Accurate segmentation of nodules in both 2D breast ultrasound (BUS) and 3D automated breast ultrasound (ABUS) is crucial for clinical diagnosis and treatment planning. Therefore, developing an automated system for nodule segmentation can enhance user independence and expedite clinical analysis. Unlike fully-supervised learning, weakly-supervised segmentation (WSS) can streamline the laborious and intricate annotation process. However, current WSS methods face challenges in achieving precise nodule segmentation, as many of them depend on inaccurate activation maps or inefficient pseudo-mask generation algorithms. In this study, we introduce a novel multi-agent reinforcement learning-based WSS framework called Flip Learning, which relies solely on 2D/3D boxes for accurate segmentation. Specifically, multiple agents are employed to erase the target from the box to facilitate classification tag flipping, with the erased region serving as the predicted segmentation mask. The key contributions of this research are as follows: (1) Adoption of a superpixel/supervoxel-based approach to encode the standardized environment, capturing boundary priors and expediting the learning process. (2) Introduction of three meticulously designed rewards, comprising a classification score reward and two intensity distribution rewards, to steer the agents' erasing process precisely, thereby avoiding both under- and over-segmentation. (3) Implementation of a progressive curriculum learning strategy to enable agents to interact with the environment in a progressively challenging manner, thereby enhancing learning efficiency. Extensively validated on the large in-house BUS and ABUS datasets, our Flip Learning method outperforms state-of-the-art WSS methods and foundation models, and achieves comparable performance as fully-supervised learning algorithms.
Weakly supervised segmentation methods can delineate thyroid nodules in ultrasound images efficiently using training data with coarse labels, but suffer from: 1) low-confidence pseudo-labels that follow topological priors, introducing significant label noise, and 2) low-rationality loss functions that rigidly compare segmentation with labels, ignoring discriminative information for nodules with diverse and complex shapes. To solve these issues, we clarify the objective and references for weakly supervised ultrasound image segmentation, presenting a framework with high-confidence pseudo-labels to represent topological and anatomical information and high-rationality losses to capture multi-level discriminative features. Specifically, we fuse geometric transformations of four-point annotations and MedSAM model results prompted by specific annotations to generate high-confidence box, foreground, and background labels. Our high-rationality learning strategy includes: 1) Alignment loss measuring spatial consistency between segmentation and box label, and topological continuity within the foreground label, guiding the network to perceive nodule location; 2) Contrastive loss pulling features from labeled foreground regions while pushing features from labeled foreground and background regions, guiding the network to learn nodule and background feature distribution; 3) Prototype correlation loss measuring consistency between correlation maps derived by comparing features with foreground and background prototypes, refining uncertain regions to accurate nodule edges. Experimental results show that our method achieves state-of-the-art performance on the TN3K and DDTI datasets. The code is available at https://github.com/bluehenglee/MLI-MSC.
Weakly supervised segmentation has the potential to greatly reduce the annotation effort for training segmentation models for small structures such as hyper-reflective foci (HRF) in optical coherence tomography (OCT). However, most weakly supervised methods either involve a strong downsampling of input images, or only achieve localization at a coarse resolution, both of which are unsatisfactory for small structures. We propose a novel framework that increases the spatial resolution of a traditional attention-based Multiple Instance Learning (MIL) approach by using Layer-wise Relevance Propagation (LRP) to prompt the Segment Anything Model (SAM~2), and increases recall with iterative inference. Moreover, we demonstrate that replacing MIL with a Compact Convolutional Transformer (CCT), which adds a positional encoding, and permits an exchange of information between different regions of the OCT image, leads to a further and substantial increase in segmentation accuracy.
Weakly-supervised medical image segmentation is gaining traction as it requires only rough annotations rather than accurate pixel-to-pixel labels, thereby reducing the workload for specialists. Although some progress has been made, there is still a considerable performance gap between the label-efficient methods and fully-supervised one, which can be attributed to the uncertainty nature of these weak labels. To address this issue, we propose a novel weak annotation method coupled with its learning framework EAUWSeg to eliminate the annotation uncertainty. Specifically, we first propose the Bounded Polygon Annotation (BPAnno) by simply labeling two polygons for a lesion. Then, the tailored learning mechanism that explicitly treat bounded polygons as two separated annotations is proposed to learn invariant feature by providing adversarial supervision signal for model training. Subsequently, a confidence-auxiliary consistency learner incorporates with a classification-guided confidence generator is designed to provide reliable supervision signal for pixels in uncertain region by leveraging the feature presentation consistency across pixels within the same category as well as class-specific information encapsulated in bounded polygons annotation. Experimental results demonstrate that EAUWSeg outperforms existing weakly-supervised segmentation methods. Furthermore, compared to fully-supervised counterparts, the proposed method not only delivers superior performance but also costs much less annotation workload. This underscores the superiority and effectiveness of our approach.
Creating fully annotated labels for medical image segmentation is prohibitively time-intensive and costly, emphasizing the necessity for innovative approaches that minimize reliance on detailed annotations. Scribble annotations offer a more cost-effective alternative, significantly reducing the expenses associated with full annotations. However, scribble annotations offer limited and imprecise information, failing to capture the detailed structural and boundary characteristics necessary for accurate organ delineation. To address these challenges, we propose HELPNet, a novel scribble-based weakly supervised segmentation framework, designed to bridge the gap between annotation efficiency and segmentation performance. HELPNet integrates three modules. The Hierarchical perturbations consistency (HPC) module enhances feature learning by employing density-controlled jigsaw perturbations across global, local, and focal views, enabling robust modeling of multi-scale structural representations. Building on this, the Entropy-guided pseudo-label (EGPL) module evaluates the confidence of segmentation predictions using entropy, generating high-quality pseudo-labels. Finally, the structural prior refinement (SPR) module incorporates connectivity and bounded priors to enhance the precision and reliability and pseudo-labels. Experimental results on three public datasets ACDC, MSCMRseg, and CHAOS show that HELPNet significantly outperforms state-of-the-art methods for scribble-based weakly supervised segmentation and achieves performance comparable to fully supervised methods. The code is available at https://github.com/IPMI-NWU/HELPNet.
The features of self-supervised vision transformers (ViTs) contain strong semantic and positional information relevant to downstream tasks like object localization and segmentation. Recent works combine these features with traditional methods like clustering, graph partitioning or region correlations to achieve impressive baselines without finetuning or training additional networks. We leverage upsampled features from ViT networks (e.g DINOv2) in two workflows: in a clustering based approach for object localization and segmentation, and paired with standard classifiers in weakly supervised materials segmentation. Both show strong performance on benchmarks, especially in weakly supervised segmentation where the ViT features capture complex relationships inaccessible to classical approaches. We expect the flexibility and generalizability of these features will both speed up and strengthen materials characterization, from segmentation to property-prediction.
Scribble-based weakly supervised segmentation techniques offer comparable performance to fully supervised methods while significantly reducing annotation costs, making them an appealing alternative. Existing methods often rely on auxiliary tasks to enforce semantic consistency and use hard pseudo labels for supervision. However, these methods often overlook the unique requirements of models trained with sparse annotations. Since the model must predict pixel-wise segmentation maps with limited annotations, the ability to handle varying levels of annotation richness is critical. In this paper, we adopt the principle of `from few to more' and propose MaCo, a weakly supervised framework designed for medical image segmentation. MaCo employs masked context modeling (MCM) and continuous pseudo labels (CPL). MCM uses an attention-based masking strategy to disrupt the input image, compelling the model's predictions to remain consistent with those of the original image. CPL converts scribble annotations into continuous pixel-wise labels by applying an exponential decay function to distance maps, resulting in continuous maps that represent the confidence of each pixel belonging to a specific category, rather than using hard pseudo labels. We evaluate MaCo against other weakly supervised methods using three public datasets. The results indicate that MaCo outperforms competing methods across all datasets, setting a new record in weakly supervised medical image segmentation.
In this work, we introduce Scribbles for All, a label and training data generation algorithm for semantic segmentation trained on scribble labels. Training or fine-tuning semantic segmentation models with weak supervision has become an important topic recently and was subject to significant advances in model quality. In this setting, scribbles are a promising label type to achieve high quality segmentation results while requiring a much lower annotation effort than usual pixel-wise dense semantic segmentation annotations. The main limitation of scribbles as source for weak supervision is the lack of challenging datasets for scribble segmentation, which hinders the development of novel methods and conclusive evaluations. To overcome this limitation, Scribbles for All provides scribble labels for several popular segmentation datasets and provides an algorithm to automatically generate scribble labels for any dataset with dense annotations, paving the way for new insights and model advancements in the field of weakly supervised segmentation. In addition to providing datasets and algorithm, we evaluate state-of-the-art segmentation models on our datasets and show that models trained with our synthetic labels perform competitively with respect to models trained on manual labels. Thus, our datasets enable state-of-the-art research into methods for scribble-labeled semantic segmentation. The datasets, scribble generation algorithm, and baselines are publicly available at https://github.com/wbkit/Scribbles4All
Accurate assessment of lymph node size in 3D CT scans is crucial for cancer staging, therapeutic management, and monitoring treatment response. Existing state-of-the-art segmentation frameworks in medical imaging often rely on fully annotated datasets. However, for lymph node segmentation, these datasets are typically small due to the extensive time and expertise required to annotate the numerous lymph nodes in 3D CT scans. Weakly-supervised learning, which leverages incomplete or noisy annotations, has recently gained interest in the medical imaging community as a potential solution. Despite the variety of weakly-supervised techniques proposed, most have been validated only on private datasets or small publicly available datasets. To address this limitation, the Mediastinal Lymph Node Quantification (LNQ) challenge was organized in conjunction with the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023). This challenge aimed to advance weakly-supervised segmentation methods by providing a new, partially annotated dataset and a robust evaluation framework. A total of 16 teams from 5 countries submitted predictions to the validation leaderboard, and 6 teams from 3 countries participated in the evaluation phase. The results highlighted both the potential and the current limitations of weakly-supervised approaches. On one hand, weakly-supervised approaches obtained relatively good performance with a median Dice score of $61.0\%$. On the other hand, top-ranked teams, with a median Dice score exceeding $70\%$, boosted their performance by leveraging smaller but fully annotated datasets to combine weak supervision and full supervision. This highlights both the promise of weakly-supervised methods and the ongoing need for high-quality, fully annotated data to achieve higher segmentation performance.
Heatmaps generated on inputs of image classification networks via explainable AI methods like Grad-CAM and LRP have been observed to resemble segmentations of input images in many cases. Consequently, heatmaps have also been leveraged for achieving weakly supervised segmentation with image-level supervision. On the other hand, losses can be imposed on differentiable heatmaps, which has been shown to serve for (1)~improving heatmaps to be more human-interpretable, (2)~regularization of networks towards better generalization, (3)~training diverse ensembles of networks, and (4)~for explicitly ignoring confounding input features. Due to the latter use case, the paradigm of imposing losses on heatmaps is often referred to as "Right for the right reasons". We unify these two lines of research by investigating semi-supervised segmentation as a novel use case for the Right for the Right Reasons paradigm. First, we show formal parallels between differentiable heatmap architectures and standard encoder-decoder architectures for image segmentation. Second, we show that such differentiable heatmap architectures yield competitive results when trained with standard segmentation losses. Third, we show that such architectures allow for training with weak supervision in the form of image-level labels and small numbers of pixel-level labels, outperforming comparable encoder-decoder models. Code is available at \url{https://github.com/Kainmueller-Lab/TW-autoencoder}.
Weakly-supervised segmentation (WSS) methods, reliant on image-level labels indicating object presence, lack explicit correspondence between labels and regions of interest (ROIs), posing a significant challenge. Despite this, WSS methods have attracted attention due to their much lower annotation costs compared to fully-supervised segmentation. Leveraging reinforcement learning (RL) self-play, we propose a novel WSS method that gamifies image segmentation of a ROI. We formulate segmentation as a competition between two agents that compete to select ROI-containing patches until exhaustion of all such patches. The score at each time-step, used to compute the reward for agent training, represents likelihood of object presence within the selection, determined by an object presence detector pre-trained using only image-level binary classification labels of object presence. Additionally, we propose a game termination condition that can be called by either side upon exhaustion of all ROI-containing patches, followed by the selection of a final patch from each. Upon termination, the agent is incentivised if ROI-containing patches are exhausted or disincentivised if an ROI-containing patch is found by the competitor. This competitive setup ensures minimisation of over- or under-segmentation, a common problem with WSS methods. Extensive experimentation across four datasets demonstrates significant performance improvements over recent state-of-the-art methods. Code: https://github.com/s-sd/spurl/tree/main/wss
Weakly supervised segmentation methods have gained significant attention due to their ability to reduce the reliance on costly pixel-level annotations during model training. However, the current weakly supervised nuclei segmentation approaches typically follow a two-stage pseudo-label generation and network training process. The performance of the nuclei segmentation heavily relies on the quality of the generated pseudo-labels, thereby limiting its effectiveness. This paper introduces a novel domain-adaptive weakly supervised nuclei segmentation framework using cross-task interaction strategies to overcome the challenge of pseudo-label generation. Specifically, we utilize weakly annotated data to train an auxiliary detection task, which assists the domain adaptation of the segmentation network. To enhance the efficiency of domain adaptation, we design a consistent feature constraint module integrating prior knowledge from the source domain. Furthermore, we develop pseudo-label optimization and interactive training methods to improve the domain transfer capability. To validate the effectiveness of our proposed method, we conduct extensive comparative and ablation experiments on six datasets. The results demonstrate the superiority of our approach over existing weakly supervised approaches. Remarkably, our method achieves comparable or even better performance than fully supervised methods. Our code will be released in https://github.com/zhangye-zoe/DAWN.
Annotating lots of 3D medical images for training segmentation models is time-consuming. The goal of weakly supervised semantic segmentation is to train segmentation models without using any ground truth segmentation masks. Our work addresses the case where only image-level categorical labels, indicating the presence or absence of a particular region of interest (such as tumours or lesions), are available. Most existing methods rely on class activation mapping (CAM). We propose a novel approach, ToNNO, which is based on the Tomographic reconstruction of a Neural Network's Output. Our technique extracts stacks of slices with different angles from the input 3D volume, feeds these slices to a 2D encoder, and applies the inverse Radon transform in order to reconstruct a 3D heatmap of the encoder's predictions. This generic method allows to perform dense prediction tasks on 3D volumes using any 2D image encoder. We apply it to weakly supervised medical image segmentation by training the 2D encoder to output high values for slices containing the regions of interest. We test it on four large scale medical image datasets and outperform 2D CAM methods. We then extend ToNNO by combining tomographic reconstruction with CAM methods, proposing Averaged CAM and Tomographic CAM, which obtain even better results.
Foundation models have exhibited unprecedented capabilities in tackling many domains and tasks. Models such as CLIP are currently widely used to bridge cross-modal representations, and text-to-image diffusion models are arguably the leading models in terms of realistic image generation. Image generative models are trained on massive datasets that provide them with powerful internal spatial representations. In this work, we explore the potential benefits of such representations, beyond image generation, in particular, for dense visual prediction tasks. We focus on the task of image segmentation, which is traditionally solved by training models on closed-vocabulary datasets, with pixel-level annotations. To avoid the annotation cost or training large diffusion models, we constraint our setup to be zero-shot and training-free. In a nutshell, our pipeline leverages different and relatively small-sized, open-source foundation models for zero-shot open-vocabulary segmentation. The pipeline is as follows: the image is passed to both a captioner model (i.e. BLIP) and a diffusion model (i.e., Stable Diffusion Model) to generate a text description and visual representation, respectively. The features are clustered and binarized to obtain class agnostic masks for each object. These masks are then mapped to a textual class, using the CLIP model to support open-vocabulary. Finally, we add a refinement step that allows to obtain a more precise segmentation mask. Our approach (dubbed FreeSeg-Diff), which does not rely on any training, outperforms many training-based approaches on both Pascal VOC and COCO datasets. In addition, we show very competitive results compared to the recent weakly-supervised segmentation approaches. We provide comprehensive experiments showing the superiority of diffusion model features compared to other pretrained models. Project page: https://bcorrad.github.io/freesegdiff/
For robotic surgical videos, instrument presence annotations are typically recorded with video streams, which offering the potential to reduce the manually annotated costs for segmentation. However, weakly supervised surgical instrument segmentation with only instrument presence labels has been rarely explored in surgical domain due to the highly under-constrained challenges. Temporal properties can enhance representation learning by capturing sequential dependencies and patterns over time even in incomplete supervision situations. From this, we take the inherent temporal attributes of surgical video into account and extend a two-stage weakly supervised segmentation paradigm from different perspectives. Firstly, we make temporal equivariance constraint to enhance pixel-wise temporal consistency between adjacent features. Secondly, we constrain class-aware semantic continuity between global and local regions across temporal dimension. Finally, we generate temporal-enhanced pseudo masks from consecutive frames to suppress irrelevant regions. Extensive experiments are validated on two surgical video datasets, including one cholecystectomy surgery benchmark and one real robotic left lateral segment liver surgery dataset. We annotate instance-wise instrument labels with fixed time-steps which are double checked by a clinician with 3-years experience to evaluate segmentation results. Experimental results demonstrate the promising performances of our method, which consistently achieves comparable or favorable results with previous state-of-the-art approaches.
Vertebral body (VB) segmentation is an important preliminary step towards medical visual diagnosis for spinal diseases. However, most previous works require pixel/voxel-wise strong supervisions, which is expensive, tedious and time-consuming for experts to annotate. In this paper, we propose a Weakly supervised Iterative Spinal Segmentation (WISS) method leveraging only four corner landmark weak labels on a single sagittal slice to achieve automatic volumetric segmentation from CT images for VBs. WISS first segments VBs on an annotated sagittal slice in an iterative self-training manner. This self-training method alternates between training and refining labels in the training set. Then WISS proceeds to segment the whole VBs slice by slice with a slice-propagation method to obtain volumetric segmentations. We evaluate the performance of WISS on a private spinal metastases CT dataset and the public lumbar CT dataset. On the first dataset, WISS achieves distinct improvements with regard to two different backbones. For the second dataset, WISS achieves dice coefficients of $91.7\%$ and $83.7\%$ for mid-sagittal slices and 3D CT volumes, respectively, saving a lot of labeling costs and only sacrificing a little segmentation performance.
This paper proposes a dynamic interactive and weakly supervised segmentation method with minimal user interactions to address two major challenges in the segmentation of whole slide histopathology images. First, the lack of hand-annotated datasets to train algorithms. Second, the lack of interactive paradigms to enable a dialogue between the pathologist and the machine, which can be a major obstacle for use in clinical routine. We therefore propose a fast and user oriented method to bridge this gap by giving the pathologist control over the final result while limiting the number of interactions needed to achieve a good result (over 90\% on all our metrics with only 4 correction scribbles).
Weakly-supervised segmentation (WSS) has emerged as a solution to mitigate the conflict between annotation cost and model performance by adopting sparse annotation formats (e.g., point, scribble, block, etc.). Typical approaches attempt to exploit anatomy and topology priors to directly expand sparse annotations into pseudo-labels. However, due to a lack of attention to the ambiguous edges in medical images and insufficient exploration of sparse supervision, existing approaches tend to generate erroneous and overconfident pseudo proposals in noisy regions, leading to cumulative model error and performance degradation. In this work, we propose a novel WSS approach, named ProCNS, encompassing two synergistic modules devised with the principles of progressive prototype calibration and noise suppression. Specifically, we design a Prototype-based Regional Spatial Affinity (PRSA) loss to maximize the pair-wise affinities between spatial and semantic elements, providing our model of interest with more reliable guidance. The affinities are derived from the input images and the prototype-refined predictions. Meanwhile, we propose an Adaptive Noise Perception and Masking (ANPM) module to obtain more enriched and representative prototype representations, which adaptively identifies and masks noisy regions within the pseudo proposals, reducing potential erroneous interference during prototype computation. Furthermore, we generate specialized soft pseudo-labels for the noisy regions identified by ANPM, providing supplementary supervision. Extensive experiments on six medical image segmentation tasks involving different modalities demonstrate that the proposed framework significantly outperforms representative state-of-the-art methods.
Single-point annotation in visual tasks, with the goal of minimizing labelling costs, is becoming increasingly prominent in research. Recently, visual foundation models, such as Segment Anything (SAM), have gained widespread usage due to their robust zero-shot capabilities and exceptional annotation performance. However, SAM's class-agnostic output and high confidence in local segmentation introduce 'semantic ambiguity', posing a challenge for precise category-specific segmentation. In this paper, we introduce a cost-effective category-specific segmenter using SAM. To tackle this challenge, we have devised a Semantic-Aware Instance Segmentation Network (SAPNet) that integrates Multiple Instance Learning (MIL) with matching capability and SAM with point prompts. SAPNet strategically selects the most representative mask proposals generated by SAM to supervise segmentation, with a specific focus on object category information. Moreover, we introduce the Point Distance Guidance and Box Mining Strategy to mitigate inherent challenges: 'group' and 'local' issues in weakly supervised segmentation. These strategies serve to further enhance the overall segmentation performance. The experimental results on Pascal VOC and COCO demonstrate the promising performance of our proposed SAPNet, emphasizing its semantic matching capabilities and its potential to advance point-prompted instance segmentation. The code will be made publicly available.
Polyp segmentation plays a vital role in accurately locating polyps at an early stage, which holds significant clinical importance for the prevention of colorectal cancer. Various polyp segmentation methods have been developed using fully-supervised deep learning techniques. However, pixel-wise annotation for polyp images by physicians during the diagnosis is both time-consuming and expensive. Moreover, visual foundation models such as the Segment Anything Model (SAM) have shown remarkable performance. Nevertheless, directly applying SAM to medical segmentation may not produce satisfactory results due to the inherent absence of medical knowledge. In this paper, we propose a novel SAM-guided Collaborative Learning Network (SAM-CLNet) for scribble-supervised polyp segmentation, enabling a collaborative learning process between our segmentation network and SAM to boost the model performance. Specifically, we first propose a Cross-level Enhancement and Aggregation Network (CEA-Net) for weakly-supervised polyp segmentation. Within CEA-Net, we propose a Cross-level Enhancement Module (CEM) that integrates the adjacent features to enhance the representation capabilities of different resolution features. Additionally, a Feature Aggregation Module (FAM) is employed to capture richer features across multiple levels. Moreover, we present a box-augmentation strategy that combines the segmentation maps generated by CEA-Net with scribble annotations to create more precise prompts. These prompts are then fed into SAM, generating segmentation SAM-guided masks, which can provide additional supervision to train CEA-Net effectively. Furthermore, we present an Image-level Filtering Mechanism to filter out unreliable SAM-guided masks. Extensive experimental results show that our SAM-CLNet outperforms state-of-the-art weakly-supervised segmentation methods.