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arXiv2023

Partition-A-Medical-Image: Extracting Multiple Representative Sub-regions for Few-shot Medical Image Segmentation

Few-shot Medical Image Segmentation (FSMIS) is a more promising solution for medical image segmentation tasks where high-quality annotations are naturally scarce. However, current mainstream methods primarily focus on extracting holistic representations from support images with large intra-class variations in appearance and background, and encounter difficulties in adapting to query images. In this work, we present an approach to extract multiple representative sub-regions from a given support medical image, enabling fine-grained selection over the generated image regions. Specifically, the foreground of the support image is decomposed into distinct regions, which are subsequently used to derive region-level representations via a designed Regional Prototypical Learning (RPL) module. We then introduce a novel Prototypical Representation Debiasing (PRD) module based on a two-way elimination mechanism which suppresses the disturbance of regional representations by a self-support, Multi-direction Self-debiasing (MS) block, and a support-query, Interactive Debiasing (ID) block. Finally, an Assembled Prediction (AP) module is devised to balance and integrate predictions of multiple prototypical representations learned using stacked PRD modules. Results obtained through extensive experiments on three publicly accessible medical imaging datasets demonstrate consistent improvements over the leading FSMIS methods. The source code is available at https://github.com/YazhouZhu19/PAMI.

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arXiv2024

Manifold-Aware Local Feature Modeling for Semi-Supervised Medical Image Segmentation

Achieving precise medical image segmentation is vital for effective treatment planning and accurate disease diagnosis. Traditional fully-supervised deep learning methods, though highly precise, are heavily reliant on large volumes of labeled data, which are often difficult to obtain due to the expertise required for medical annotations. This has led to the rise of semi-supervised learning approaches that utilize both labeled and unlabeled data to mitigate the label scarcity issue. In this paper, we introduce the Manifold-Aware Local Feature Modeling Network (MANet), which enhances the U-Net architecture by incorporating manifold supervision signals. This approach focuses on improving boundary accuracy, which is crucial for reliable medical diagnosis. To further extend the versatility of our method, we propose two variants: MA-Sobel and MA-Canny. The MA-Sobel variant employs the Sobel operator, which is effective for both 2D and 3D data, while the MA-Canny variant utilizes the Canny operator, specifically designed for 2D images, to refine boundary detection. These variants allow our method to adapt to various medical image modalities and dimensionalities, ensuring broader applicability. Our extensive experiments on datasets such as ACDC, LA, and Pancreas-NIH demonstrate that MANet consistently surpasses state-of-the-art methods in performance metrics like Dice and Jaccard scores. The proposed method also shows improved generalization across various semi-supervised segmentation networks, highlighting its robustness and effectiveness. Visual analysis of segmentation results confirms that MANet offers clearer and more accurate class boundaries, underscoring the value of manifold information in medical image segmentation.

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arXiv2022

CDDSA: Contrastive Domain Disentanglement and Style Augmentation for Generalizable Medical Image Segmentation

Generalization to previously unseen images with potential domain shifts and different styles is essential for clinically applicable medical image segmentation, and the ability to disentangle domain-specific and domain-invariant features is key for achieving Domain Generalization (DG). However, existing DG methods can hardly achieve effective disentanglement to get high generalizability. To deal with this problem, we propose an efficient Contrastive Domain Disentanglement and Style Augmentation (CDDSA) framework for generalizable medical image segmentation. First, a disentangle network is proposed to decompose an image into a domain-invariant anatomical representation and a domain-specific style code, where the former is sent to a segmentation model that is not affected by the domain shift, and the disentangle network is regularized by a decoder that combines the anatomical and style codes to reconstruct the input image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Thirdly, to further improve generalizability, we propose a style augmentation method based on the disentanglement representation to synthesize images in various unseen styles with shared anatomical structures. Our method was validated on a public multi-site fundus image dataset for optic cup and disc segmentation and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset for nasopharynx Gross Tumor Volume (GTVnx) segmentation. Experimental results showed that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in domain-generalizable segmentation.

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arXiv2026

A Unified Variational Framework for Deep Weakly Supervised Image Segmentation

We propose a unified variational framework for image segmentation under sparse pixel-level supervision. Our method is based on a simplex-constrained Potts model with a smooth perimeter regularizer, yielding a convex, smooth energy functional that can be used as a training loss in weakly supervised deep learning paradigms or optimized efficiently using iterative methods. Sparse labels are incorporated into the data fidelity term by constructing a fuzzy membership function via a function extension problem in a Reproducing Kernel Hilbert Space (RKHS), which can effectively capture inhomogeneous intensity statistics. The derived discrete loss for training standard networks demonstrates robustness and consistent improvements over non-training and partial cross-entropy (PCE) baselines in experiments, achieving comparable performance without requiring ground-truth segmentation images.

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arXiv2025

Geometric Feature Prompting of Image Segmentation Models

Advances in machine learning, especially the introduction of transformer architectures and vision transformers, have led to the development of highly capable computer vision foundation models. The segment anything model (known colloquially as SAM and more recently SAM 2), is a highly capable foundation model for segmentation of natural images and has been further applied to medical and scientific image segmentation tasks. SAM relies on prompts -- points or regions of interest in an image -- to generate associated segmentations. In this manuscript we propose the use of a geometrically motivated prompt generator to produce prompt points that are colocated with particular features of interest. Focused prompting enables the automatic generation of sensitive and specific segmentations in a scientific image analysis task using SAM with relatively few point prompts. The image analysis task examined is the segmentation of plant roots in rhizotron or minirhizotron images, which has historically been a difficult task to automate. Hand annotation of rhizotron images is laborious and often subjective; SAM, initialized with GeomPrompt local ridge prompts has the potential to dramatically improve rhizotron image processing. The authors have concurrently released an open source software suite called geomprompt https://pypi.org/project/geomprompt/ that can produce point prompts in a format that enables direct integration with the segment-anything package.

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arXiv2025

A Novel Convolutional-Free Method for 3D Medical Imaging Segmentation

Segmentation of 3D medical images is a critical task for accurate diagnosis and treatment planning. Convolutional neural networks (CNNs) have dominated the field, achieving significant success in 3D medical image segmentation. However, CNNs struggle with capturing long-range dependencies and global context, limiting their performance, particularly for fine and complex structures. Recent transformer-based models, such as TransUNet and nnFormer, have demonstrated promise in addressing these limitations, though they still rely on hybrid CNN-transformer architectures. This paper introduces a novel, fully convolutional-free model based on transformer architecture and self-attention mechanisms for 3D medical image segmentation. Our approach focuses on improving multi-semantic segmentation accuracy and addressing domain adaptation challenges between thick and thin slice CT images. We propose a joint loss function that facilitates effective segmentation of thin slices based on thick slice annotations, overcoming limitations in dataset availability. Furthermore, we present a benchmark dataset for multi-semantic segmentation on thin slices, addressing a gap in current medical imaging research. Our experiments demonstrate the superiority of the proposed model over traditional and hybrid architectures, offering new insights into the future of convolution-free medical image segmentation.

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arXiv2019

MIScnn: A Framework for Medical Image Segmentation with Convolutional Neural Networks and Deep Learning

The increased availability and usage of modern medical imaging induced a strong need for automatic medical image segmentation. Still, current image segmentation platforms do not provide the required functionalities for plain setup of medical image segmentation pipelines. Already implemented pipelines are commonly standalone software, optimized on a specific public data set. Therefore, this paper introduces the open-source Python library MIScnn. The aim of MIScnn is to provide an intuitive API allowing fast building of medical image segmentation pipelines including data I/O, preprocessing, data augmentation, patch-wise analysis, metrics, a library with state-of-the-art deep learning models and model utilization like training, prediction, as well as fully automatic evaluation (e.g. cross-validation). Similarly, high configurability and multiple open interfaces allow full pipeline customization. Running a cross-validation with MIScnn on the Kidney Tumor Segmentation Challenge 2019 data set (multi-class semantic segmentation with 300 CT scans) resulted into a powerful predictor based on the standard 3D U-Net model. With this experiment, we could show that the MIScnn framework enables researchers to rapidly set up a complete medical image segmentation pipeline by using just a few lines of code. The source code for MIScnn is available in the Git repository: https://github.com/frankkramer-lab/MIScnn.

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arXiv2022

4D Segmentation Algorithm with application to 3D+time Image Segmentation

In this paper, we introduce and study a novel segmentation method for 4D images based on surface evolution governed by a nonlinear partial differential equation, the generalized subjective surface equation. The new method uses 4D digital image information and information from a thresholded 4D image in a local neighborhood. Thus, the 4D image segmentation is accomplished by defining the edge detector function's input as the weighted sum of the norm of gradients of presmoothed 4D image and norm of presmoothed thresholded 4D image in a local neighborhood. Additionally, we design and study a numerical method based on the finite volume approach for solving the new model. The reduced diamond cell approach is used for approximating the gradient of the solution. We use a semi-implicit finite volume scheme for the numerical discretization and show that our numerical scheme is unconditionally stable. The new 4D method was tested on artificial data and applied to real data representing 3D+time microscopy images of cell nuclei within the zebrafish pectoral fin and hind-brain. In a real application, processing 3D+time microscopy images amounts to solving a linear system with several billion unknowns and requires over $1000$ GB of memory; thus, it may not be possible to process these images on a serial machine without parallel implementation utilizing the MPI. Consequently, we develop and present in the paper OpenMP and MPI parallel implementation of designed algorithms. Finally, we include cell tracking results to show how our new method serves as a basis for finding trajectories of cells during embryogenesis.

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arXiv2016

Unsupervised Image Segmentation using the Deffuant-Weisbuch Model from Social Dynamics

Unsupervised image segmentation algorithms aim at identifying disjoint homogeneous regions in an image, and have been subject to considerable attention in the machine vision community. In this paper, a popular theoretical model with it's origins in statistical physics and social dynamics, known as the Deffuant-Weisbuch model, is applied to the image segmentation problem. The Deffuant-Weisbuch model has been found to be useful in modelling the evolution of a closed system of interacting agents characterised by their opinions or beliefs, leading to the formation of clusters of agents who share a similar opinion or belief at steady state. In the context of image segmentation, this paper considers a pixel as an agent and it's colour property as it's opinion, with opinion updates as per the Deffuant-Weisbuch model. Apart from applying the basic model to image segmentation, this paper incorporates adjacency and neighbourhood information in the model, which factors in the local similarity and smoothness properties of images. Convergence is reached when the number of unique pixel opinions, i.e., the number of colour centres, matches the pre-specified number of clusters. Experiments are performed on a set of images from the Berkeley Image Segmentation Dataset and the results are analysed both qualitatively and quantitatively, which indicate that this simple and intuitive method is promising for image segmentation. To the best of the knowledge of the author, this is the first work where a theoretical model from statistical physics and social dynamics has been successfully applied to image processing.

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arXiv2016

A regularization-based approach for unsupervised image segmentation

We propose a novel unsupervised image segmentation algorithm, which aims to segment an image into several coherent parts. It requires no user input, no supervised learning phase and assumes an unknown number of segments. It achieves this by first over-segmenting the image into several hundred superpixels. These are iteratively joined on the basis of a discriminative classifier trained on color and texture information obtained from each superpixel. The output of the classifier is regularized by a Markov random field that lends more influence to neighbouring superpixels that are more similar. In each iteration, similar superpixels fall under the same label, until only a few coherent regions remain in the image. The algorithm was tested on a standard evaluation data set, where it performs on par with state-of-the-art algorithms in term of precision and greatly outperforms the state of the art by reducing the oversegmentation of the object of interest.

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arXiv2023

Few Shot Medical Image Segmentation with Cross Attention Transformer

Medical image segmentation has made significant progress in recent years. Deep learning-based methods are recognized as data-hungry techniques, requiring large amounts of data with manual annotations. However, manual annotation is expensive in the field of medical image analysis, which requires domain-specific expertise. To address this challenge, few-shot learning has the potential to learn new classes from only a few examples. In this work, we propose a novel framework for few-shot medical image segmentation, termed CAT-Net, based on cross masked attention Transformer. Our proposed network mines the correlations between the support image and query image, limiting them to focus only on useful foreground information and boosting the representation capacity of both the support prototype and query features. We further design an iterative refinement framework that refines the query image segmentation iteratively and promotes the support feature in turn. We validated the proposed method on three public datasets: Abd-CT, Abd-MRI, and Card-MRI. Experimental results demonstrate the superior performance of our method compared to state-of-the-art methods and the effectiveness of each component. Code: https://github.com/hust-linyi/CAT-Net.

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arXiv2016

Combinatorial Energy Learning for Image Segmentation

We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS) places a particular emphasis on modeling the inherent combinatorial nature of dense image segmentation problems. We propose efficient algorithms for learning deep neural networks to model the energy function, and for local optimization of this energy in the space of supervoxel agglomerations. We extensively evaluate our method on a publicly available 3-D microscopy dataset with 25 billion voxels of ground truth data. On an 11 billion voxel test set, we find that our method improves volumetric reconstruction accuracy by more than 20% as compared to two state-of-the-art baseline methods: graph-based segmentation of the output of a 3-D convolutional neural network trained to predict boundaries, as well as a random forest classifier trained to agglomerate supervoxels that were generated by a 3-D convolutional neural network.

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arXiv2022

Weakly Supervised Volumetric Image Segmentation with Deformed Templates

There are many approaches to weakly-supervised training of networks to segment 2D images. By contrast, existing approaches to segmenting volumetric images rely on full-supervision of a subset of 2D slices of the 3D volume. We propose an approach to volume segmentation that is truly weakly-supervised in the sense that we only need to provide a sparse set of 3D points on the surface of target objects instead of detailed 2D masks. We use the 3D points to deform a 3D template so that it roughly matches the target object outlines and we introduce an architecture that exploits the supervision it provides to train a network to find accurate boundaries. We evaluate our approach on Computed Tomography (CT), Magnetic Resonance Imagery (MRI) and Electron Microscopy (EM) image datasets and show that it substantially reduces the required amount of effort.

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arXiv2018

Adaptive strategy for superpixel-based region-growing image segmentation

This work presents a region-growing image segmentation approach based on superpixel decomposition. From an initial contour-constrained over-segmentation of the input image, the image segmentation is achieved by iteratively merging similar superpixels into regions. This approach raises two key issues: (1) how to compute the similarity between superpixels in order to perform accurate merging and (2) in which order those superpixels must be merged together. In this perspective, we firstly introduce a robust adaptive multi-scale superpixel similarity in which region comparisons are made both at content and common border level. Secondly, we propose a global merging strategy to efficiently guide the region merging process. Such strategy uses an adpative merging criterion to ensure that best region aggregations are given highest priorities. This allows to reach a final segmentation into consistent regions with strong boundary adherence. We perform experiments on the BSDS500 image dataset to highlight to which extent our method compares favorably against other well-known image segmentation algorithms. The obtained results demonstrate the promising potential of the proposed approach.

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arXiv2025

AMLP: Adjustable Masking Lesion Patches for Self-Supervised Medical Image Segmentation

Self-supervised masked image modeling (MIM) methods have shown promising performances on analyzing natural images. However, directly applying such methods to medical image segmentation tasks still cannot achieve satisfactory results. The challenges arise from the facts that (i) medical images are inherently more complex compared to natural images, and the subjects in medical images often exhibit more distinct contour features; (ii) moreover, the conventional high and fixed masking ratio in MIM is likely to mask the background, limiting the scope of learnable information. To address these problems, we propose a new self-supervised medical image segmentation framework, called Adjustable Masking Lesion Patches (AMLP), which employs Masked Patch Selection~(MPS) strategy to identify patches with high probabilities of containing lesions to help model achieve precise lesion reconstruction. To improve the categorization of patches in MPS, we further introduce Relative Reconstruction Loss (RRL) to better learn hard-to-reconstruct lesion patches. Then, Category Consistency Loss (CCL) is proposed to refine patch categorization based on reconstruction difficulty, enhancing difference between lesions and backgrounds. Moreover, an Adjustable Masking Ratio (AMR) strategy is proposed to gradually increase the masking ratio over training to expand~the scope of learnable mutual information. Extensive~experiments on two medical segmentation datasets demonstrate the superior performances of the proposed AMLP w.r.t. the SOTA self-supervised methods; the results prove that AMLP effectively addresses the challenges of applying masked modeling to medical images and capturing accurate lesion details that are crucial for segmentation tasks.

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arXiv2023

Hierarchical Open-vocabulary Universal Image Segmentation

Open-vocabulary image segmentation aims to partition an image into semantic regions according to arbitrary text descriptions. However, complex visual scenes can be naturally decomposed into simpler parts and abstracted at multiple levels of granularity, introducing inherent segmentation ambiguity. Unlike existing methods that typically sidestep this ambiguity and treat it as an external factor, our approach actively incorporates a hierarchical representation encompassing different semantic-levels into the learning process. We propose a decoupled text-image fusion mechanism and representation learning modules for both "things" and "stuff". Additionally, we systematically examine the differences that exist in the textual and visual features between these types of categories. Our resulting model, named HIPIE, tackles HIerarchical, oPen-vocabulary, and unIvErsal segmentation tasks within a unified framework. Benchmarked on over 40 datasets, e.g., ADE20K, COCO, Pascal-VOC Part, RefCOCO/RefCOCOg, ODinW and SeginW, HIPIE achieves the state-of-the-art results at various levels of image comprehension, including semantic-level (e.g., semantic segmentation), instance-level (e.g., panoptic/referring segmentation and object detection), as well as part-level (e.g., part/subpart segmentation) tasks. Our code is released at https://github.com/berkeley-hipie/HIPIE.

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arXiv2024

HMT-UNet: A hybird Mamba-Transformer Vision UNet for Medical Image Segmentation

In the field of medical image segmentation, models based on both CNN and Transformer have been thoroughly investigated. However, CNNs have limited modeling capabilities for long-range dependencies, making it challenging to exploit the semantic information within images fully. On the other hand, the quadratic computational complexity poses a challenge for Transformers. State Space Models (SSMs), such as Mamba, have been recognized as a promising method. They not only demonstrate superior performance in modeling long-range interactions, but also preserve a linear computational complexity. The hybrid mechanism of SSM (State Space Model) and Transformer, after meticulous design, can enhance its capability for efficient modeling of visual features. Extensive experiments have demonstrated that integrating the self-attention mechanism into the hybrid part behind the layers of Mamba's architecture can greatly improve the modeling capacity to capture long-range spatial dependencies. In this paper, leveraging the hybrid mechanism of SSM, we propose a U-shape architecture model for medical image segmentation, named Hybird Transformer vision Mamba UNet (HTM-UNet). We conduct comprehensive experiments on the ISIC17, ISIC18, CVC-300, CVC-ClinicDB, Kvasir, CVC-ColonDB, ETIS-Larib PolypDB public datasets and ZD-LCI-GIM private dataset. The results indicate that HTM-UNet exhibits competitive performance in medical image segmentation tasks. Our code is available at https://github.com/simzhangbest/HMT-Unet.

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arXiv2019

Computing Valid p-values for Image Segmentation by Selective Inference

Image segmentation is one of the most fundamental tasks of computer vision. In many practical applications, it is essential to properly evaluate the reliability of individual segmentation results. In this study, we propose a novel framework to provide the statistical significance of segmentation results in the form of p-values. Specifically, we consider a statistical hypothesis test for determining the difference between the object and the background regions. This problem is challenging because the difference can be deceptively large (called segmentation bias) due to the adaptation of the segmentation algorithm to the data. To overcome this difficulty, we introduce a statistical approach called selective inference, and develop a framework to compute valid p-values in which the segmentation bias is properly accounted for. Although the proposed framework is potentially applicable to various segmentation algorithms, we focus in this paper on graph cut-based and threshold-based segmentation algorithms, and develop two specific methods to compute valid p-values for the segmentation results obtained by these algorithms. We prove the theoretical validity of these two methods and demonstrate their practicality by applying them to segmentation problems for medical images.

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