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arXiv2022

Scribble2D5: Weakly-Supervised Volumetric Image Segmentation via Scribble Annotations

Recently, weakly-supervised image segmentation using weak annotations like scribbles has gained great attention, since such annotations are much easier to obtain compared to time-consuming and label-intensive labeling at the pixel/voxel level. However, because scribbles lack structure information of region of interest (ROI), existing scribble-based methods suffer from poor boundary localization. Furthermore, most current methods are designed for 2D image segmentation, which do not fully leverage the volumetric information if directly applied to image slices. In this paper, we propose a scribble-based volumetric image segmentation, Scribble2D5, which tackles 3D anisotropic image segmentation and improves boundary prediction. To achieve this, we augment a 2.5D attention UNet with a proposed label propagation module to extend semantic information from scribbles and a combination of static and active boundary prediction to learn ROI's boundary and regularize its shape. Extensive experiments on three public datasets demonstrate Scribble2D5 significantly outperforms current scribble-based methods and approaches the performance of fully-supervised ones. Our code is available online.

cs.CV↗

arXiv2025

SuperCL: Superpixel Guided Contrastive Learning for Medical Image Segmentation Pre-training

Medical image segmentation is a critical yet challenging task, primarily due to the difficulty of obtaining extensive datasets of high-quality, expert-annotated images. Contrastive learning presents a potential but still problematic solution to this issue. Because most existing methods focus on extracting instance-level or pixel-to-pixel representation, which ignores the characteristics between intra-image similar pixel groups. Moreover, when considering contrastive pairs generation, most SOTA methods mainly rely on manually setting thresholds, which requires a large number of gradient experiments and lacks efficiency and generalization. To address these issues, we propose a novel contrastive learning approach named SuperCL for medical image segmentation pre-training. Specifically, our SuperCL exploits the structural prior and pixel correlation of images by introducing two novel contrastive pairs generation strategies: Intra-image Local Contrastive Pairs (ILCP) Generation and Inter-image Global Contrastive Pairs (IGCP) Generation. Considering superpixel cluster aligns well with the concept of contrastive pairs generation, we utilize the superpixel map to generate pseudo masks for both ILCP and IGCP to guide supervised contrastive learning. Moreover, we also propose two modules named Average SuperPixel Feature Map Generation (ASP) and Connected Components Label Generation (CCL) to better exploit the prior structural information for IGCP. Finally, experiments on 8 medical image datasets indicate our SuperCL outperforms existing 12 methods. i.e. Our SuperCL achieves a superior performance with more precise predictions from visualization figures and 3.15%, 5.44%, 7.89% DSC higher than the previous best results on MMWHS, CHAOS, Spleen with 10% annotations. Our code will be released after acceptance.

cs.CV↗

arXiv2022

Modeling Annotator Preference and Stochastic Annotation Error for Medical Image Segmentation

Manual annotation of medical images is highly subjective, leading to inevitable and huge annotation biases. Deep learning models may surpass human performance on a variety of tasks, but they may also mimic or amplify these biases. Although we can have multiple annotators and fuse their annotations to reduce stochastic errors, we cannot use this strategy to handle the bias caused by annotators' preferences. In this paper, we highlight the issue of annotator-related biases on medical image segmentation tasks, and propose a Preference-involved Annotation Distribution Learning (PADL) framework to address it from the perspective of disentangling an annotator's preference from stochastic errors using distribution learning so as to produce not only a meta segmentation but also the segmentation possibly made by each annotator. Under this framework, a stochastic error modeling (SEM) module estimates the meta segmentation map and average stochastic error map, and a series of human preference modeling (HPM) modules estimate each annotator's segmentation and the corresponding stochastic error. We evaluated our PADL framework on two medical image benchmarks with different imaging modalities, which have been annotated by multiple medical professionals, and achieved promising performance on all five medical image segmentation tasks.

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arXiv2021

Attention Toward Neighbors: A Context Aware Framework for High Resolution Image Segmentation

High-resolution image segmentation remains challenging and error-prone due to the enormous size of intermediate feature maps. Conventional methods avoid this problem by using patch based approaches where each patch is segmented independently. However, independent patch segmentation induces errors, particularly at the patch boundary due to the lack of contextual information in very high-resolution images where the patch size is much smaller compared to the full image. To overcome these limitations, in this paper, we propose a novel framework to segment a particular patch by incorporating contextual information from its neighboring patches. This allows the segmentation network to see the target patch with a wider field of view without the need of larger feature maps. Comparative analysis from a number of experiments shows that our proposed framework is able to segment high resolution images with significantly improved mean Intersection over Union and overall accuracy.

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arXiv2024

Surveying Image Segmentation Approaches in Astronomy

Image segmentation plays a critical role in unlocking the mysteries of the universe, providing astronomers with a clearer perspective on celestial objects within complex astronomical images and data cubes. Manual segmentation, while traditional, is not only time-consuming but also susceptible to biases introduced by human intervention. As a result, automated segmentation methods have become essential for achieving robust and consistent results in astronomical studies. This review begins by summarizing traditional and classical segmentation methods widely used in astronomical tasks. Despite the significant improvements these methods have brought to segmentation outcomes, they fail to meet astronomers' expectations, requiring additional human correction, further intensifying the labor-intensive nature of the segmentation process. The review then focuses on the transformative impact of machine learning, particularly deep learning, on segmentation tasks in astronomy. It introduces state-of-the-art machine learning approaches, highlighting their applications and the remarkable advancements they bring to segmentation accuracy in both astronomical images and data cubes. As the field of machine learning continues to evolve rapidly, it is anticipated that astronomers will increasingly leverage these sophisticated techniques to enhance segmentation tasks in their research projects. In essence, this review serves as a comprehensive guide to the evolution of segmentation methods in astronomy, emphasizing the transition from classical approaches to cutting-edge machine learning methodologies. We encourage astronomers to embrace these advancements, fostering a more streamlined and accurate segmentation process that aligns with the ever-expanding frontiers of astronomical exploration.

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arXiv2019

Anatomical Priors for Image Segmentation via Post-Processing with Denoising Autoencoders

Deep convolutional neural networks (CNN) proved to be highly accurate to perform anatomical segmentation of medical images. However, some of the most popular CNN architectures for image segmentation still rely on post-processing strategies (e.g. Conditional Random Fields) to incorporate connectivity constraints into the resulting masks. These post-processing steps are based on the assumption that objects are usually continuous and therefore nearby pixels should be assigned the same object label. Even if it is a valid assumption in general, these methods do not offer a straightforward way to incorporate more complex priors like convexity or arbitrary shape restrictions. In this work we propose Post-DAE, a post-processing method based on denoising autoencoders (DAE) trained using only segmentation masks. We learn a low-dimensional space of anatomically plausible segmentations, and use it as a post-processing step to impose shape constraints on the resulting masks obtained with arbitrary segmentation methods. Our approach is independent of image modality and intensity information since it employs only segmentation masks for training. This enables the use of anatomical segmentations that do not need to be paired with intensity images, making the approach very flexible. Our experimental results on anatomical segmentation of X-ray images show that Post-DAE can improve the quality of noisy and incorrect segmentation masks obtained with a variety of standard methods, by bringing them back to a feasible space, with almost no extra computational time.

eess.IV↗

arXiv2024

RRSIS: Referring Remote Sensing Image Segmentation

Localizing desired objects from remote sensing images is of great use in practical applications. Referring image segmentation, which aims at segmenting out the objects to which a given expression refers, has been extensively studied in natural images. However, almost no research attention is given to this task of remote sensing imagery. Considering its potential for real-world applications, in this paper, we introduce referring remote sensing image segmentation (RRSIS) to fill in this gap and make some insightful explorations. Specifically, we create a new dataset, called RefSegRS, for this task, enabling us to evaluate different methods. Afterward, we benchmark referring image segmentation methods of natural images on the RefSegRS dataset and find that these models show limited efficacy in detecting small and scattered objects. To alleviate this issue, we propose a language-guided cross-scale enhancement (LGCE) module that utilizes linguistic features to adaptively enhance multi-scale visual features by integrating both deep and shallow features. The proposed dataset, benchmarking results, and the designed LGCE module provide insights into the design of a better RRSIS model. We will make our dataset and code publicly available.

cs.CV↗

arXiv2025

SAM-Guided Robust Representation Learning for One-Shot 3D Medical Image Segmentation

One-shot medical image segmentation (MIS) is crucial for medical analysis due to the burden of medical experts on manual annotation. The recent emergence of the segment anything model (SAM) has demonstrated remarkable adaptation in MIS but cannot be directly applied to one-shot medical image segmentation (MIS) due to its reliance on labor-intensive user interactions and the high computational cost. To cope with these limitations, we propose a novel SAM-guided robust representation learning framework, named RRL-MedSAM, to adapt SAM to one-shot 3D MIS, which exploits the strong generalization capabilities of the SAM encoder to learn better feature representation. We devise a dual-stage knowledge distillation (DSKD) strategy to distill general knowledge between natural and medical images from the foundation model to train a lightweight encoder, and then adopt a mutual exponential moving average (mutual-EMA) to update the weights of the general lightweight encoder and medical-specific encoder. Specifically, pseudo labels from the registration network are used to perform mutual supervision for such two encoders. Moreover, we introduce an auto-prompting (AP) segmentation decoder which adopts the mask generated from the general lightweight model as a prompt to assist the medical-specific model in boosting the final segmentation performance. Extensive experiments conducted on three public datasets, i.e., OASIS, CT-lung demonstrate that the proposed RRL-MedSAM outperforms state-of-the-art one-shot MIS methods for both segmentation and registration tasks. Especially, our lightweight encoder uses only 3\% of the parameters compared to the encoder of SAM-Base.

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arXiv2025

Image Segmentation: Inducing graph-based learning

This study explores the potential of graph neural networks (GNNs) to enhance semantic segmentation across diverse image modalities. We evaluate the effectiveness of a novel GNN-based U-Net architecture on three distinct datasets: PascalVOC, a standard benchmark for natural image segmentation, WoodScape, a challenging dataset of fisheye images commonly used in autonomous driving, introducing significant geometric distortions; and ISIC2016, a dataset of dermoscopic images for skin lesion segmentation. We compare our proposed UNet-GNN model against established convolutional neural networks (CNNs) based segmentation models, including U-Net and U-Net++, as well as the transformer-based SwinUNet. Unlike these methods, which primarily rely on local convolutional operations or global self-attention, GNNs explicitly model relationships between image regions by constructing and operating on a graph representation of the image features. This approach allows the model to capture long-range dependencies and complex spatial relationships, which we hypothesize will be particularly beneficial for handling geometric distortions present in fisheye imagery and capturing intricate boundaries in medical images. Our analysis demonstrates the versatility of GNNs in addressing diverse segmentation challenges and highlights their potential to improve segmentation accuracy in various applications, including autonomous driving and medical image analysis.

cs.CV↗

arXiv2026

RS2-SAM2: Customized SAM2 for Referring Remote Sensing Image Segmentation

Referring Remote Sensing Image Segmentation (RRSIS) aims to segment target objects in remote sensing (RS) images based on textual descriptions. Although Segment Anything Model 2 (SAM2) has shown remarkable performance in various segmentation tasks, its application to RRSIS presents several challenges, including understanding the text-described RS scenes and generating effective prompts from text. To address these issues, we propose \textbf{RS2-SAM2}, a novel framework that adapts SAM2 to RRSIS by aligning the adapted RS features and textual features while providing pseudo-mask-based dense prompts. Specifically, we employ a union encoder to jointly encode the visual and textual inputs, generating aligned visual and text embeddings as well as multimodal class tokens. A bidirectional hierarchical fusion module is introduced to adapt SAM2 to RS scenes and align adapted visual features with the visually enhanced text embeddings, improving the model's interpretation of text-described RS scenes. To provide precise target cues for SAM2, we design a mask prompt generator, which takes the visual embeddings and class tokens as input and produces a pseudo-mask as the dense prompt of SAM2. Experimental results on several RRSIS benchmarks demonstrate that RS2-SAM2 achieves state-of-the-art performance.

cs.CV↗

arXiv2023

Multi-Modal Evaluation Approach for Medical Image Segmentation

Manual segmentation of medical images (e.g., segmenting tumors in CT scans) is a high-effort task that can be accelerated with machine learning techniques. However, selecting the right segmentation approach depends on the evaluation function, particularly in medical image segmentation where we must deal with dependency between voxels. For instance, in contrast to classical systems where the predictions are either correct or incorrect, predictions in medical image segmentation may be partially correct and incorrect simultaneously. In this paper, we explore this expressiveness to extract the useful properties of these systems and formally define a novel multi-modal evaluation (MME) approach to measure the effectiveness of different segmentation methods. This approach improves the segmentation evaluation by introducing new relevant and interpretable characteristics, including detection property, boundary alignment, uniformity, total volume, and relative volume. Our proposed approach is open-source and publicly available for use. We have conducted several reproducible experiments, including the segmentation of pancreas, liver tumors, and multi-organs datasets, to show the applicability of the proposed approach.

cs.CV↗

arXiv2020

Kullback-Leibler Divergence-Based Fuzzy $C$-Means Clustering Incorporating Morphological Reconstruction and Wavelet Frames for Image Segmentation

Although spatial information of images usually enhance the robustness of the Fuzzy C-Means (FCM) algorithm, it greatly increases the computational costs for image segmentation. To achieve a sound trade-off between the segmentation performance and the speed of clustering, we come up with a Kullback-Leibler (KL) divergence-based FCM algorithm by incorporating a tight wavelet frame transform and a morphological reconstruction operation. To enhance FCM's robustness, an observed image is first filtered by using the morphological reconstruction. A tight wavelet frame system is employed to decompose the observed and filtered images so as to form their feature sets. Considering these feature sets as data of clustering, an modified FCM algorithm is proposed, which introduces a KL divergence term in the partition matrix into its objective function. The KL divergence term aims to make membership degrees of each image pixel closer to those of its neighbors, which brings that the membership partition becomes more suitable and the parameter setting of FCM becomes simplified. On the basis of the obtained partition matrix and prototypes, the segmented feature set is reconstructed by minimizing the inverse process of the modified objective function. To modify abnormal features produced in the reconstruction process, each reconstructed feature is reassigned to the closest prototype. As a result, the segmentation accuracy of KL divergence-based FCM is further improved. What's more, the segmented image is reconstructed by using a tight wavelet frame reconstruction operation. Finally, supporting experiments coping with synthetic, medical and color images are reported. Experimental results exhibit that the proposed algorithm works well and comes with better segmentation performance than other comparative algorithms. Moreover, the proposed algorithm requires less time than most of the FCM-related algorithms.

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arXiv2013

Robust Image Segmentation in Low Depth Of Field Images

In photography, low depth of field (DOF) is an important technique to emphasize the object of interest (OOI) within an image. Thus, low DOF images are widely used in the application area of macro, portrait or sports photography. When viewing a low DOF image, the viewer implicitly concentrates on the regions that are sharper regions of the image and thus segments the image into regions of interest and non regions of interest which has a major impact on the perception of the image. Thus, a robust algorithm for the fully automatic detection of the OOI in low DOF images provides valuable information for subsequent image processing and image retrieval. In this paper we propose a robust and parameterless algorithm for the fully automatic segmentation of low DOF images. We compare our method with three similar methods and show the superior robustness even though our algorithm does not require any parameters to be set by hand. The experiments are conducted on a real world data set with high and low DOF images.

cs.CV↗

arXiv2022

Multi-rater Prism: Learning self-calibrated medical image segmentation from multiple raters

In medical image segmentation, it is often necessary to collect opinions from multiple experts to make the final decision. This clinical routine helps to mitigate individual bias. But when data is multiply annotated, standard deep learning models are often not applicable. In this paper, we propose a novel neural network framework, called Multi-Rater Prism (MrPrism) to learn the medical image segmentation from multiple labels. Inspired by the iterative half-quadratic optimization, the proposed MrPrism will combine the multi-rater confidences assignment task and calibrated segmentation task in a recurrent manner. In this recurrent process, MrPrism can learn inter-observer variability taking into account the image semantic properties, and finally converges to a self-calibrated segmentation result reflecting the inter-observer agreement. Specifically, we propose Converging Prism (ConP) and Diverging Prism (DivP) to process the two tasks iteratively. ConP learns calibrated segmentation based on the multi-rater confidence maps estimated by DivP. DivP generates multi-rater confidence maps based on the segmentation masks estimated by ConP. The experimental results show that by recurrently running ConP and DivP, the two tasks can achieve mutual improvement. The final converged segmentation result of MrPrism outperforms state-of-the-art (SOTA) strategies on a wide range of medical image segmentation tasks.

eess.IV↗

arXiv2025

Multi-level Asymmetric Contrastive Learning for Volumetric Medical Image Segmentation Pre-training

Medical image segmentation is a fundamental yet challenging task due to the arduous process of acquiring large volumes of high-quality labeled data from experts. Contrastive learning offers a promising but still problematic solution to this dilemma. Firstly existing medical contrastive learning strategies focus on extracting image-level representation, which ignores abundant multi-level representations. Furthermore they underutilize the decoder either by random initialization or separate pre-training from the encoder, thereby neglecting the potential collaboration between the encoder and decoder. To address these issues, we propose a novel multi-level asymmetric contrastive learning framework named MACL for volumetric medical image segmentation pre-training. Specifically, we design an asymmetric contrastive learning structure to pre-train encoder and decoder simultaneously to provide better initialization for segmentation models. Moreover, we develop a multi-level contrastive learning strategy that integrates correspondences across feature-level, image-level, and pixel-level representations to ensure the encoder and decoder capture comprehensive details from representations of varying scales and granularities during the pre-training phase. Finally, experiments on 8 medical image datasets indicate our MACL framework outperforms existing 11 contrastive learning strategies. i.e. Our MACL achieves a superior performance with more precise predictions from visualization figures and 1.72%, 7.87%, 2.49% and 1.48% Dice higher than previous best results on ACDC, MMWHS, HVSMR and CHAOS with 10% labeled data, respectively. And our MACL also has a strong generalization ability among 5 variant U-Net backbones. Our code will be released at https://github.com/stevezs315/MACL.

cs.CV↗

arXiv2023

Volumetric Medical Image Segmentation via Scribble Annotations and Shape Priors

Recently, weakly-supervised image segmentation using weak annotations like scribbles has gained great attention in computer vision and medical image analysis, since such annotations are much easier to obtain compared to time-consuming and labor-intensive labeling at the pixel/voxel level. However, due to a lack of structure supervision on regions of interest (ROIs), existing scribble-based methods suffer from poor boundary localization. Furthermore, most current methods are designed for 2D image segmentation, which do not fully leverage the volumetric information if directly applied to each image slice. In this paper, we propose a scribble-based volumetric image segmentation, Scribble2D5, which tackles 3D anisotropic image segmentation and aims to its improve boundary prediction. To achieve this, we augment a 2.5D attention UNet with a proposed label propagation module to extend semantic information from scribbles and use a combination of static and active boundary prediction to learn ROI's boundary and regularize its shape. Also, we propose an optional add-on component, which incorporates the shape prior information from unpaired segmentation masks to further improve model accuracy. Extensive experiments on three public datasets and one private dataset demonstrate our Scribble2D5 achieves state-of-the-art performance on volumetric image segmentation using scribbles and shape prior if available.

cs.CV↗

arXiv2020

Deep Convolutional Neural Networks with Spatial Regularization, Volume and Star-shape Priori for Image Segmentation

We use Deep Convolutional Neural Networks (DCNNs) for image segmentation problems. DCNNs can well extract the features from natural images. However, the classification functions in the existing network architecture of CNNs are simple and lack capabilities to handle important spatial information in a way that have been done for many well-known traditional variational models. Prior such as spatial regularity, volume prior and object shapes cannot be well handled by existing DCNNs. We propose a novel Soft Threshold Dynamics (STD) framework which can easily integrate many spatial priors of the classical variational models into the DCNNs for image segmentation. The novelty of our method is to interpret the softmax activation function as a dual variable in a variational problem, and thus many spatial priors can be imposed in the dual space. From this viewpoint, we can build a STD based framework which can enable the outputs of DCNNs to have many special priors such as spatial regularity, volume constraints and star-shape priori. The proposed method is a general mathematical framework and it can be applied to any semantic segmentation DCNNs. To show the efficiency and accuracy of our method, we applied it to the popular DeepLabV3+ image segmentation network, and the experiments results show that our method can work efficiently on data-driven image segmentation DCNNs.

cs.CV↗

arXiv2019

Mixed-Supervised Dual-Network for Medical Image Segmentation

Deep learning based medical image segmentation models usually require large datasets with high-quality dense segmentations to train, which are very time-consuming and expensive to prepare. One way to tackle this challenge is by using the mixed-supervised learning framework, in which only a part of data is densely annotated with segmentation label and the rest is weakly labeled with bounding boxes. The model is trained jointly in a multi-task learning setting. In this paper, we propose Mixed-Supervised Dual-Network (MSDN), a novel architecture which consists of two separate networks for the detection and segmentation tasks respectively, and a series of connection modules between the layers of the two networks. These connection modules are used to transfer useful information from the auxiliary detection task to help the segmentation task. We propose to use a recent technique called "Squeeze and Excitation" in the connection module to boost the transfer. We conduct experiments on two medical image segmentation datasets. The proposed MSDN model outperforms multiple baselines.

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