Image Segmentation

Improving the reliability and completeness of colonoscopic inspection is critical for reducing missed lesions and improving colorectal cancer prevention. Reliable scene understanding is essential for navigation, reconstruction, and assessment of inspection completeness. Anatomical structures such as mucosal folds provide stable geometric cues for endoscope localization, while surgical instruments introduce dynamic occlusions that complicate visual interpretation. However, existing gastrointestinal endoscopy datasets largely focus on disease detection or artifact segmentation, leaving a gap in precise annotations of structural landmarks and instruments. We introduce SegCol, a dataset and benchmark for semantic segmentation of colon fold edges and surgical instruments derived from the EndoMapper dataset. SegCol provides manually annotated pixel-level masks for three instrument classes and thin fold-edge structures across temporally consistent image sequences. It forms the basis of the SegCol Challenge, organized as part of the EndoVis Challenge at MICCAI 2024, evaluating both supervised segmentation and annotation-efficient active learning. We further study segmentation metrics, including Dice, ODS/OIS, AP, and CLDice, under structural perturbations and different object geometries, and analyze participating methods, architectural choices, and active learning strategies. Our findings show that metric behavior strongly depends on target structure, highlighting the need for carefully selected evaluation protocols in endoscopic segmentation. Details are available at https://www.synapse.org/Synapse:syn54124209/wiki/626563, and code at https://github.com/surgical-vision/segcol_challenge.

Robots need to be able to understand their surroundings in order to operate safely and robustly, and to interact with the surrounding environment. Robots deployed in unconstrained real-world scenarios must additionally be able to deal with novel situations and objects that have never been seen before. In this article, we tackle the problem of open-world panoptic segmentation, i.e., the task of discovering new semantic categories and new object instances at test time, while enforcing consistency among the categories that we incrementally discover. We present Con2MAV, a general method for open-world panoptic segmentation. Experiments across a wide range of datasets, from road scenes to underwater environments, highlight its compelling capabilities in open-world segmentation and its competitive performance on known classes. We will open-source the implementation of our approach upon acceptance. In addition, we propose PANIC (Panoptic ANomalies In Context), a benchmark for evaluating open-world segmentation tasks in autonomous driving scenarios. This dataset, recorded with a multi-modal sensor suite mounted on a car, and then manually annotated, provides high-quality, pixel-wise annotations of anomalous objects at both semantic and instance level. PANIC contains 800 images, more than 50 unknown classes, i.e., classes that do not appear in the training set, and over 4,000 object instances, providing a comprehensive benchmark for evaluating open-world segmentation methods in autonomous driving scenarios. We provide competitions for multiple open-world segmentation tasks on a hidden test set. Our dataset and competitions are available at https://www.ipb.uni-bonn.de/data/panic.

Large-scale pre-trained audio and image models demonstrate an unprecedented degree of generalization, making them suitable for a wide range of applications. Here, we tackle the specific task of sound-prompted segmentation, aiming to segment image regions corresponding to objects heard in an audio signal. Most existing approaches tackle this problem by fine-tuning pre-trained models or by training additional modules specifically for the task. We adopt a different strategy: we introduce a training-free approach that leverages Non-negative Matrix Factorization (NMF) to co-factorize audio and visual features from pre-trained models so as to reveal shared interpretable concepts. These concepts are passed on to an open-vocabulary segmentation model for precise segmentation maps. By using frozen pre-trained models, our method achieves high generalization and establishes state-of-the-art performance in unsupervised sound-prompted segmentation, significantly surpassing previous unsupervised methods.

Segmentation of cellular structures in electron microscopy (EM) images is fundamental to analyzing the morphology of neurons and glial cells in the healthy and diseased brain tissue. Current neuronal segmentation applications are based on convolutional neural networks (CNNs) and do not effectively capture global relationships within images. Here, we present DendriteSAM, a vision foundation model based on Segment Anything, for interactive and automatic segmentation of dendrites in EM images. The model is trained on high-resolution EM data from healthy rat hippocampus and is tested on diseased rat and human data. Our evaluation results demonstrate better mask quality compared to the original and other fine-tuned models, leveraging the features learned during training. This study introduces the first implementation of vision foundation models in dendrite segmentation, paving the path for computer-assisted diagnosis of neuronal anomalies.

Early detection of vision-threatening conditions such as diabetic retinopathy, glaucoma, and age-related macular degeneration depends on retinal fundus image analysis, but manual assessment is slow and expert-dependent. Automated convolutional neural networks classify fundus images accurately yet act as black boxes, and existing retinal vessel segmentation methods lose discriminative power under pathology and seldom exploit attention or transformer backbones. Using the FIVES and DRIVE fundus datasets, we develop a two-pipeline framework that pairs four-class disease classification with attention- and transformer-based vessel segmentation, organised in three stages: (1) FIVES images are augmented by rotation and horizontal and vertical flips and used to fine-tune eight ImageNet-pretrained CNNs: ResNet101, DenseNet169, Xception, InceptionV3, DenseNet121, InceptionResNetV2, ResNet50, and EfficientNetB0. (2) Five gradient-based explanation methods, Grad-CAM, Grad-CAM++, Score-CAM, Faster Score-CAM, and Layer-CAM, are computed on the final convolutional block of each classifier and compared qualitatively across architectures. (3) Ten U-Net variants are benchmarked for vessel segmentation: TransUNet (hybrid CNN--Transformer encoder) and Attention U-Net (gated skip connections), evaluated with ResNet50V2, ResNet101V2, and ResNet152V2 backbones, along with additional Attention U-Net configurations using DenseNet backbones, and the fully transformer-based Swin-UNet. ResNet101 gives the highest classification accuracy: 94.17% (F1 0.942) $>$ 88.33% for EfficientNetB0. For segmentation, the architecture ranking is consistent on both datasets: Attention U-Net $>$ TransUNet $>$ Swin-UNet. The strongest configuration is Attention U-Net with a ResNet101V2 backbone: FIVES IoU 0.722, Dice 0.838; DRIVE IoU 0.648, Dice 0.787, lifting DRIVE IoU 60.80 $\rightarrow$ 64.83 over a prior custom U-Net.

In this paper, we propose a novel locally statistical variational active contour model based on I-divergence-TV denoising model, which hybrides geodesic active contour (GAC) model with active contours without edges (ACWE) model, and can be used to segment images corrupted by multiplicative gamma noise. By adding a diffusion term into the level set evolution (LSE) equation of the proposed model, we construct a reaction-diffusion (RD) equation, which can gradually regularize the level set function (LSF) to be piecewise constant in each segment domain and gain the stable solution. We further transform the proposed model into a general ROF model by adding a proximity term ,and it can be solved by a fast denoising algorithm proposed by Jia-Zhao or soved by BM3D and NLM denoising algorithm, which also provide a unified solution framework for formally generalized-ROF-like subproblems arising in multivariate splitting algorithms.

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to influence the risk, severity, and outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy remains a manual and time-consuming expert task. The CoW is commonly imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), yet few datasets with annotated CoW anatomy exist, and there have been no established benchmarks for comparing CoW segmentation algorithms. We organized the TopCoW benchmark challenge alongside the release of an annotated CoW dataset with 125 paired MRA and CTA scans from the same patients. Voxel-level annotations for 13 vessel components were created using virtual reality technology and verified by clinical experts. Participants submitted algorithms for CoW segmentation and variant classification, which we evaluated on internal and external test sets comprising 226 scans from over five centers. The benchmark includes voxel-level segmentation, CoW component detection, CoW variant classification, and two clinical application tasks. We received submissions from over 250 participants across six continents. Top-performing teams achieved over 90% Dice scores for CoW segmentation, over 80% F1 scores for detecting key vessel components, and over 70% balanced accuracy in CoW variant classification across nearly all test sets. The best algorithms also supported clinically relevant downstream tasks by accurately classifying fetal-type posterior cerebral arteries and localizing aneurysms in relation to CoW anatomy. This benchmark demonstrated the utility of CoW segmentation algorithms for some downstream clinical applications with explainability.

In this paper, we propose a novel variational active contour model based on Aubert-Aujol (AA) denoising model, which hybrides geodesic active contour (GAC) model with active contours without edges (ACWE) model and can be used to segment images corrupted by multiplicative gamma noise. We transform the proposed model into classic ROF model by adding a proximity term.[26] was submitted on 29-Aug-2013, and our early edition was ever submitted to TGRS on 12-Jun-2012, Venkatakrishnan et al.[27] proposed their PnP algorithm on 29-May-2013, so Venkatakrishnan and we proposed the PnP algorithm almost simultaneously. Inspired by a fast denosing algorithm proposed by Jia-Zhao recently, we propose two fast fixed point algorithms to solve SAR image segmentation question.

In this paper, we propose a novel variational active contour model based on I-divergence-TV model to segment Synthetic aperture radar (SAR) images with multiplicative gamma noise, which hybrides edge-based model with region-based model. The proposed model can efficiently stop the contours at weak or blurred edges, and can automatically detect the exterior and interior boundaries of images. We further transform the proposed model into a general ROF model by adding a proximity term ,and it can be solved by a fast denoising algorithm proposed by Jia-Zhao or soved by BM3D and NLM denoising algorithm, which also provide a unified solution framework for formally generalized-ROF-like subproblems arising in multivariate splitting algorithms[25]. [25] was submitted on 29-Aug-2013, and our early edition was ever submitted to TGRS on 12-Jun-2012, Venkatakrishnan et al. [26] proposed their PnP algorithm on 29-May-2013, so Venkatakrishnan and we proposed the PnP algorithm almost simultaneously.

In this paper, we propose a novel locally statistical active contour model (LACM) based on Aubert-Aujol (AA) denoising model and variational level set method, which can be used for SAR images segmentation with intensity inhomogeneity. Then we transform the proposed model into a global optimization model by using convex relaxation technique. Firstly, we apply the Split Bregman technique to transform the global optimization model into two alternating optimization processes of Shrink operator and Laplace operator, which is called SB_LACM model. Moreover, we propose two fast models to solve the global optimization model , which are more efficient than the SB_LACM model. The first model is: we add the proximal function to transform the global optimization model to a general ROF model[29], which can be solved by a fast denoising algorithm proposed by R.-Q.Jia, and H.Zhao; [29] was submitted on 29-Aug-2013, and our early edition was ever submitted to TGRS on 12-Jun-2012, Venkatakrishnan et al. [30] proposed their PnP algorithm on 29-May-2013, so Venkatakrishnan and we proposed the PnP algorithm almost simultaneously. Thus we obtain a fast segmentation algorithm with global optimization solver that does not involve partial differential equations or difference equation, and only need simple difference computation. The second model is: we use a different splitting approach than one model to transform the global optimization model into a differentiable term and a general ROF model term, which can be solved by the same technique as the first model.

We present a method for multiclass thresholding of histograms whose modes may overlap so strongly that they merge into a unimodal distribution. The histogram is approximated by a nonparametric kernel density (KD) estimate, a mixture of Gaussians with one component per bin and a common bandwidth, whose parameters are determined by Expectation-Maximization (EM) iterations. Because the estimate is a Gaussian mixture, the semigroup property of Gaussian convolution yields its scale-space representation in closed form, at bandwidths both larger and smaller than the fitted one. The algorithm increases or decreases the bandwidth until the number of local minima of the estimate equals the number of requested classes minus one, and returns the positions of those minima as the threshold values. We validate the method on synthetic histograms with known thresholds, and we apply it to the histogram of X-ray computed tomography images of a natural porous sample in which the three phases strongly overlap. The porosity computed from the resulting segmentation agrees with the direct experimental measurement to within 4%, whereas K-means clustering misestimates it by 52%.