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arXiv2016

An Interactive Medical Image Segmentation Framework Using Iterative Refinement

Image segmentation is often performed on medical images for identifying diseases in clinical evaluation. Hence it has become one of the major research areas. Conventional image segmentation techniques are unable to provide satisfactory segmentation results for medical images as they contain irregularities. They need to be pre-processed before segmentation. In order to obtain the most suitable method for medical image segmentation, we propose a two stage algorithm. The first stage automatically generates a binary marker image of the region of interest using mathematical morphology. This marker serves as the mask image for the second stage which uses GrabCut on the input image thus resulting in an efficient segmented result. The obtained result can be further refined by user interaction which can be done using the Graphical User Interface (GUI). Experimental results show that the proposed method is accurate and provides satisfactory segmentation results with minimum user interaction on medical as well as natural images.

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arXiv2020

Going to Extremes: Weakly Supervised Medical Image Segmentation

Medical image annotation is a major hurdle for developing precise and robust machine learning models. Annotation is expensive, time-consuming, and often requires expert knowledge, particularly in the medical field. Here, we suggest using minimal user interaction in the form of extreme point clicks to train a segmentation model which, in effect, can be used to speed up medical image annotation. An initial segmentation is generated based on the extreme points utilizing the random walker algorithm. This initial segmentation is then used as a noisy supervision signal to train a fully convolutional network that can segment the organ of interest, based on the provided user clicks. Through experimentation on several medical imaging datasets, we show that the predictions of the network can be refined using several rounds of training with the prediction from the same weakly annotated data. Further improvements are shown utilizing the clicked points within a custom-designed loss and attention mechanism. Our approach has the potential to speed up the process of generating new training datasets for the development of new machine learning and deep learning-based models for, but not exclusively, medical image analysis.

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arXiv2022

Bridging 2D and 3D Segmentation Networks for Computation Efficient Volumetric Medical Image Segmentation: An Empirical Study of 2.5D Solutions

Recently, deep convolutional neural networks have achieved great success for medical image segmentation. However, unlike segmentation of natural images, most medical images such as MRI and CT are volumetric data. In order to make full use of volumetric information, 3D CNNs are widely used. However, 3D CNNs suffer from higher inference time and computation cost, which hinders their further clinical applications. Additionally, with the increased number of parameters, the risk of overfitting is higher, especially for medical images where data and annotations are expensive to acquire. To issue this problem, many 2.5D segmentation methods have been proposed to make use of volumetric spatial information with less computation cost. Despite these works lead to improvements on a variety of segmentation tasks, to the best of our knowledge, there has not previously been a large-scale empirical comparison of these methods. In this paper, we aim to present a review of the latest developments of 2.5D methods for volumetric medical image segmentation. Additionally, to compare the performance and effectiveness of these methods, we provide an empirical study of these methods on three representative segmentation tasks involving different modalities and targets. Our experimental results highlight that 3D CNNs may not always be the best choice. Despite all these 2.5D methods can bring performance gains to 2D baseline, not all the methods hold the benefits on different datasets. We hope the results and conclusions of our study will prove useful for the community on exploring and developing efficient volumetric medical image segmentation methods.

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arXiv2025

Intelligent Communication Mixture-of-Experts Boosted-Medical Image Segmentation Foundation Model

Foundation models for medical image segmentation have achieved remarkable performance. Adaptive fine-tuning of natural image segmentation foundation models is crucial for medical image segmentation tasks. However, some limitations exist in existing fine-tuning methods: 1) insufficient representation of high-level features and 2) the fine-tuning process disrupts the structural integrity of pretrained weights. Inspired by these critical problems, we propose an intelligent communication mixture-of-experts boosted-medical image segmentation foundation model, named IC-MoE, with twofold ideas: 1) We construct basic experts, semantic experts, and adaptive experts. Moreover, we implement a pixel probability adaptive voting strategy, which enables expert selection and fusion through label consistency and load balancing. This approach preliminarily enhances the representation capability of high-level features while preserving the structural integrity of pretrained weights. 2) We propose a semantic-guided contrastive learning method to address the issue of weak supervision in contrastive learning. This method further enhances the representation capability of high-level features while preserving the structural integrity of pretrained weights. Extensive experiments across three public medical image segmentation datasets demonstrate that the IC-MoE outperforms other SOTA models. Consequently, the proposed IC-MoE effectively supplements foundational medical image segmentation models with high-level features and pretrained structural integrity. We also validate the superior generalizability of the IC-MoE across diverse medical image segmentation scenarios.

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arXiv2023

Exploring Generalizable Distillation for Efficient Medical Image Segmentation

Efficient medical image segmentation aims to provide accurate pixel-wise predictions for medical images with a lightweight implementation framework. However, lightweight frameworks generally fail to achieve superior performance and suffer from poor generalizable ability on cross-domain tasks. In this paper, we explore the generalizable knowledge distillation for the efficient segmentation of cross-domain medical images. Considering the domain gaps between different medical datasets, we propose the Model-Specific Alignment Networks (MSAN) to obtain the domain-invariant representations. Meanwhile, a customized Alignment Consistency Training (ACT) strategy is designed to promote the MSAN training. Considering the domain-invariant representative vectors in MSAN, we propose two generalizable knowledge distillation schemes for cross-domain distillation, Dual Contrastive Graph Distillation (DCGD) and Domain-Invariant Cross Distillation (DICD). Specifically, in DCGD, two types of implicit contrastive graphs are designed to represent the intra-coupling and inter-coupling semantic correlations from the perspective of data distribution. In DICD, the domain-invariant semantic vectors from the two models (i.e., teacher and student) are leveraged to cross-reconstruct features by the header exchange of MSAN, which achieves improvement in the generalization of both the encoder and decoder in the student model. Furthermore, a metric named Frechet Semantic Distance (FSD) is tailored to verify the effectiveness of the regularized domain-invariant features. Extensive experiments conducted on the Liver and Retinal Vessel Segmentation datasets demonstrate the superiority of our method, in terms of performance and generalization on lightweight frameworks.

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arXiv2024

Image Segmentation in Foundation Model Era: A Survey

Image segmentation is a long-standing challenge in computer vision, studied continuously over several decades, as evidenced by seminal algorithms such as N-Cut, FCN, and MaskFormer. With the advent of foundation models (FMs), contemporary segmentation methodologies have embarked on a new epoch by either adapting FMs (e.g., CLIP, Stable Diffusion, DINO) for image segmentation or developing dedicated segmentation foundation models (e.g., SAM). These approaches not only deliver superior segmentation performance, but also herald newfound segmentation capabilities previously unseen in deep learning context. However, current research in image segmentation lacks a detailed analysis of distinct characteristics, challenges, and solutions associated with these advancements. This survey seeks to fill this gap by providing a thorough review of cutting-edge research centered around FM-driven image segmentation. We investigate two basic lines of research -- generic image segmentation (i.e., semantic segmentation, instance segmentation, panoptic segmentation), and promptable image segmentation (i.e., interactive segmentation, referring segmentation, few-shot segmentation) -- by delineating their respective task settings, background concepts, and key challenges. Furthermore, we provide insights into the emergence of segmentation knowledge from FMs like CLIP, Stable Diffusion, and DINO. An exhaustive overview of over 300 segmentation approaches is provided to encapsulate the breadth of current research efforts. Subsequently, we engage in a discussion of open issues and potential avenues for future research. We envisage that this fresh, comprehensive, and systematic survey catalyzes the evolution of advanced image segmentation systems. A public website is created to continuously track developments in this fast advancing field: \url{https://github.com/stanley-313/ImageSegFM-Survey}.

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arXiv2021

Annotation-efficient deep learning for automatic medical image segmentation

Automatic medical image segmentation plays a critical role in scientific research and medical care. Existing high-performance deep learning methods typically rely on large training datasets with high-quality manual annotations, which are difficult to obtain in many clinical applications. Here, we introduce Annotation-effIcient Deep lEarning (AIDE), an open-source framework to handle imperfect training datasets. Methodological analyses and empirical evaluations are conducted, and we demonstrate that AIDE surpasses conventional fully-supervised models by presenting better performance on open datasets possessing scarce or noisy annotations. We further test AIDE in a real-life case study for breast tumor segmentation. Three datasets containing 11,852 breast images from three medical centers are employed, and AIDE, utilizing 10% training annotations, consistently produces segmentation maps comparable to those generated by fully-supervised counterparts or provided by independent radiologists. The 10-fold enhanced efficiency in utilizing expert labels has the potential to promote a wide range of biomedical applications.

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arXiv2026

Leveraging Causal Reasoning Method for Explaining Medical Image Segmentation Models

Medical image segmentation plays a vital role in clinical decision-making, enabling precise localization of lesions and guiding interventions. Despite significant advances in segmentation accuracy, the black-box nature of most deep models has raised growing concerns about their trustworthiness in high-stakes medical scenarios. Current explanation techniques have primarily focused on classification tasks, leaving the segmentation domain relatively underexplored. We introduced an explanation model for segmentation task which employs the causal inference framework and backpropagates the average treatment effect (ATE) into a quantification metric to determine the influence of input regions, as well as network components, on target segmentation areas. Through comparison with recent segmentation explainability techniques on two representative medical imaging datasets, we demonstrated that our approach provides more faithful explanations than existing approaches. Furthermore, we carried out a systematic causal analysis of multiple foundational segmentation models using our method, which reveals significant heterogeneity in perceptual strategies across different models, and even between different inputs for the same model. Suggesting the potential of our method to provide notable insights for optimizing segmentation models. Our code can be found at https://github.com/lcmmai/PdCR.

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arXiv2024

Dual Structure-Aware Image Filterings for Semi-supervised Medical Image Segmentation

Semi-supervised image segmentation has attracted great attention recently. The key is how to leverage unlabeled images in the training process. Most methods maintain consistent predictions of the unlabeled images under variations (e.g., adding noise/perturbations, or creating alternative versions) in the image and/or model level. In most image-level variation, medical images often have prior structure information, which has not been well explored. In this paper, we propose novel dual structure-aware image filterings (DSAIF) as the image-level variations for semi-supervised medical image segmentation. Motivated by connected filtering that simplifies image via filtering in structure-aware tree-based image representation, we resort to the dual contrast invariant Max-tree and Min-tree representation. Specifically, we propose a novel connected filtering that removes topologically equivalent nodes (i.e. connected components) having no siblings in the Max/Min-tree. This results in two filtered images preserving topologically critical structure. Applying the proposed DSAIF to mutually supervised networks decreases the consensus of their erroneous predictions on unlabeled images. This helps to alleviate the confirmation bias issue of overfitting to noisy pseudo labels of unlabeled images, and thus effectively improves the segmentation performance. Extensive experimental results on three benchmark datasets demonstrate that the proposed method significantly/consistently outperforms some state-of-the-art methods. The source codes will be publicly available.

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arXiv2023

Mixing Data Augmentation with Preserving Foreground Regions in Medical Image Segmentation

The development of medical image segmentation using deep learning can significantly support doctors' diagnoses. Deep learning needs large amounts of data for training, which also requires data augmentation to extend diversity for preventing overfitting. However, the existing methods for data augmentation of medical image segmentation are mainly based on models which need to update parameters and cost extra computing resources. We proposed data augmentation methods designed to train a high accuracy deep learning network for medical image segmentation. The proposed data augmentation approaches are called KeepMask and KeepMix, which can create medical images by better identifying the boundary of the organ with no more parameters. Our methods achieved better performance and obtained more precise boundaries for medical image segmentation on datasets. The dice coefficient of our methods achieved 94.15% (3.04% higher than baseline) on CHAOS and 74.70% (5.25% higher than baseline) on MSD spleen with Unet.

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arXiv2017

FPGA based Parallelized Architecture of Efficient Graph based Image Segmentation Algorithm

Efficient and real time segmentation of color images has a variety of importance in many fields of computer vision such as image compression, medical imaging, mapping and autonomous navigation. Being one of the most computationally expensive operation, it is usually done through software imple- mentation using high-performance processors. In robotic systems, however, with the constrained platform dimensions and the need for portability, low power consumption and simultaneously the need for real time image segmentation, we envision hardware parallelism as the way forward to achieve higher acceleration. Field-programmable gate arrays (FPGAs) are among the best suited for this task as they provide high computing power in a small physical area. They exceed the computing speed of software based implementations by breaking the paradigm of sequential execution and accomplishing more per clock cycle operations by enabling hardware level parallelization at an architectural level. In this paper, we propose three novel architectures of a well known Efficient Graph based Image Segmentation algorithm. These proposed implementations optimizes time and power consumption when compared to software implementations. The hybrid design proposed, has notable furtherance of acceleration capabilities delivering atleast 2X speed gain over other implemen- tations, which henceforth allows real time image segmentation that can be deployed on Mobile Robotic systems.

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arXiv2013

Co-Sparse Textural Similarity for Image Segmentation

We propose an algorithm for segmenting natural images based on texture and color information, which leverages the co-sparse analysis model for image segmentation within a convex multilabel optimization framework. As a key ingredient of this method, we introduce a novel textural similarity measure, which builds upon the co-sparse representation of image patches. We propose a Bayesian approach to merge textural similarity with information about color and location. Combined with recently developed convex multilabel optimization methods this leads to an efficient algorithm for both supervised and unsupervised segmentation, which is easily parallelized on graphics hardware. The approach provides competitive results in unsupervised segmentation and outperforms state-of-the-art interactive segmentation methods on the Graz Benchmark.

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arXiv2020

Color Image Segmentation using Adaptive Particle Swarm Optimization and Fuzzy C-means

Segmentation partitions an image into different regions containing pixels with similar attributes. A standard non-contextual variant of Fuzzy C-means clustering algorithm (FCM), considering its simplicity is generally used in image segmentation. Using FCM has its disadvantages like it is dependent on the initial guess of the number of clusters and highly sensitive to noise. Satisfactory visual segments cannot be obtained using FCM. Particle Swarm Optimization (PSO) belongs to the class of evolutionary algorithms and has good convergence speed and fewer parameters compared to Genetic Algorithms (GAs). An optimized version of PSO can be combined with FCM to act as a proper initializer for the algorithm thereby reducing its sensitivity to initial guess. A hybrid PSO algorithm named Adaptive Particle Swarm Optimization (APSO) which improves in the calculation of various hyper parameters like inertia weight, learning factors over standard PSO, using insights from swarm behaviour, leading to improvement in cluster quality can be used. This paper presents a new image segmentation algorithm called Adaptive Particle Swarm Optimization and Fuzzy C-means Clustering Algorithm (APSOF), which is based on Adaptive Particle Swarm Optimization (APSO) and Fuzzy C-means clustering. Experimental results show that APSOF algorithm has edge over FCM in correctly identifying the optimum cluster centers, there by leading to accurate classification of the image pixels. Hence, APSOF algorithm has superior performance in comparison with classic Particle Swarm Optimization (PSO) and Fuzzy C-means clustering algorithm (FCM) for image segmentation.

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arXiv2020

Contrastive Rendering for Ultrasound Image Segmentation

Ultrasound (US) image segmentation embraced its significant improvement in deep learning era. However, the lack of sharp boundaries in US images still remains an inherent challenge for segmentation. Previous methods often resort to global context, multi-scale cues or auxiliary guidance to estimate the boundaries. It is hard for these methods to approach pixel-level learning for fine-grained boundary generating. In this paper, we propose a novel and effective framework to improve boundary estimation in US images. Our work has three highlights. First, we propose to formulate the boundary estimation as a rendering task, which can recognize ambiguous points (pixels/voxels) and calibrate the boundary prediction via enriched feature representation learning. Second, we introduce point-wise contrastive learning to enhance the similarity of points from the same class and contrastively decrease the similarity of points from different classes. Boundary ambiguities are therefore further addressed. Third, both rendering and contrastive learning tasks contribute to consistent improvement while reducing network parameters. As a proof-of-concept, we performed validation experiments on a challenging dataset of 86 ovarian US volumes. Results show that our proposed method outperforms state-of-the-art methods and has the potential to be used in clinical practice.

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arXiv2018

Multi-Level Contextual Network for Biomedical Image Segmentation

Accurate and reliable image segmentation is an essential part of biomedical image analysis. In this paper, we consider the problem of biomedical image segmentation using deep convolutional neural networks. We propose a new end-to-end network architecture that effectively integrates local and global contextual patterns of histologic primitives to obtain a more reliable segmentation result. Specifically, we introduce a deep fully convolution residual network with a new skip connection strategy to control the contextual information passed forward. Moreover, our trained model is also computationally inexpensive due to its small number of network parameters. We evaluate our method on two public datasets for epithelium segmentation and tubule segmentation tasks. Our experimental results show that the proposed method provides a fast and effective way of producing a pixel-wise dense prediction of biomedical images.

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arXiv2023

G-CASCADE: Efficient Cascaded Graph Convolutional Decoding for 2D Medical Image Segmentation

In recent years, medical image segmentation has become an important application in the field of computer-aided diagnosis. In this paper, we are the first to propose a new graph convolution-based decoder namely, Cascaded Graph Convolutional Attention Decoder (G-CASCADE), for 2D medical image segmentation. G-CASCADE progressively refines multi-stage feature maps generated by hierarchical transformer encoders with an efficient graph convolution block. The encoder utilizes the self-attention mechanism to capture long-range dependencies, while the decoder refines the feature maps preserving long-range information due to the global receptive fields of the graph convolution block. Rigorous evaluations of our decoder with multiple transformer encoders on five medical image segmentation tasks (i.e., Abdomen organs, Cardiac organs, Polyp lesions, Skin lesions, and Retinal vessels) show that our model outperforms other state-of-the-art (SOTA) methods. We also demonstrate that our decoder achieves better DICE scores than the SOTA CASCADE decoder with 80.8% fewer parameters and 82.3% fewer FLOPs. Our decoder can easily be used with other hierarchical encoders for general-purpose semantic and medical image segmentation tasks.

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arXiv2024

Enhancing the Reliability of Segment Anything Model for Auto-Prompting Medical Image Segmentation with Uncertainty Rectification

The Segment Anything Model (SAM) has recently emerged as a groundbreaking foundation model for prompt-driven image segmentation tasks. However, both the original SAM and its medical variants require slice-by-slice manual prompting of target structures, which directly increase the burden for applications. Despite attempts of auto-prompting to turn SAM into a fully automatic manner, it still exhibits subpar performance and lacks of reliability especially in the field of medical imaging. In this paper, we propose UR-SAM, an uncertainty rectified SAM framework to enhance the reliability for auto-prompting medical image segmentation. Building upon a localization framework for automatic prompt generation, our method incorporates a prompt augmentation module to obtain a series of input prompts for SAM for uncertainty estimation and an uncertainty-based rectification module to further utilize the distribution of estimated uncertainty to improve the segmentation performance. Extensive experiments on two public 3D medical datasets covering the segmentation of 35 organs demonstrate that without supplementary training or fine-tuning, our method further improves the segmentation performance with up to 10.7 % and 13.8 % in dice similarity coefficient, demonstrating efficiency and broad capabilities for medical image segmentation without manual prompting.

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arXiv2019

A General Framework for Complex Network-Based Image Segmentation

With the recent advances in complex networks theory, graph-based techniques for image segmentation has attracted great attention recently. In order to segment the image into meaningful connected components, this paper proposes an image segmentation general framework using complex networks based community detection algorithms. If we consider regions as communities, using community detection algorithms directly can lead to an over-segmented image. To address this problem, we start by splitting the image into small regions using an initial segmentation. The obtained regions are used for building the complex network. To produce meaningful connected components and detect homogeneous communities, some combinations of color and texture based features are employed in order to quantify the regions similarities. To sum up, the network of regions is constructed adaptively to avoid many small regions in the image, and then, community detection algorithms are applied on the resulting adaptive similarity matrix to obtain the final segmented image. Experiments are conducted on Berkeley Segmentation Dataset and four of the most influential community detection algorithms are tested. Experimental results have shown that the proposed general framework increases the segmentation performances compared to some existing methods.

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