interpretability of the generative diffusion model in the context of breast cancer segmentation. Extensive experiments have demonstrated the superiority of our model over the current state-of-the-art approaches, confirming its effectiveness as a flexible diffusion denoising method suitable for medical image research. Our code will be publicly available later.
Within this work, we introduce LIMIS: The first purely language-based interactive medical image segmentation model. We achieve this by adapting Grounded SAM to the medical domain and designing a language-based model interaction strategy that allows radiologists to incorporate their knowledge into the segmentation process. LIMIS produces high-quality initial segmentation masks by leveraging medical foundation models and allows users to adapt segmentation masks using only language, opening up interactive segmentation to scenarios where physicians require using their hands for other tasks. We evaluate LIMIS on three publicly available medical datasets in terms of performance and usability with experts from the medical domain confirming its high-quality segmentation masks and its interactive usability.