Daily Papers

Application of deep learning on histopathological whole slide images (WSIs) holds promise of improving diagnostic efficiency and reproducibility but is largely dependent on the ability to write computer code or purchase commercial solutions. We present a code-free pipeline utilizing free-to-use, open-source software (QuPath, DeepMIB, and FastPathology) for creating and deploying deep learning-based segmentation models for computational pathology. We demonstrate the pipeline on a use case of separating epithelium from stroma in colonic mucosa. A dataset of 251 annotated WSIs, comprising 140 hematoxylin-eosin (HE)-stained and 111 CD3 immunostained colon biopsy WSIs, were developed through active learning using the pipeline. On a hold-out test set of 36 HE and 21 CD3-stained WSIs a mean intersection over union score of 96.6% and 95.3% was achieved on epithelium segmentation. We demonstrate pathologist-level segmentation accuracy and clinical acceptable runtime performance and show that pathologists without programming experience can create near state-of-the-art segmentation solutions for histopathological WSIs using only free-to-use software. The study further demonstrates the strength of open-source solutions in its ability to create generalizable, open pipelines, of which trained models and predictions can seamlessly be exported in open formats and thereby used in external solutions. All scripts, trained models, a video tutorial, and the full dataset of 251 WSIs with ~31k epithelium annotations are made openly available at https://github.com/andreped/NoCodeSeg to accelerate research in the field.

The development of deep segmentation models for computational pathology (CPath) can help foster the investigation of interpretable morphological biomarkers. Yet, there is a major bottleneck in the success of such approaches because supervised deep learning models require an abundance of accurately labelled data. This issue is exacerbated in the field of CPath because the generation of detailed annotations usually demands the input of a pathologist to be able to distinguish between different tissue constructs and nuclei. Manually labelling nuclei may not be a feasible approach for collecting large-scale annotated datasets, especially when a single image region can contain thousands of different cells. However, solely relying on automatic generation of annotations will limit the accuracy and reliability of ground truth. Therefore, to help overcome the above challenges, we propose a multi-stage annotation pipeline to enable the collection of large-scale datasets for histology image analysis, with pathologist-in-the-loop refinement steps. Using this pipeline, we generate the largest known nuclear instance segmentation and classification dataset, containing nearly half a million labelled nuclei in H&E stained colon tissue. We have released the dataset and encourage the research community to utilise it to drive forward the development of downstream cell-based models in CPath.

It has recently been shown that deep learning models for anatomical segmentation in medical images can exhibit biases against certain sub-populations defined in terms of protected attributes like sex or ethnicity. In this context, auditing fairness of deep segmentation models becomes crucial. However, such audit process generally requires access to ground-truth segmentation masks for the target population, which may not always be available, especially when going from development to deployment. Here we propose a new method to anticipate model biases in biomedical image segmentation in the absence of ground-truth annotations. Our unsupervised bias discovery method leverages the reverse classification accuracy framework to estimate segmentation quality. Through numerical experiments in synthetic and realistic scenarios we show how our method is able to successfully anticipate fairness issues in the absence of ground-truth labels, constituting a novel and valuable tool in this field.

Medical image segmentation aims to delineate the anatomical or pathological structures of interest, playing a crucial role in clinical diagnosis. A substantial amount of high-quality annotated data is crucial for constructing high-precision deep segmentation models. However, medical annotation is highly cumbersome and time-consuming, especially for medical videos or 3D volumes, due to the huge labeling space and poor inter-frame consistency. Recently, a fundamental task named Moving Object Segmentation (MOS) has made significant advancements in natural images. Its objective is to delineate moving objects from the background within image sequences, requiring only minimal annotations. In this paper, we propose the first foundation model, named iMOS, for MOS in medical images. Extensive experiments on a large multi-modal medical dataset validate the effectiveness of the proposed iMOS. Specifically, with the annotation of only a small number of images in the sequence, iMOS can achieve satisfactory tracking and segmentation performance of moving objects throughout the entire sequence in bi-directions. We hope that the proposed iMOS can help accelerate the annotation speed of experts, and boost the development of medical foundation models.

Image-based crack detection algorithms are increasingly in demand in infrastructure monitoring, as early detection of cracks is of paramount importance for timely maintenance planning. While deep learning has significantly advanced crack detection algorithms, existing models often require extensive labeled datasets and high computational costs for fine-tuning, limiting their adaptability across diverse conditions. This study introduces an efficient selective fine-tuning strategy, focusing on tuning normalization components, to enhance the adaptability of segmentation models for crack detection. The proposed method is applied to the Segment Anything Model (SAM) and five well-established segmentation models. Experimental results demonstrate that selective fine-tuning of only normalization parameters outperforms full fine-tuning and other common fine-tuning techniques in both performance and computational efficiency, while improving generalization. The proposed approach yields a SAM-based model, Segment Any Crack (SAC), achieving a 61.22\% F1-score and 44.13\% IoU on the OmniCrack30k benchmark dataset, along with the highest performance across three zero-shot datasets and the lowest standard deviation. The results highlight the effectiveness of the adaptation approach in improving segmentation accuracy while significantly reducing computational overhead.

This study introduces Landslide4Sense, a reference benchmark for landslide detection from remote sensing. The repository features 3,799 image patches fusing optical layers from Sentinel-2 sensors with the digital elevation model and slope layer derived from ALOS PALSAR. The added topographical information facilitates the accurate detection of landslide borders, which recent researches have shown to be challenging using optical data alone. The extensive data set supports deep learning (DL) studies in landslide detection and the development and validation of methods for the systematic update of landslide inventories. The benchmark data set has been collected at four different times and geographical locations: Iburi (September 2018), Kodagu (August 2018), Gorkha (April 2015), and Taiwan (August 2009). Each image pixel is labelled as belonging to a landslide or not, incorporating various sources and thorough manual annotation. We then evaluate the landslide detection performance of 11 state-of-the-art DL segmentation models: U-Net, ResU-Net, PSPNet, ContextNet, DeepLab-v2, DeepLab-v3+, FCN-8s, LinkNet, FRRN-A, FRRN-B, and SQNet. All models were trained from scratch on patches from one quarter of each study area and tested on independent patches from the other three quarters. Our experiments demonstrate that ResU-Net outperformed the other models for the landslide detection task. We make the multi-source landslide benchmark data (Landslide4Sense) and the tested DL models publicly available at https://www.iarai.ac.at/landslide4sense, establishing an important resource for remote sensing, computer vision, and machine learning communities in studies of image classification in general and applications to landslide detection in particular.

Manually annotating object segmentation masks is very time consuming. Interactive object segmentation methods offer a more efficient alternative where a human annotator and a machine segmentation model collaborate. In this paper we make several contributions to interactive segmentation: (1) we systematically explore in simulation the design space of deep interactive segmentation models and report new insights and caveats; (2) we execute a large-scale annotation campaign with real human annotators, producing masks for 2.5M instances on the OpenImages dataset. We plan to release this data publicly, forming the largest existing dataset for instance segmentation. Moreover, by re-annotating part of the COCO dataset, we show that we can produce instance masks 3 times faster than traditional polygon drawing tools while also providing better quality. (3) We present a technique for automatically estimating the quality of the produced masks which exploits indirect signals from the annotation process.

Landslides pose severe threats to infrastructure, economies, and human lives, necessitating accurate detection and predictive mapping across diverse geographic regions. With advancements in deep learning and remote sensing, automated landslide detection has become increasingly effective. This study presents a comprehensive approach integrating multi-source satellite imagery and deep learning models to enhance landslide identification and prediction. We leverage Sentinel-2 multispectral data and ALOS PALSAR-derived slope and Digital Elevation Model (DEM) layers to capture critical environmental features influencing landslide occurrences. Various geospatial analysis techniques are employed to assess the impact of terra in characteristics, vegetation cover, and rainfall on detection accuracy. Additionally, we evaluate the performance of multiple stateof-the-art deep learning segmentation models, including U-Net, DeepLabV3+, and Res-Net, to determine their effectiveness in landslide detection. The proposed framework contributes to the development of reliable early warning systems, improved disaster risk management, and sustainable land-use planning. Our findings provide valuable insights into the potential of deep learning and multi-source remote sensing in creating robust, scalable, and transferable landslide prediction models.

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

Clinically deployed deep learning-based segmentation models are known to fail on data outside of their training distributions. While clinicians review the segmentations, these models tend to perform well in most instances, which could exacerbate automation bias. Therefore, detecting out-of-distribution images at inference is critical to warn the clinicians that the model likely failed. This work applied the Mahalanobis distance (MD) post hoc to the bottleneck features of four Swin UNETR and nnU-net models that segmented the liver on T1-weighted magnetic resonance imaging and computed tomography. By reducing the dimensions of the bottleneck features with either principal component analysis or uniform manifold approximation and projection, images the models failed on were detected with high performance and minimal computational load. In addition, this work explored a non-parametric alternative to the MD, a k-th nearest neighbors distance (KNN). KNN drastically improved scalability and performance over MD when both were applied to raw and average-pooled bottleneck features.

Semantic scene understanding is crucial for robust and safe autonomous navigation, particularly so in off-road environments. Recent deep learning advances for 3D semantic segmentation rely heavily on large sets of training data, however existing autonomy datasets either represent urban environments or lack multimodal off-road data. We fill this gap with RELLIS-3D, a multimodal dataset collected in an off-road environment, which contains annotations for 13,556 LiDAR scans and 6,235 images. The data was collected on the Rellis Campus of Texas A\&M University and presents challenges to existing algorithms related to class imbalance and environmental topography. Additionally, we evaluate the current state-of-the-art deep learning semantic segmentation models on this dataset. Experimental results show that RELLIS-3D presents challenges for algorithms designed for segmentation in urban environments. This novel dataset provides the resources needed by researchers to continue to develop more advanced algorithms and investigate new research directions to enhance autonomous navigation in off-road environments. RELLIS-3D is available at https://github.com/unmannedlab/RELLIS-3D

Large-scale models pre-trained on large-scale datasets have profoundly advanced the development of deep learning. However, the state-of-the-art models for medical image segmentation are still small-scale, with their parameters only in the tens of millions. Further scaling them up to higher orders of magnitude is rarely explored. An overarching goal of exploring large-scale models is to train them on large-scale medical segmentation datasets for better transfer capacities. In this work, we design a series of Scalable and Transferable U-Net (STU-Net) models, with parameter sizes ranging from 14 million to 1.4 billion. Notably, the 1.4B STU-Net is the largest medical image segmentation model to date. Our STU-Net is based on nnU-Net framework due to its popularity and impressive performance. We first refine the default convolutional blocks in nnU-Net to make them scalable. Then, we empirically evaluate different scaling combinations of network depth and width, discovering that it is optimal to scale model depth and width together. We train our scalable STU-Net models on a large-scale TotalSegmentator dataset and find that increasing model size brings a stronger performance gain. This observation reveals that a large model is promising in medical image segmentation. Furthermore, we evaluate the transferability of our model on 14 downstream datasets for direct inference and 3 datasets for further fine-tuning, covering various modalities and segmentation targets. We observe good performance of our pre-trained model in both direct inference and fine-tuning. The code and pre-trained models are available at https://github.com/Ziyan-Huang/STU-Net.

Accurately detecting and classifying damage in analogue media such as paintings, photographs, textiles, mosaics, and frescoes is essential for cultural heritage preservation. While machine learning models excel in correcting degradation if the damage operator is known a priori, we show that they fail to robustly predict where the damage is even after supervised training; thus, reliable damage detection remains a challenge. Motivated by this, we introduce ARTeFACT, a dataset for damage detection in diverse types analogue media, with over 11,000 annotations covering 15 kinds of damage across various subjects, media, and historical provenance. Furthermore, we contribute human-verified text prompts describing the semantic contents of the images, and derive additional textual descriptions of the annotated damage. We evaluate CNN, Transformer, diffusion-based segmentation models, and foundation vision models in zero-shot, supervised, unsupervised and text-guided settings, revealing their limitations in generalising across media types. Our dataset is available at https://daniela997.github.io/ARTeFACT/{https://daniela997.github.io/ARTeFACT/} as the first-of-its-kind benchmark for analogue media damage detection and restoration.

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

Automatic and consistent meningioma segmentation in T1-weighted MRI volumes and corresponding volumetric assessment is of use for diagnosis, treatment planning, and tumor growth evaluation. In this paper, we optimized the segmentation and processing speed performances using a large number of both surgically treated meningiomas and untreated meningiomas followed at the outpatient clinic. We studied two different 3D neural network architectures: (i) a simple encoder-decoder similar to a 3D U-Net, and (ii) a lightweight multi-scale architecture (PLS-Net). In addition, we studied the impact of different training schemes. For the validation studies, we used 698 T1-weighted MR volumes from St. Olav University Hospital, Trondheim, Norway. The models were evaluated in terms of detection accuracy, segmentation accuracy and training/inference speed. While both architectures reached a similar Dice score of 70% on average, the PLS-Net was more accurate with an F1-score of up to 88%. The highest accuracy was achieved for the largest meningiomas. Speed-wise, the PLS-Net architecture tended to converge in about 50 hours while 130 hours were necessary for U-Net. Inference with PLS-Net takes less than a second on GPU and about 15 seconds on CPU. Overall, with the use of mixed precision training, it was possible to train competitive segmentation models in a relatively short amount of time using the lightweight PLS-Net architecture. In the future, the focus should be brought toward the segmentation of small meningiomas (less than 2ml) to improve clinical relevance for automatic and early diagnosis as well as speed of growth estimates.

Clinicians are often very sceptical about applying automatic image processing approaches, especially deep learning based methods, in practice. One main reason for this is the black-box nature of these approaches and the inherent problem of missing insights of the automatically derived decisions. In order to increase trust in these methods, this paper presents approaches that help to interpret and explain the results of deep learning algorithms by depicting the anatomical areas which influence the decision of the algorithm most. Moreover, this research presents a unified framework, TorchEsegeta, for applying various interpretability and explainability techniques for deep learning models and generate visual interpretations and explanations for clinicians to corroborate their clinical findings. In addition, this will aid in gaining confidence in such methods. The framework builds on existing interpretability and explainability techniques that are currently focusing on classification models, extending them to segmentation tasks. In addition, these methods have been adapted to 3D models for volumetric analysis. The proposed framework provides methods to quantitatively compare visual explanations using infidelity and sensitivity metrics. This framework can be used by data scientists to perform post-hoc interpretations and explanations of their models, develop more explainable tools and present the findings to clinicians to increase their faith in such models. The proposed framework was evaluated based on a use case scenario of vessel segmentation models trained on Time-of-fight (TOF) Magnetic Resonance Angiogram (MRA) images of the human brain. Quantitative and qualitative results of a comparative study of different models and interpretability methods are presented. Furthermore, this paper provides an extensive overview of several existing interpretability and explainability methods.

Deep learning-based semantic segmentation models achieve impressive results yet remain limited in handling distribution shifts between training and test data. In this paper, we present SDGPA (Synthetic Data Generation and Progressive Adaptation), a novel method that tackles zero-shot domain adaptive semantic segmentation, in which no target images are available, but only a text description of the target domain's style is provided. To compensate for the lack of target domain training data, we utilize a pretrained off-the-shelf text-to-image diffusion model, which generates training images by transferring source domain images to target style. Directly editing source domain images introduces noise that harms segmentation because the layout of source images cannot be precisely maintained. To address inaccurate layouts in synthetic data, we propose a method that crops the source image, edits small patches individually, and then merges them back together, which helps improve spatial precision. Recognizing the large domain gap, SDGPA constructs an augmented intermediate domain, leveraging easier adaptation subtasks to enable more stable model adaptation to the target domain. Additionally, to mitigate the impact of noise in synthetic data, we design a progressive adaptation strategy, ensuring robust learning throughout the training process. Extensive experiments demonstrate that our method achieves state-of-the-art performance in zero-shot semantic segmentation. The code is available at https://github.com/ROUJINN/SDGPA

Deep Neural Networks (DNNs)-based semantic segmentation models trained on a source domain often struggle to generalize to unseen target domains, i.e., a domain gap problem. Texture often contributes to the domain gap, making DNNs vulnerable to domain shift because they are prone to be texture-biased. Existing Domain Generalized Semantic Segmentation (DGSS) methods have alleviated the domain gap problem by guiding models to prioritize shape over texture. On the other hand, shape and texture are two prominent and complementary cues in semantic segmentation. This paper argues that leveraging texture is crucial for improving performance in DGSS. Specifically, we propose a novel framework, coined Texture Learning Domain Randomization (TLDR). TLDR includes two novel losses to effectively enhance texture learning in DGSS: (1) a texture regularization loss to prevent overfitting to source domain textures by using texture features from an ImageNet pre-trained model and (2) a texture generalization loss that utilizes random style images to learn diverse texture representations in a self-supervised manner. Extensive experimental results demonstrate the superiority of the proposed TLDR; e.g., TLDR achieves 46.5 mIoU on GTA-to-Cityscapes using ResNet-50, which improves the prior state-of-the-art method by 1.9 mIoU. The source code is available at https://github.com/ssssshwan/TLDR.

This paper contributes to the "BraTS 2024 Brain MR Image Synthesis Challenge" and presents a conditional Wavelet Diffusion Model (cWDM) for directly solving a paired image-to-image translation task on high-resolution volumes. While deep learning-based brain tumor segmentation models have demonstrated clear clinical utility, they typically require MR scans from various modalities (T1, T1ce, T2, FLAIR) as input. However, due to time constraints or imaging artifacts, some of these modalities may be missing, hindering the application of well-performing segmentation algorithms in clinical routine. To address this issue, we propose a method that synthesizes one missing modality image conditioned on three available images, enabling the application of downstream segmentation models. We treat this paired image-to-image translation task as a conditional generation problem and solve it by combining a Wavelet Diffusion Model for high-resolution 3D image synthesis with a simple conditioning strategy. This approach allows us to directly apply our model to full-resolution volumes, avoiding artifacts caused by slice- or patch-wise data processing. While this work focuses on a specific application, the presented method can be applied to all kinds of paired image-to-image translation problems, such as CT leftrightarrow MR and MR leftrightarrow PET translation, or mask-conditioned anatomically guided image generation.

The world is covered with millions of buildings, and precisely knowing each instance's position and extents is vital to a multitude of applications. Recently, automated building footprint segmentation models have shown superior detection accuracy thanks to the usage of Convolutional Neural Networks (CNN). However, even the latest evolutions struggle to precisely delineating borders, which often leads to geometric distortions and inadvertent fusion of adjacent building instances. We propose to overcome this issue by exploiting the distinct geometric properties of buildings. To this end, we present Deep Structured Active Contours (DSAC), a novel framework that integrates priors and constraints into the segmentation process, such as continuous boundaries, smooth edges, and sharp corners. To do so, DSAC employs Active Contour Models (ACM), a family of constraint- and prior-based polygonal models. We learn ACM parameterizations per instance using a CNN, and show how to incorporate all components in a structured output model, making DSAC trainable end-to-end. We evaluate DSAC on three challenging building instance segmentation datasets, where it compares favorably against state-of-the-art. Code will be made available.

Machine learning requires data, but acquiring and labeling real-world data is challenging, expensive, and time-consuming. More importantly, it is nearly impossible to alter real data post-acquisition (e.g., change the illumination of a room), making it very difficult to measure how specific properties of the data affect performance. In this paper, we present AI Playground (AIP), an open-source, Unreal Engine-based tool for generating and labeling virtual image data. With AIP, it is trivial to capture the same image under different conditions (e.g., fidelity, lighting, etc.) and with different ground truths (e.g., depth or surface normal values). AIP is easily extendable and can be used with or without code. To validate our proposed tool, we generated eight datasets of otherwise identical but varying lighting and fidelity conditions. We then trained deep neural networks to predict (1) depth values, (2) surface normals, or (3) object labels and assessed each network's intra- and cross-dataset performance. Among other insights, we verified that sensitivity to different settings is problem-dependent. We confirmed the findings of other studies that segmentation models are very sensitive to fidelity, but we also found that they are just as sensitive to lighting. In contrast, depth and normal estimation models seem to be less sensitive to fidelity or lighting and more sensitive to the structure of the image. Finally, we tested our trained depth-estimation networks on two real-world datasets and obtained results comparable to training on real data alone, confirming that our virtual environments are realistic enough for real-world tasks.

Domain Adaptation (DA) is important for deep learning-based medical image segmentation models to deal with testing images from a new target domain. As the source-domain data are usually unavailable when a trained model is deployed at a new center, Source-Free Domain Adaptation (SFDA) is appealing for data and annotation-efficient adaptation to the target domain. However, existing SFDA methods have a limited performance due to lack of sufficient supervision with source-domain images unavailable and target-domain images unlabeled. We propose a novel Uncertainty-aware Pseudo Label guided (UPL) SFDA method for medical image segmentation. Specifically, we propose Target Domain Growing (TDG) to enhance the diversity of predictions in the target domain by duplicating the pre-trained model's prediction head multiple times with perturbations. The different predictions in these duplicated heads are used to obtain pseudo labels for unlabeled target-domain images and their uncertainty to identify reliable pseudo labels. We also propose a Twice Forward pass Supervision (TFS) strategy that uses reliable pseudo labels obtained in one forward pass to supervise predictions in the next forward pass. The adaptation is further regularized by a mean prediction-based entropy minimization term that encourages confident and consistent results in different prediction heads. UPL-SFDA was validated with a multi-site heart MRI segmentation dataset, a cross-modality fetal brain segmentation dataset, and a 3D fetal tissue segmentation dataset. It improved the average Dice by 5.54, 5.01 and 6.89 percentage points for the three tasks compared with the baseline, respectively, and outperformed several state-of-the-art SFDA methods.

Medical image segmentation has recently demonstrated impressive progress with deep neural networks, yet the heterogeneous modalities and scarcity of mask annotations limit the development of segmentation models on unannotated modalities. This paper investigates a new paradigm for leveraging generative models in medical applications: controllably synthesizing data for unannotated modalities, without requiring registered data pairs. Specifically, we make the following contributions in this paper: (i) we collect and curate a large-scale radiology image-text dataset, MedGen-1M, comprising modality labels, attributes, region, and organ information, along with a subset of organ mask annotations, to support research in controllable medical image generation; (ii) we propose a diffusion-based data engine, termed MRGen, which enables generation conditioned on text prompts and masks, synthesizing MR images for diverse modalities lacking mask annotations, to train segmentation models on unannotated modalities; (iii) we conduct extensive experiments across various modalities, illustrating that our data engine can effectively synthesize training samples and extend MRI segmentation towards unannotated modalities.

Placenta volume measurement from 3D ultrasound images is critical for predicting pregnancy outcomes, and manual annotation is the gold standard. However, such manual annotation is expensive and time-consuming. Automated segmentation algorithms can often successfully segment the placenta, but these methods may not consistently produce robust segmentations suitable for practical use. Recently, inspired by the Segment Anything Model (SAM), deep learning-based interactive segmentation models have been widely applied in the medical imaging domain. These models produce a segmentation from visual prompts provided to indicate the target region, which may offer a feasible solution for practical use. However, none of these models are specifically designed for interactively segmenting 3D ultrasound images, which remain challenging due to the inherent noise of this modality. In this paper, we evaluate publicly available state-of-the-art 3D interactive segmentation models in contrast to a human-in-the-loop approach for the placenta segmentation task. The Dice score, normalized surface Dice, averaged symmetric surface distance, and 95-percent Hausdorff distance are used as evaluation metrics. We consider a Dice score of 0.95 a successful segmentation. Our results indicate that the human-in-the-loop segmentation model reaches this standard. Moreover, we assess the efficiency of the human-in-the-loop model as a function of the amount of prompts. Our results demonstrate that the human-in-the-loop model is both effective and efficient for interactive placenta segmentation. The code is available at https://github.com/MedICL-VU/PRISM-placenta.

Semi-supervised learning (SSL) has become a promising solution to alleviate the annotation burden of deep learning-based medical image segmentation models. While recent advances in foundation model-driven SSL have pushed the boundary to extremely limited annotation scenarios, they fail to maintain robust competitive performance in complex imaging modalities. In this paper, we propose SemiSAM-O1, an annotation-efficient framework using only one annotated template case for segmentation. SemiSAM-O1 extends the specialist-generalist collaborative learning framework to the extreme one-label setting by fully exploiting the foundation model's feature representation capability beyond its prompting interface. SemiSAM-O1 operates in two stages. In the first stage, the foundation model's encoder extracts dense features from all volumes, and class prototypes derived from the single annotated template are propagated to the unlabeled pool via feature similarity to produce coarse initial pseudo-labels. In the second stage, an iterative training-and-refinement loop progressively improves both the segmentation model and the pseudo-labels over multiple rounds, where each round trains the model from scratch on current pseudo-labels and generates updated predictions with voxel-wise uncertainty estimates. An uncertainty-guided refinement step further leverages the foundation model's global feature space to correct high-uncertainty regions by aggregating labels from their most similar confident neighbors, establishing a virtuous cycle of mutual improvement. Extensive experiments on a wide range of segmentation tasks across different modalities and anatomical targets demonstrate that SemiSAM-O1 significantly narrows the performance gap between one-label semi-supervised learning and full supervision, while significantly reducing the computational overhead of online foundation model inference.

Deep learning (DL) has become the dominant approach for medical image segmentation, yet ensuring the reliability and clinical applicability of these models requires addressing key challenges such as annotation variability, calibration, and uncertainty estimation. This is why we created the Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS), which highlights the critical role of multiple annotators in establishing a more comprehensive ground truth, emphasizing that segmentation is inherently subjective and that leveraging inter-annotator variability is essential for robust model evaluation. Seven teams participated in the challenge, submitting a variety of DL models evaluated using metrics such as Dice Similarity Coefficient (DSC), Expected Calibration Error (ECE), and Continuous Ranked Probability Score (CRPS). By incorporating consensus and dissensus ground truth, we assess how DL models handle uncertainty and whether their confidence estimates align with true segmentation performance. Our findings reinforce the importance of well-calibrated models, as better calibration is strongly correlated with the quality of the results. Furthermore, we demonstrate that segmentation models trained on diverse datasets and enriched with pre-trained knowledge exhibit greater robustness, particularly in cases deviating from standard anatomical structures. Notably, the best-performing models achieved high DSC and well-calibrated uncertainty estimates. This work underscores the need for multi-annotator ground truth, thorough calibration assessments, and uncertainty-aware evaluations to develop trustworthy and clinically reliable DL-based medical image segmentation models.

Vision Transformers (ViTs) have recently achieved strong results in semantic segmentation, yet their deployment on resource-constrained devices remains limited due to their high memory footprint and computational cost. Quantization offers an effective strategy to improve efficiency, but ViT-based segmentation models are notoriously fragile under low precision, as quantization errors accumulate across deep encoder-decoder pipelines. We introduce I-Segmenter, the first fully integer-only ViT segmentation framework. Building on the Segmenter architecture, I-Segmenter systematically replaces floating-point operations with integer-only counterparts. To further stabilize both training and inference, we propose lambda-ShiftGELU, a novel activation function that mitigates the limitations of uniform quantization in handling long-tailed activation distributions. In addition, we remove the L2 normalization layer and replace bilinear interpolation in the decoder with nearest neighbor upsampling, ensuring integer-only execution throughout the computational graph. Extensive experiments show that I-Segmenter achieves accuracy within a reasonable margin of its FP32 baseline (5.1 % on average), while reducing model size by up to 3.8x and enabling up to 1.2x faster inference with optimized runtimes. Notably, even in one-shot PTQ with a single calibration image, I-Segmenter delivers competitive accuracy, underscoring its practicality for real-world deployment.

Do deep learning models for instance segmentation generalize to novel objects in a systematic way? For classification, such behavior has been questioned. In this study, we aim to understand if certain design decisions such as framework, architecture or pre-training contribute to the semantic understanding of instance segmentation. To answer this question, we consider a special case of robustness and compare pre-trained models on a challenging benchmark for object-centric, out-of-distribution texture. We do not introduce another method in this work. Instead, we take a step back and evaluate a broad range of existing literature. This includes Cascade and Mask R-CNN, Swin Transformer, BMask, YOLACT(++), DETR, BCNet, SOTR and SOLOv2. We find that YOLACT++, SOTR and SOLOv2 are significantly more robust to out-of-distribution texture than other frameworks. In addition, we show that deeper and dynamic architectures improve robustness whereas training schedules, data augmentation and pre-training have only a minor impact. In summary we evaluate 68 models on 61 versions of MS COCO for a total of 4148 evaluations.

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

Tuberculosis (TB) is a chronic lung disease that occurs due to bacterial infection and is one of the top 10 leading causes of death. Accurate and early detection of TB is very important, otherwise, it could be life-threatening. In this work, we have detected TB reliably from the chest X-ray images using image pre-processing, data augmentation, image segmentation, and deep-learning classification techniques. Several public databases were used to create a database of 700 TB infected and 3500 normal chest X-ray images for this study. Nine different deep CNNs (ResNet18, ResNet50, ResNet101, ChexNet, InceptionV3, Vgg19, DenseNet201, SqueezeNet, and MobileNet), which were used for transfer learning from their pre-trained initial weights and trained, validated and tested for classifying TB and non-TB normal cases. Three different experiments were carried out in this work: segmentation of X-ray images using two different U-net models, classification using X-ray images, and segmented lung images. The accuracy, precision, sensitivity, F1-score, specificity in the detection of tuberculosis using X-ray images were 97.07 %, 97.34 %, 97.07 %, 97.14 % and 97.36 % respectively. However, segmented lungs for the classification outperformed than whole X-ray image-based classification and accuracy, precision, sensitivity, F1-score, specificity were 99.9 %, 99.91 %, 99.9 %, 99.9 %, and 99.52 % respectively. The paper also used a visualization technique to confirm that CNN learns dominantly from the segmented lung regions results in higher detection accuracy. The proposed method with state-of-the-art performance can be useful in the computer-aided faster diagnosis of tuberculosis.

Deep learning has advanced two fundamentally different paradigms for instance segmentation: specialized models optimized through task-specific fine-tuning and generalist foundation models capable of zero-shot segmentation. This work presents a comprehensive comparison between SAM3 (Segment Anything Model, also called SAMv3) operating in zero-shot mode and three variants of Ultralytics YOLO11 (nano, medium, and large) fine-tuned for instance segmentation. The evaluation is conducted on the MinneApple dataset, a dense benchmark comprising 670 orchard images with 28,179 annotated apple instances, enabling rigorous validation of model behavior under high object density and occlusion. Our analysis shows IoU choices can inflate performance gaps by up to 30%. At the appropriate IoU = 0.15 threshold, YOLO models achieve 68.9%, 72.2%, and 71.9% F1, while SAM3 reaches 59.8% in pure zero-shot mode. However, YOLO exhibits steep degradation 48-50 points across IoU ranges whereas SAM3 drops only 4 points, revealing 12 times superior boundary stability of SAM3. This highlights the strength of SAMv3 in mask precision versus specialization in detection completeness of YOLO11. We provide open-source code, evaluation pipelines, and methodological recommendations, contributing to a deeper understanding of when specialized fine-tuned models or generalist foundation models are preferable for dense instance segmentation tasks. This project repository is available on GitHub as https://github.com/Applied-AI-Research-Lab/Segment-Anything-Model-SAM3-Zero-Shot-Segmentation-Against-Fine-Tuned-YOLO-Detectors

Training deep networks with limited labeled data while achieving a strong generalization ability is key in the quest to reduce human annotation efforts. This is the goal of semi-supervised learning, which exploits more widely available unlabeled data to complement small labeled data sets. In this paper, we propose a novel framework for discriminative pixel-level tasks using a generative model of both images and labels. Concretely, we learn a generative adversarial network that captures the joint image-label distribution and is trained efficiently using a large set of unlabeled images supplemented with only few labeled ones. We build our architecture on top of StyleGAN2, augmented with a label synthesis branch. Image labeling at test time is achieved by first embedding the target image into the joint latent space via an encoder network and test-time optimization, and then generating the label from the inferred embedding. We evaluate our approach in two important domains: medical image segmentation and part-based face segmentation. We demonstrate strong in-domain performance compared to several baselines, and are the first to showcase extreme out-of-domain generalization, such as transferring from CT to MRI in medical imaging, and photographs of real faces to paintings, sculptures, and even cartoons and animal faces. Project Page: https://nv-tlabs.github.io/semanticGAN/

Deep Convolutional Neural Networks (DCNNs) have recently shown state of the art performance in high level vision tasks, such as image classification and object detection. This work brings together methods from DCNNs and probabilistic graphical models for addressing the task of pixel-level classification (also called "semantic image segmentation"). We show that responses at the final layer of DCNNs are not sufficiently localized for accurate object segmentation. This is due to the very invariance properties that make DCNNs good for high level tasks. We overcome this poor localization property of deep networks by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF). Qualitatively, our "DeepLab" system is able to localize segment boundaries at a level of accuracy which is beyond previous methods. Quantitatively, our method sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 71.6% IOU accuracy in the test set. We show how these results can be obtained efficiently: Careful network re-purposing and a novel application of the 'hole' algorithm from the wavelet community allow dense computation of neural net responses at 8 frames per second on a modern GPU.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

This investigation reports on the results of convolutional neural networks developed for the recently introduced PathologicAL Myopia (PALM) dataset, which consists of 1200 fundus images. We propose a new Optic Nerve Head (ONH)-based prediction enhancement for the segmentation of atrophy and fovea. Models trained with 400 available training images achieved an AUC of 0.9867 for pathological myopia classification, and a Euclidean distance of 58.27 pixels on the fovea localization task, evaluated on a test set of 400 images. Dice and F1 metrics for semantic segmentation of lesions scored 0.9303 and 0.9869 on optic disc, 0.8001 and 0.9135 on retinal atrophy, and 0.8073 and 0.7059 on retinal detachment, respectively. Our work was acknowledged with an award in the context of the "PathologicAL Myopia detection from retinal images" challenge held during the IEEE International Symposium on Biomedical Imaging (April 2019). Considering that (pathological) myopia cases are often identified as false positives and negatives in classification systems for glaucoma, we envision that the current work could aid in future research to discriminate between glaucomatous and highly-myopic eyes, complemented by the localization and segmentation of landmarks such as fovea, optic disc and atrophy.

In this work we address the task of semantic image segmentation with Deep Learning and make three main contributions that are experimentally shown to have substantial practical merit. First, we highlight convolution with upsampled filters, or 'atrous convolution', as a powerful tool in dense prediction tasks. Atrous convolution allows us to explicitly control the resolution at which feature responses are computed within Deep Convolutional Neural Networks. It also allows us to effectively enlarge the field of view of filters to incorporate larger context without increasing the number of parameters or the amount of computation. Second, we propose atrous spatial pyramid pooling (ASPP) to robustly segment objects at multiple scales. ASPP probes an incoming convolutional feature layer with filters at multiple sampling rates and effective fields-of-views, thus capturing objects as well as image context at multiple scales. Third, we improve the localization of object boundaries by combining methods from DCNNs and probabilistic graphical models. The commonly deployed combination of max-pooling and downsampling in DCNNs achieves invariance but has a toll on localization accuracy. We overcome this by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF), which is shown both qualitatively and quantitatively to improve localization performance. Our proposed "DeepLab" system sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 79.7% mIOU in the test set, and advances the results on three other datasets: PASCAL-Context, PASCAL-Person-Part, and Cityscapes. All of our code is made publicly available online.

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

This report presents an overview of the AIM 2025 RipSeg Challenge, a competition designed to advance techniques for automatic rip current segmentation in still images. Rip currents are dangerous, fast-moving flows that pose a major risk to beach safety worldwide, making accurate visual detection an important and underexplored research task. The challenge builds on RipVIS, the largest available rip current dataset, and focuses on single-class instance segmentation, where precise delineation is critical to fully capture the extent of rip currents. The dataset spans diverse locations, rip current types, and camera orientations, providing a realistic and challenging benchmark. In total, 75 participants registered for this first edition, resulting in 5 valid test submissions. Teams were evaluated on a composite score combining F_1, F_2, AP_{50}, and AP_{[50:95]}, ensuring robust and application-relevant rankings. The top-performing methods leveraged deep learning architectures, domain adaptation techniques, pretrained models, and domain generalization strategies to improve performance under diverse conditions. This report outlines the dataset details, competition framework, evaluation metrics, and final results, providing insights into the current state of rip current segmentation. We conclude with a discussion of key challenges, lessons learned from the submissions, and future directions for expanding RipSeg.

Semantic image segmentation, the process of classifying each pixel in an image into a particular class, plays an important role in many visual understanding systems. As the predominant criterion for evaluating the performance of statistical models, loss functions are crucial for shaping the development of deep learning-based segmentation algorithms and improving their overall performance. To aid researchers in identifying the optimal loss function for their particular application, this survey provides a comprehensive and unified review of 25 loss functions utilized in image segmentation. We provide a novel taxonomy and thorough review of how these loss functions are customized and leveraged in image segmentation, with a systematic categorization emphasizing their significant features and applications. Furthermore, to evaluate the efficacy of these methods in real-world scenarios, we propose unbiased evaluations of some distinct and renowned loss functions on established medical and natural image datasets. We conclude this review by identifying current challenges and unveiling future research opportunities. Finally, we have compiled the reviewed studies that have open-source implementations on our GitHub page.

The rapid advancement of deep learning has facilitated the automated processing of electron microscopy (EM) big data stacks. However, designing a framework that eliminates manual labeling and adapts to domain gaps remains challenging. Current research remains entangled in the dilemma of pursuing complete automation while still requiring simulations or slight manual annotations. Here we demonstrate tandem generative adversarial network (tGAN), a fully label-free and simulation-free pipeline capable of generating EM images for computer vision training. The tGAN can assimilate key features from new data stacks, thus producing a tailored virtual dataset for the training of automated EM analysis tools. Using segmenting nanoparticles for analyzing size distribution of supported catalysts as the demonstration, our findings showcased that the recognition accuracy of tGAN even exceeds the manually-labeling method by 5%. It can also be adaptively deployed to various data domains without further manual manipulation, which is verified by transfer learning from HAADF-STEM to BF-TEM. This generalizability may enable it to extend its application to a broader range of imaging characterizations, liberating microscopists and materials scientists from tedious dataset annotations.

Deep learning models have shown their potential for several applications. However, most of the models are opaque and difficult to trust due to their complex reasoning - commonly known as the black-box problem. Some fields, such as medicine, require a high degree of transparency to accept and adopt such technologies. Consequently, creating explainable/interpretable models or applying post-hoc methods on classifiers to build trust in deep learning models are required. Moreover, deep learning methods can be used for segmentation tasks, which typically require hard-to-obtain, time-consuming manually-annotated segmentation labels for training. This paper introduces three inherently-explainable classifiers to tackle both of these problems as one. The localisation heatmaps provided by the networks -- representing the models' focus areas and being used in classification decision-making -- can be directly interpreted, without requiring any post-hoc methods to derive information for model explanation. The models are trained by using the input image and only the classification labels as ground-truth in a supervised fashion - without using any information about the location of the region of interest (i.e. the segmentation labels), making the segmentation training of the models weakly-supervised through classification labels. The final segmentation is obtained by thresholding these heatmaps. The models were employed for the task of multi-class brain tumour classification using two different datasets, resulting in the best F1-score of 0.93 for the supervised classification task while securing a median Dice score of 0.67pm0.08 for the weakly-supervised segmentation task. Furthermore, the obtained accuracy on a subset of tumour-only images outperformed the state-of-the-art glioma tumour grading binary classifiers with the best model achieving 98.7\% accuracy.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Deep learning-based image generation has seen significant advancements with diffusion models, notably improving the quality of generated images. Despite these developments, generating images with unseen characteristics beneficial for downstream tasks has received limited attention. To bridge this gap, we propose Style-Extracting Diffusion Models, featuring two conditioning mechanisms. Specifically, we utilize 1) a style conditioning mechanism which allows to inject style information of previously unseen images during image generation and 2) a content conditioning which can be targeted to a downstream task, e.g., layout for segmentation. We introduce a trainable style encoder to extract style information from images, and an aggregation block that merges style information from multiple style inputs. This architecture enables the generation of images with unseen styles in a zero-shot manner, by leveraging styles from unseen images, resulting in more diverse generations. In this work, we use the image layout as target condition and first show the capability of our method on a natural image dataset as a proof-of-concept. We further demonstrate its versatility in histopathology, where we combine prior knowledge about tissue composition and unannotated data to create diverse synthetic images with known layouts. This allows us to generate additional synthetic data to train a segmentation network in a semi-supervised fashion. We verify the added value of the generated images by showing improved segmentation results and lower performance variability between patients when synthetic images are included during segmentation training. Our code will be made publicly available at [LINK].

The transition to renewable energy, particularly solar, is key to mitigating climate change. Google's Solar API aids this transition by estimating solar potential from aerial imagery, but its impact is constrained by geographical coverage. This paper proposes expanding the API's reach using satellite imagery, enabling global solar potential assessment. We tackle challenges involved in building a Digital Surface Model (DSM) and roof instance segmentation from lower resolution and single oblique views using deep learning models. Our models, trained on aligned satellite and aerial datasets, produce 25cm DSMs and roof segments. With ~1m DSM MAE on buildings, ~5deg roof pitch error and ~56% IOU on roof segmentation, they significantly enhance the Solar API's potential to promote solar adoption.

Medical image segmentation is an important analysis task in clinical practice and research. Deep learning has massively advanced the field, but current approaches are mostly based on models trained for a specific task. Training such models or adapting them to a new condition is costly due to the need for (manually) labeled data. The emergence of vision foundation models, especially Segment Anything, offers a path to universal segmentation for medical images, overcoming these issues. Here, we study how to improve Segment Anything for medical images by comparing different finetuning strategies on a large and diverse dataset. We evaluate the finetuned models on a wide range of interactive and (automatic) semantic segmentation tasks. We find that the performance can be clearly improved for interactive segmentation. However, semantic segmentation does not benefit from pretraining on medical images. Our best model, MedicoSAM, is publicly available at https://github.com/computational-cell-analytics/medico-sam. We show that it is compatible with existing tools for data annotation and believe that it will be of great practical value.

Semantic segmentation is a key technology for autonomous vehicles to understand the surrounding scenes. The appealing performances of contemporary models usually come at the expense of heavy computations and lengthy inference time, which is intolerable for self-driving. Using light-weight architectures (encoder-decoder or two-pathway) or reasoning on low-resolution images, recent methods realize very fast scene parsing, even running at more than 100 FPS on a single 1080Ti GPU. However, there is still a significant gap in performance between these real-time methods and the models based on dilation backbones. To tackle this problem, we proposed a family of efficient backbones specially designed for real-time semantic segmentation. The proposed deep dual-resolution networks (DDRNets) are composed of two deep branches between which multiple bilateral fusions are performed. Additionally, we design a new contextual information extractor named Deep Aggregation Pyramid Pooling Module (DAPPM) to enlarge effective receptive fields and fuse multi-scale context based on low-resolution feature maps. Our method achieves a new state-of-the-art trade-off between accuracy and speed on both Cityscapes and CamVid dataset. In particular, on a single 2080Ti GPU, DDRNet-23-slim yields 77.4% mIoU at 102 FPS on Cityscapes test set and 74.7% mIoU at 230 FPS on CamVid test set. With widely used test augmentation, our method is superior to most state-of-the-art models and requires much less computation. Codes and trained models are available online.

Cell segmentation is a major bottleneck in extracting quantitative single-cell information from microscopy data. The challenge is exasperated in the setting of microstructured environments. While deep learning approaches have proven useful for general cell segmentation tasks, existing segmentation tools for the yeast-microstructure setting rely on traditional machine learning approaches. Here we present convolutional neural networks trained for multiclass segmenting of individual yeast cells and discerning these from cell-similar microstructures. We give an overview of the datasets recorded for training, validating and testing the networks, as well as a typical use-case. We showcase the method's contribution to segmenting yeast in microstructured environments with a typical synthetic biology application in mind. The models achieve robust segmentation results, outperforming the previous state-of-the-art in both accuracy and speed. The combination of fast and accurate segmentation is not only beneficial for a posteriori data processing, it also makes online monitoring of thousands of trapped cells or closed-loop optimal experimental design feasible from an image processing perspective.

Brain tumors pose a significant threat to human life, therefore it is very much necessary to detect them accurately in the early stages for better diagnosis and treatment. Brain tumors can be detected by the radiologist manually from the MRI scan images of the patients. However, the incidence of brain tumors has risen amongst children and adolescents in recent years, resulting in a substantial volume of data, as a result, it is time-consuming and difficult to detect manually. With the emergence of Artificial intelligence in the modern world and its vast application in the medical field, we can make an approach to the CAD (Computer Aided Diagnosis) system for the early detection of Brain tumors automatically. All the existing models for this task are not completely generalized and perform poorly on the validation data. So, we have proposed two novel Deep Learning Architectures - (a) SAETCN (Self-Attention Enhancement Tumor Classification Network) for the classification of different kinds of brain tumors. We have achieved an accuracy of 99.38% on the validation dataset making it one of the few Novel Deep learning-based architecture that is capable of detecting brain tumors accurately. We have trained the model on the dataset, which contains images of 3 types of tumors (glioma, meningioma, and pituitary tumors) and non-tumor cases. and (b) SAS-Net (Self-Attentive Segmentation Network) for the accurate segmentation of brain tumors. We have achieved an overall pixel accuracy of 99.23%.

Semantic segmentation has made significant progress in recent years thanks to deep neural networks, but the common objective of generating a single segmentation output that accurately matches the image's content may not be suitable for safety-critical domains such as medical diagnostics and autonomous driving. Instead, multiple possible correct segmentation maps may be required to reflect the true distribution of annotation maps. In this context, stochastic semantic segmentation methods must learn to predict conditional distributions of labels given the image, but this is challenging due to the typically multimodal distributions, high-dimensional output spaces, and limited annotation data. To address these challenges, we propose a conditional categorical diffusion model (CCDM) for semantic segmentation based on Denoising Diffusion Probabilistic Models. Our model is conditioned to the input image, enabling it to generate multiple segmentation label maps that account for the aleatoric uncertainty arising from divergent ground truth annotations. Our experimental results show that CCDM achieves state-of-the-art performance on LIDC, a stochastic semantic segmentation dataset, and outperforms established baselines on the classical segmentation dataset Cityscapes.

Extent of resection after surgery is one of the main prognostic factors for patients diagnosed with glioblastoma. To achieve this, accurate segmentation and classification of residual tumor from post-operative MR images is essential. The current standard method for estimating it is subject to high inter- and intra-rater variability, and an automated method for segmentation of residual tumor in early post-operative MRI could lead to a more accurate estimation of extent of resection. In this study, two state-of-the-art neural network architectures for pre-operative segmentation were trained for the task. The models were extensively validated on a multicenter dataset with nearly 1000 patients, from 12 hospitals in Europe and the United States. The best performance achieved was a 61\% Dice score, and the best classification performance was about 80\% balanced accuracy, with a demonstrated ability to generalize across hospitals. In addition, the segmentation performance of the best models was on par with human expert raters. The predicted segmentations can be used to accurately classify the patients into those with residual tumor, and those with gross total resection.

Accurate segmentation of organs and tumors in CT and MRI scans is essential for diagnosis, treatment planning, and disease monitoring. While deep learning has advanced automated segmentation, most models remain task-specific, lacking generalizability across modalities and institutions. Vision foundation models (FMs) pretrained on billion-scale natural images offer powerful and transferable representations. However, adapting them to medical imaging faces two key challenges: (1) the ViT backbone of most foundation models still underperform specialized CNNs on medical image segmentation, and (2) the large domain gap between natural and medical images limits transferability. We introduce MedDINOv3, a simple and effective framework for adapting DINOv3 to medical segmentation. We first revisit plain ViTs and design a simple and effective architecture with multi-scale token aggregation. Then, we perform domain-adaptive pretraining on CT-3M, a curated collection of 3.87M axial CT slices, using a multi-stage DINOv3 recipe to learn robust dense features. MedDINOv3 matches or exceeds state-of-the-art performance across four segmentation benchmarks, demonstrating the potential of vision foundation models as unified backbones for medical image segmentation. The code is available at https://github.com/ricklisz/MedDINOv3.

This paper addresses the visualisation of image classification models, learnt using deep Convolutional Networks (ConvNets). We consider two visualisation techniques, based on computing the gradient of the class score with respect to the input image. The first one generates an image, which maximises the class score [Erhan et al., 2009], thus visualising the notion of the class, captured by a ConvNet. The second technique computes a class saliency map, specific to a given image and class. We show that such maps can be employed for weakly supervised object segmentation using classification ConvNets. Finally, we establish the connection between the gradient-based ConvNet visualisation methods and deconvolutional networks [Zeiler et al., 2013].

Robust principal component analysis (RPCA) decomposes an observation matrix into low-rank background and sparse object components. This capability has enabled its application in tasks ranging from image restoration to segmentation. However, traditional RPCA models suffer from computational burdens caused by matrix operations, reliance on finely tuned hyperparameters, and rigid priors that limit adaptability in dynamic scenarios. To solve these limitations, we propose RPCANet++, a sparse object segmentation framework that fuses the interpretability of RPCA with efficient deep architectures. Our approach unfolds a relaxed RPCA model into a structured network comprising a Background Approximation Module (BAM), an Object Extraction Module (OEM), and an Image Restoration Module (IRM). To mitigate inter-stage transmission loss in the BAM, we introduce a Memory-Augmented Module (MAM) to enhance background feature preservation, while a Deep Contrast Prior Module (DCPM) leverages saliency cues to expedite object extraction. Extensive experiments on diverse datasets demonstrate that RPCANet++ achieves state-of-the-art performance under various imaging scenarios. We further improve interpretability via visual and numerical low-rankness and sparsity measurements. By combining the theoretical strengths of RPCA with the efficiency of deep networks, our approach sets a new baseline for reliable and interpretable sparse object segmentation. Codes are available at our Project Webpage https://fengyiwu98.github.io/rpcanetx.

Gliomas are aggressive brain tumors that require accurate imaging-based diagnosis, with segmentation playing a critical role in evaluating morphology and treatment decisions. Manual delineation of gliomas is time-consuming and prone to variability, motivating the use of deep learning to improve consistency and alleviate clinical workload. However, existing methods often fail to fully exploit the information available in multi-parametric MRI (mp-MRI), particularly inter-slice contextual features, and typically require considerable computational resources while lacking robustness across tumor type variations. We present GBT-SAM, a parameter-efficient deep learning framework that adapts the Segment Anything Model (SAM), a large-scale vision model, to volumetric mp-MRI data. GBT-SAM reduces input complexity by selecting fewer than 2.6\% of slices per scan while incorporating all four MRI modalities, preserving essential tumor-related information with minimal cost. Furthermore, our model is trained by a two-step fine-tuning strategy that incorporates a depth-aware module to capture inter-slice correlations and lightweight adaptation layers, resulting in just 6.5M trainable parameters, which is the lowest among SAM-based approaches. GBT-SAM achieves a Dice Score of 93.54 on the BraTS Adult Glioma dataset and demonstrates robust performance on Meningioma, Pediatric Glioma, and Sub-Saharan Glioma datasets. These results highlight GBT-SAM's potential as a computationally efficient and domain-robust framework for brain tumor segmentation using mp-MRI. Our code and models are available at https://github.com/vpulab/med-sam-brain .

We propose a new class of implicit networks, the multiscale deep equilibrium model (MDEQ), suited to large-scale and highly hierarchical pattern recognition domains. An MDEQ directly solves for and backpropagates through the equilibrium points of multiple feature resolutions simultaneously, using implicit differentiation to avoid storing intermediate states (and thus requiring only O(1) memory consumption). These simultaneously-learned multi-resolution features allow us to train a single model on a diverse set of tasks and loss functions, such as using a single MDEQ to perform both image classification and semantic segmentation. We illustrate the effectiveness of this approach on two large-scale vision tasks: ImageNet classification and semantic segmentation on high-resolution images from the Cityscapes dataset. In both settings, MDEQs are able to match or exceed the performance of recent competitive computer vision models: the first time such performance and scale have been achieved by an implicit deep learning approach. The code and pre-trained models are at https://github.com/locuslab/mdeq .

Austenitic 347H stainless steel offers superior mechanical properties and corrosion resistance required for extreme operating conditions such as high temperature. The change in microstructure due to composition and process variations is expected to impact material properties. Identifying microstructural features such as grain boundaries thus becomes an important task in the process-microstructure-properties loop. Applying convolutional neural network (CNN) based deep-learning models is a powerful technique to detect features from material micrographs in an automated manner. Manual labeling of the images for the segmentation task poses a major bottleneck for generating training data and labels in a reliable and reproducible way within a reasonable timeframe. In this study, we attempt to overcome such limitations by utilizing multi-modal microscopy to generate labels directly instead of manual labeling. We combine scanning electron microscopy (SEM) images of 347H stainless steel as training data and electron backscatter diffraction (EBSD) micrographs as pixel-wise labels for grain boundary detection as a semantic segmentation task. We demonstrate that despite producing instrumentation drift during data collection between two modes of microscopy, this method performs comparably to similar segmentation tasks that used manual labeling. Additionally, we find that naïve pixel-wise segmentation results in small gaps and missing boundaries in the predicted grain boundary map. By incorporating topological information during model training, the connectivity of the grain boundary network and segmentation performance is improved. Finally, our approach is validated by accurate computation on downstream tasks of predicting the underlying grain morphology distributions which are the ultimate quantities of interest for microstructural characterization.

We present a simple and efficient method based on deep learning to automatically decompose sketched objects into semantically valid parts. We train a deep neural network to transfer existing segmentations and labelings from 3D models to freehand sketches without requiring numerous well-annotated sketches as training data. The network takes the binary image of a sketched object as input and produces a corresponding segmentation map with per-pixel labelings as output. A subsequent post-process procedure with multi-label graph cuts further refines the segmentation and labeling result. We validate our proposed method on two sketch datasets. Experiments show that our method outperforms the state-of-the-art method in terms of segmentation and labeling accuracy and is significantly faster, enabling further integration in interactive drawing systems. We demonstrate the efficiency of our method in a sketch-based modeling application that automatically transforms input sketches into 3D models by part assembly.

Automated segmentation of BUS images is important for precise lesion delineation and tumor characterization, but is challenged by inherent artifacts and dataset inconsistencies. In this work, we evaluate the use of a modified Residual Encoder U-Net for breast ultrasound segmentation, with a focus on uncertainty quantification. We identify and correct for data duplication in the BUSI dataset, and use a deduplicated subset for more reliable estimates of generalization performance. Epistemic uncertainty is quantified using Monte Carlo dropout, deep ensembles, and their combination. Models are benchmarked on both in-distribution and out-of-distribution datasets to demonstrate how they generalize to unseen cross-domain data. Our approach achieves state-of-the-art segmentation accuracy on the Breast-Lesion-USG dataset with in-distribution validation, and provides calibrated uncertainty estimates that effectively signal regions of low model confidence. Performance declines and increased uncertainty observed in out-of-distribution evaluation highlight the persistent challenge of domain shift in medical imaging, and the importance of integrated uncertainty modeling for trustworthy clinical deployment. Code available at: https://github.com/toufiqmusah/nn-uncertainty.git

Learning anatomical segmentation from heterogeneous labels in multi-center datasets is a common situation encountered in clinical scenarios, where certain anatomical structures are only annotated in images coming from particular medical centers, but not in the full database. Here we first show how state-of-the-art pixel-level segmentation models fail in naively learning this task due to domain memorization issues and conflicting labels. We then propose to adopt HybridGNet, a landmark-based segmentation model which learns the available anatomical structures using graph-based representations. By analyzing the latent space learned by both models, we show that HybridGNet naturally learns more domain-invariant feature representations, and provide empirical evidence in the context of chest X-ray multiclass segmentation. We hope these insights will shed light on the training of deep learning models with heterogeneous labels from public and multi-center datasets.

Deep learning has brought the most profound contribution towards biomedical image segmentation to automate the process of delineation in medical imaging. To accomplish such task, the models are required to be trained using huge amount of annotated or labelled data that highlights the region of interest with a binary mask. However, efficient generation of the annotations for such huge data requires expert biomedical analysts and extensive manual effort. It is a tedious and expensive task, while also being vulnerable to human error. To address this problem, a self-supervised learning framework, BT-Unet is proposed that uses the Barlow Twins approach to pre-train the encoder of a U-Net model via redundancy reduction in an unsupervised manner to learn data representation. Later, complete network is fine-tuned to perform actual segmentation. The BT-Unet framework can be trained with a limited number of annotated samples while having high number of unannotated samples, which is mostly the case in real-world problems. This framework is validated over multiple U-Net models over diverse datasets by generating scenarios of a limited number of labelled samples using standard evaluation metrics. With exhaustive experiment trials, it is observed that the BT-Unet framework enhances the performance of the U-Net models with significant margin under such circumstances.

Structured output representation is a generative task explored in computer vision that often times requires the mapping of low dimensional features to high dimensional structured outputs. Losses in complex spatial information in deterministic approaches such as Convolutional Neural Networks (CNN) lead to uncertainties and ambiguous structures within a single output representation. A probabilistic approach through deep Conditional Generative Models (CGM) is presented by Sohn et al. in which a particular model known as the Conditional Variational Auto-encoder (CVAE) is introduced and explored. While the original paper focuses on the task of image segmentation, this paper adopts the CVAE framework for the task of controlled output representation through attributes. This approach allows us to learn a disentangled multimodal prior distribution, resulting in more controlled and robust approach to sample generation. In this work we recreate the CVAE architecture and train it on images conditioned on various attributes obtained from two image datasets; the Large-scale CelebFaces Attributes (CelebA) dataset and the Caltech-UCSD Birds (CUB-200-2011) dataset. We attempt to generate new faces with distinct attributes such as hair color and glasses, as well as different bird species samples with various attributes. We further introduce strategies for improving generalized sample generation by applying a weighted term to the variational lower bound.

Detecting glass regions is a challenging task due to the inherent ambiguity in their transparency and reflective characteristics. Current solutions in this field remain rooted in conventional deep learning paradigms, requiring the construction of annotated datasets and the design of network architectures. However, the evident drawback with these mainstream solutions lies in the time-consuming and labor-intensive process of curating datasets, alongside the increasing complexity of model structures. In this paper, we propose to address these issues by fully harnessing the capabilities of two existing vision foundation models (VFMs): Stable Diffusion and Segment Anything Model (SAM). Firstly, we construct a Synthetic but photorealistic large-scale Glass Surface Detection dataset, dubbed S-GSD, without any labour cost via Stable Diffusion. This dataset consists of four different scales, consisting of 168k images totally with precise masks. Besides, based on the powerful segmentation ability of SAM, we devise a simple Glass surface sEgMentor named GEM, which follows the simple query-based encoder-decoder architecture. Comprehensive experiments are conducted on the large-scale glass segmentation dataset GSD-S. Our GEM establishes a new state-of-the-art performance with the help of these two VFMs, surpassing the best-reported method GlassSemNet with an IoU improvement of 2.1%. Additionally, extensive experiments demonstrate that our synthetic dataset S-GSD exhibits remarkable performance in zero-shot and transfer learning settings. Codes, datasets and models are publicly available at: https://github.com/isbrycee/GEM

Automated segmentation is a fundamental medical image analysis task, which enjoys significant advances due to the advent of deep learning. While foundation models have been useful in natural language processing and some vision tasks for some time, the foundation model developed with image segmentation in mind - Segment Anything Model (SAM) - has been developed only recently and has shown similar promise. However, there are still no systematic analyses or "best-practice" guidelines for optimal fine-tuning of SAM for medical image segmentation. This work summarizes existing fine-tuning strategies with various backbone architectures, model components, and fine-tuning algorithms across 18 combinations, and evaluates them on 17 datasets covering all common radiology modalities. Our study reveals that (1) fine-tuning SAM leads to slightly better performance than previous segmentation methods, (2) fine-tuning strategies that use parameter-efficient learning in both the encoder and decoder are superior to other strategies, (3) network architecture has a small impact on final performance, (4) further training SAM with self-supervised learning can improve final model performance. We also demonstrate the ineffectiveness of some methods popular in the literature and further expand our experiments into few-shot and prompt-based settings. Lastly, we released our code and MRI-specific fine-tuned weights, which consistently obtained superior performance over the original SAM, at https://github.com/mazurowski-lab/finetune-SAM.

Segmenting medical images is critical to facilitating both patient diagnoses and quantitative research. A major limiting factor is the lack of labeled data, as obtaining expert annotations for each new set of imaging data and task can be labor intensive and inconsistent among annotators. We present CUTS, an unsupervised deep learning framework for medical image segmentation. CUTS operates in two stages. For each image, it produces an embedding map via intra-image contrastive learning and local patch reconstruction. Then, these embeddings are partitioned at dynamic granularity levels that correspond to the data topology. CUTS yields a series of coarse-to-fine-grained segmentations that highlight features at various granularities. We applied CUTS to retinal fundus images and two types of brain MRI images to delineate structures and patterns at different scales. When evaluated against predefined anatomical masks, CUTS improved the dice coefficient and Hausdorff distance by at least 10% compared to existing unsupervised methods. Finally, CUTS showed performance on par with Segment Anything Models (SAM, MedSAM, SAM-Med2D) pre-trained on gigantic labeled datasets.

Early detection of wildfires is essential to prevent large-scale fires resulting in extensive environmental, structural, and societal damage. Uncrewed aerial vehicles (UAVs) can cover large remote areas effectively with quick deployment requiring minimal infrastructure and equipping them with small cameras and computers enables autonomous real-time detection. In remote areas, however, detection methods are limited to onboard computation due to the lack of high-bandwidth mobile networks. For accurate camera-based localisation, segmentation of the detected smoke is essential but training data for deep learning-based wildfire smoke segmentation is limited. This study shows how small specialised segmentation models can be trained using only bounding box labels, leveraging zero-shot foundation model supervision. The method offers the advantages of needing only fairly easily obtainable bounding box labels and requiring training solely for the smaller student network. The proposed method achieved 63.3% mIoU on a manually annotated and diverse wildfire dataset. The used model can perform in real-time at ~25 fps with a UAV-carried NVIDIA Jetson Orin NX computer while reliably recognising smoke, as demonstrated at real-world forest burning events. Code is available at: https://gitlab.com/fgi_nls/public/wildfire-real-time-segmentation

Lower extremity computed tomography (CT) contains clinically relevant information for body composition analysis, sarcopenia assessment, and musculoskeletal disease monitoring, but extracting these measurements at scale requires accurate tissue segmentation and an automated quantification workflow. Existing public segmentation tools are not designed for comprehensive lower extremity CT analysis, particularly for clinically important inter/intramuscular adipose tissue, and most public methods only provide mask prediction rather than an end-to-end quantification system. To address this problem, we present LegSegNet, a deep learning system for lower extremity CT tissue segmentation and body composition quantification. Given an input CT scan, LegSegNet segments bone, skeletal muscle, subcutaneous adipose tissue, and inter/intramuscular adipose tissue. It then computes quantitative tissue measurements for downstream analysis. We developed the segmentation model using 1,302 manually annotated CT slices and evaluated it on 900 held-out test slices, with all annotations reviewed by radiologists. We benchmark LegSegNet against a broad set of 2D segmentation methods, including CNN-based models, transformer-based models, and finetuned foundation models, and further evaluate its generalization on an external public CT dataset. LegSegNet achieves the best overall segmentation performance, with an average Dice score of 89.31 on the held-out test set. To our knowledge, LegSegNet is the first publicly available end-to-end system for lower extremity CT tissue segmentation and quantification, providing a practical evaluation tool for future computer vision research in medical image analysis. The code and model weights are available at: https://github.com/mazurowski-lab/LegSegNet

Point cloud segmentation is central to autonomous driving and 3D scene understanding. While voxel- and point-based methods dominate recent research due to their compatibility with deep architectures and ability to capture fine-grained geometry, they often incur high computational cost, irregular memory access, and limited real-time efficiency. In contrast, range-view methods, though relatively underexplored - can leverage mature 2D semantic segmentation techniques for fast and accurate predictions. Motivated by the rapid progress in Visual Foundation Models (VFMs) for captioning, zero-shot recognition, and multimodal tasks, we investigate whether SAM2, the current state-of-the-art VFM for segmentation tasks, can serve as a strong backbone for LiDAR point cloud segmentation in the range view. We present , to our knowledge, the first range-view framework that adapts SAM2 to 3D segmentation, coupling efficient 2D feature extraction with standard projection/back-projection to operate on point clouds. To optimize SAM2 for range-view representations, we implement several architectural modifications to the encoder: (1) a novel module that emphasizes horizontal spatial dependencies inherent in LiDAR range images, (2) a customized configuration of tailored to the geometric properties of spherical projections, and (3) an adapted mechanism in the encoder backbone specifically designed to capture the unique spatial patterns and discontinuities present in range-view pseudo-images. Our approach achieves competitive performance on SemanticKITTI while benefiting from the speed, scalability, and deployment simplicity of 2D-centric pipelines. This work highlights the viability of VFMs as general-purpose backbones for 3D perception and opens a path toward unified, foundation-model-driven LiDAR segmentation. Results lets us conclude that range-view segmentation methods using VFMs leads to promising results.

The ability to perform pixel-wise semantic segmentation in real-time is of paramount importance in mobile applications. Recent deep neural networks aimed at this task have the disadvantage of requiring a large number of floating point operations and have long run-times that hinder their usability. In this paper, we propose a novel deep neural network architecture named ENet (efficient neural network), created specifically for tasks requiring low latency operation. ENet is up to 18times faster, requires 75times less FLOPs, has 79times less parameters, and provides similar or better accuracy to existing models. We have tested it on CamVid, Cityscapes and SUN datasets and report on comparisons with existing state-of-the-art methods, and the trade-offs between accuracy and processing time of a network. We present performance measurements of the proposed architecture on embedded systems and suggest possible software improvements that could make ENet even faster.

Currently, deep learning-based instance segmentation for various applications (e.g., Agriculture) is predominantly performed using a labor-intensive process involving extensive field data collection using sophisticated sensors, followed by careful manual annotation of images, presenting significant logistical and financial challenges to researchers and organizations. The process also slows down the model development and training process. In this study, we presented a novel method for deep learning-based instance segmentation of apples in commercial orchards that eliminates the need for labor-intensive field data collection and manual annotation. Utilizing a Large Language Model (LLM), we synthetically generated orchard images and automatically annotated them using the Segment Anything Model (SAM) integrated with a YOLO11 base model. This method significantly reduces reliance on physical sensors and manual data processing, presenting a major advancement in "Agricultural AI". The synthetic, auto-annotated dataset was used to train the YOLO11 model for Apple instance segmentation, which was then validated on real orchard images. The results showed that the automatically generated annotations achieved a Dice Coefficient of 0.9513 and an IoU of 0.9303, validating the accuracy and overlap of the mask annotations. All YOLO11 configurations, trained solely on these synthetic datasets with automated annotations, accurately recognized and delineated apples, highlighting the method's efficacy. Specifically, the YOLO11m-seg configuration achieved a mask precision of 0.902 and a mask mAP@50 of 0.833 on test images collected from a commercial orchard. Additionally, the YOLO11l-seg configuration outperformed other models in validation on 40 LLM-generated images, achieving the highest mask precision and mAP@50 metrics. Keywords: YOLO, SAM, SAMv2, YOLO11, YOLOv11, Segment Anything, YOLO-SAM

Automated tracking of surgical tool keypoints in robotic surgery videos is an essential task for various downstream use cases such as skill assessment, expertise assessment, and the delineation of safety zones. In recent years, the explosion of deep learning for vision applications has led to many works in surgical instrument segmentation, while lesser focus has been on tracking specific tool keypoints, such as tool tips. In this work, we propose a novel, multi-frame context-driven deep learning framework to localize and track tool keypoints in surgical videos. We train and test our models on the annotated frames from the 2015 EndoVis Challenge dataset, resulting in state-of-the-art performance. By leveraging sophisticated deep learning models and multi-frame context, we achieve 90\% keypoint detection accuracy and a localization RMS error of 5.27 pixels. Results on a self-annotated JIGSAWS dataset with more challenging scenarios also show that the proposed multi-frame models can accurately track tool-tip and tool-base keypoints, with {<}4.2-pixel RMS error overall. Such a framework paves the way for accurately tracking surgical instrument keypoints, enabling further downstream use cases. Project and dataset webpage: https://tinyurl.com/mfc-tracker

Agentic systems built on large language models (LLMs) offer promising capabilities for automating complex workflows in healthcare AI. We introduce mAIstro, an open-source, autonomous multi-agentic framework for end-to-end development and deployment of medical AI models. The system orchestrates exploratory data analysis, radiomic feature extraction, image segmentation, classification, and regression through a natural language interface, requiring no coding from the user. Built on a modular architecture, mAIstro supports both open- and closed-source LLMs, and was evaluated using a large and diverse set of prompts across 16 open-source datasets, covering a wide range of imaging modalities, anatomical regions, and data types. The agents successfully executed all tasks, producing interpretable outputs and validated models. This work presents the first agentic framework capable of unifying data analysis, AI model development, and inference across varied healthcare applications, offering a reproducible and extensible foundation for clinical and research AI integration. The code is available at: https://github.com/eltzanis/mAIstro

Although deep models have greatly improved the accuracy and robustness of image segmentation, obtaining segmentation results with highly accurate boundaries and fine structures is still a challenging problem. In this paper, we propose a simple yet powerful Boundary-Aware Segmentation Network (BASNet), which comprises a predict-refine architecture and a hybrid loss, for highly accurate image segmentation. The predict-refine architecture consists of a densely supervised encoder-decoder network and a residual refinement module, which are respectively used to predict and refine a segmentation probability map. The hybrid loss is a combination of the binary cross entropy, structural similarity and intersection-over-union losses, which guide the network to learn three-level (ie, pixel-, patch- and map- level) hierarchy representations. We evaluate our BASNet on two reverse tasks including salient object segmentation, camouflaged object segmentation, showing that it achieves very competitive performance with sharp segmentation boundaries. Importantly, BASNet runs at over 70 fps on a single GPU which benefits many potential real applications. Based on BASNet, we further developed two (close to) commercial applications: AR COPY & PASTE, in which BASNet is integrated with augmented reality for "COPYING" and "PASTING" real-world objects, and OBJECT CUT, which is a web-based tool for automatic object background removal. Both applications have already drawn huge amount of attention and have important real-world impacts. The code and two applications will be publicly available at: https://github.com/NathanUA/BASNet.

Accurate medical image segmentation is crucial for precise anatomical delineation. Deep learning models like U-Net have shown great success but depend heavily on large datasets and struggle with domain shifts, complex structures, and limited training samples. Recent studies have explored diffusion models for segmentation by iteratively refining masks. However, these methods still retain the conventional image-to-mask mapping, making them highly sensitive to input data, which hampers stability and generalization. In contrast, we introduce DiffAtlas, a novel generative framework that models both images and masks through diffusion during training, effectively ``GenAI-fying'' atlas-based segmentation. During testing, the model is guided to generate a specific target image-mask pair, from which the corresponding mask is obtained. DiffAtlas retains the robustness of the atlas paradigm while overcoming its scalability and domain-specific limitations. Extensive experiments on CT and MRI across same-domain, cross-modality, varying-domain, and different data-scale settings using the MMWHS and TotalSegmentator datasets demonstrate that our approach outperforms existing methods, particularly in limited-data and zero-shot modality segmentation. Code is available at https://github.com/M3DV/DiffAtlas.

Rapid assessment after a natural disaster is key for prioritizing emergency resources. In the case of landslides, rapid assessment involves determining the extent of the area affected and measuring the size and location of individual landslides. Synthetic Aperture Radar (SAR) is an active remote sensing technique that is unaffected by weather conditions. Deep Learning algorithms can be applied to SAR data, but training them requires large labeled datasets. In the case of landslides, these datasets are laborious to produce for segmentation, and often they are not available for the specific region in which the event occurred. Here, we study how deep learning algorithms for landslide segmentation on SAR products can benefit from pretraining on a simpler task and from data from different regions. The method we explore consists of two training stages. First, we learn the task of identifying whether a SAR image contains any landslides or not. Then, we learn to segment in a sparsely labeled scenario where half of the data do not contain landslides. We test whether the inclusion of feature embeddings derived from stage-1 helps with landslide detection in stage-2. We find that it leads to minor improvements in the Area Under the Precision-Recall Curve, but also to a significantly lower false positive rate in areas without landslides and an improved estimate of the average number of landslide pixels in a chip. A more accurate pixel count allows to identify the most affected areas with higher confidence. This could be valuable in rapid response scenarios where prioritization of resources at a global scale is important. We make our code publicly available at https://github.com/VMBoehm/SAR-landslide-detection-pretraining.

In this paper, a semi-automatic annotation of bacteria genera and species from DIBaS dataset is implemented using clustering and thresholding algorithms. A Deep learning model is trained to achieve the semantic segmentation and classification of the bacteria species. Classification accuracy of 95% is achieved. Deep learning models find tremendous applications in biomedical image processing. Automatic segmentation of bacteria from gram-stained microscopic images is essential to diagnose respiratory and urinary tract infections, detect cancers, etc. Deep learning will aid the biologists to get reliable results in less time. Additionally, a lot of human intervention can be reduced. This work can be helpful to detect bacteria from urinary smear images, sputum smear images, etc to diagnose urinary tract infections, tuberculosis, pneumonia, etc.

Brain tumors, particularly gliomas, pose significant chall-enges due to their complex growth patterns, infiltrative nature, and the variability in brain structure across individuals, which makes accurate diagnosis and monitoring difficult. Deep learning models have been developed to accurately delineate these tumors. However, most of these models were trained on relatively homogenous high-resource datasets, limiting their robustness when deployed in underserved regions. In this study, we performed segmentation-aware offline data augmentation on the BraTS-Africa dataset to increase the data sample size and diversity to enhance generalization. We further constructed an ensemble of three distinct architectures, MedNeXt, SegMamba, and Residual-Encoder U-Net, to leverage their complementary strengths. Our best-performing model, MedNeXt, was trained on 1000 epochs and achieved the highest average lesion-wise dice and normalized surface distance scores of 0.86 and 0.81 respectively. However, the ensemble model trained for 500 epochs produced the most balanced segmentation performance across the tumour subregions. This work demonstrates that a combination of advanced augmentation and model ensembling can improve segmentation accuracy and robustness on diverse and underrepresented datasets. Code available at: https://github.com/SPARK-Academy-2025/SPARK-2025/tree/main/SPARK2025_BraTs_MODELS/SPARK_NeuroAshanti

While deep learning models have become the predominant method for medical image segmentation, they are typically not capable of generalizing to unseen segmentation tasks involving new anatomies, image modalities, or labels. Given a new segmentation task, researchers generally have to train or fine-tune models, which is time-consuming and poses a substantial barrier for clinical researchers, who often lack the resources and expertise to train neural networks. We present UniverSeg, a method for solving unseen medical segmentation tasks without additional training. Given a query image and example set of image-label pairs that define a new segmentation task, UniverSeg employs a new Cross-Block mechanism to produce accurate segmentation maps without the need for additional training. To achieve generalization to new tasks, we have gathered and standardized a collection of 53 open-access medical segmentation datasets with over 22,000 scans, which we refer to as MegaMedical. We used this collection to train UniverSeg on a diverse set of anatomies and imaging modalities. We demonstrate that UniverSeg substantially outperforms several related methods on unseen tasks, and thoroughly analyze and draw insights about important aspects of the proposed system. The UniverSeg source code and model weights are freely available at https://universeg.csail.mit.edu

Deep-learning models have been successful in biomedical image segmentation. To generalize for real-world deployment, test-time augmentation (TTA) methods are often used to transform the test image into different versions that are hopefully closer to the training domain. Unfortunately, due to the vast diversity of instance scale and image styles, many augmented test images produce undesirable results, thus lowering the overall performance. This work proposes a new TTA framework, S^3-TTA, which selects the suitable image scale and style for each test image based on a transformation consistency metric. In addition, S^3-TTA constructs an end-to-end augmentation-segmentation joint-training pipeline to ensure a task-oriented augmentation. On public benchmarks for cell and lung segmentation, S^3-TTA demonstrates improvements over the prior art by 3.4% and 1.3%, respectively, by simply augmenting the input data in testing phase.

Deep learning models have emerged as the cornerstone of medical image segmentation, but their efficacy hinges on the availability of extensive manually labeled datasets and their adaptability to unforeseen categories remains a challenge. Few-shot segmentation (FSS) offers a promising solution by endowing models with the capacity to learn novel classes from limited labeled examples. A leading method for FSS is ALPNet, which compares features between the query image and the few available support segmented images. A key question about using ALPNet is how to design its features. In this work, we delve into the potential of using features from DINOv2, which is a foundational self-supervised learning model in computer vision. Leveraging the strengths of ALPNet and harnessing the feature extraction capabilities of DINOv2, we present a novel approach to few-shot segmentation that not only enhances performance but also paves the way for more robust and adaptable medical image analysis.

Information on trees at the individual level is crucial for monitoring forest ecosystems and planning forest management. Current monitoring methods involve ground measurements, requiring extensive cost, time and labor. Advances in drone remote sensing and computer vision offer great potential for mapping individual trees from aerial imagery at broad-scale. Large pre-trained vision models, such as the Segment Anything Model (SAM), represent a particularly compelling choice given limited labeled data. In this work, we compare methods leveraging SAM for the task of automatic tree crown instance segmentation in high resolution drone imagery in three use cases: 1) boreal plantations, 2) temperate forests and 3) tropical forests. We also study the integration of elevation data into models, in the form of Digital Surface Model (DSM) information, which can readily be obtained at no additional cost from RGB drone imagery. We present BalSAM, a model leveraging SAM and DSM information, which shows potential over other methods, particularly in the context of plantations. We find that methods using SAM out-of-the-box do not outperform a custom Mask R-CNN, even with well-designed prompts. However, efficiently tuning SAM end-to-end and integrating DSM information are both promising avenues for tree crown instance segmentation models.

In this paper, we focus on image inpainting task, aiming at recovering the missing area of an incomplete image given the context information. Recent development in deep generative models enables an efficient end-to-end framework for image synthesis and inpainting tasks, but existing methods based on generative models don't exploit the segmentation information to constrain the object shapes, which usually lead to blurry results on the boundary. To tackle this problem, we propose to introduce the semantic segmentation information, which disentangles the inter-class difference and intra-class variation for image inpainting. This leads to much clearer recovered boundary between semantically different regions and better texture within semantically consistent segments. Our model factorizes the image inpainting process into segmentation prediction (SP-Net) and segmentation guidance (SG-Net) as two steps, which predict the segmentation labels in the missing area first, and then generate segmentation guided inpainting results. Experiments on multiple public datasets show that our approach outperforms existing methods in optimizing the image inpainting quality, and the interactive segmentation guidance provides possibilities for multi-modal predictions of image inpainting.

Semantic segmentation and change detection are two fundamental challenges in remote sensing, requiring models to capture either spatial semantics or temporal differences from satellite imagery. Existing deep learning models often struggle with temporal inconsistencies or in capturing fine-grained spatial structures, require extensive pretraining, and offer limited interpretability - especially in real-world remote sensing scenarios. Recent advances in diffusion models show that Gaussian noise can be systematically leveraged to learn expressive data representations through denoising. Motivated by this, we investigate whether the noise process in diffusion models can be effectively utilized for discriminative tasks. We propose Noise2Map, a unified diffusion-based framework that repurposes the denoising process for fast, end-to-end discriminative learning. Unlike prior work that uses diffusion only for generation or feature extraction, Noise2Map directly predicts semantic or change maps using task-specific noise schedules and timestep conditioning, avoiding the costly sampling procedures of traditional diffusion models. The model is pretrained via self-supervised denoising and fine-tuned with supervision, enabling both interpretability and robustness. Our architecture supports both tasks (SS and CD) through a shared backbone and task-specific noise schedulers. Extensive evaluations on the SpaceNet7, WHU, and xView2 buildings damaged by wildfires datasets demonstrate that Noise2Map ranks on average 1st among seven models on semantic segmentation and 1st on change detection by a cross-dataset rank metric (average F1 primary, IoU tie-break). Ablation studies highlight the robustness of our model against different training noise schedulers and timestep control in the diffusion process, as well as the ability of the model to perform multi-task learning.

The recent surge in performance for image analysis of digitised pathology slides can largely be attributed to the advances in deep learning. Deep models can be used to initially localise various structures in the tissue and hence facilitate the extraction of interpretable features for biomarker discovery. However, these models are typically trained for a single task and therefore scale poorly as we wish to adapt the model for an increasing number of different tasks. Also, supervised deep learning models are very data hungry and therefore rely on large amounts of training data to perform well. In this paper, we present a multi-task learning approach for segmentation and classification of nuclei, glands, lumina and different tissue regions that leverages data from multiple independent data sources. While ensuring that our tasks are aligned by the same tissue type and resolution, we enable meaningful simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve the performance of additional tasks via transfer learning, including nuclear classification and signet ring cell detection. As part of this work, we train our developed Cerberus model on a huge amount of data, consisting of over 600K objects for segmentation and 440K patches for classification. We use our approach to process 599 colorectal whole-slide images from TCGA, where we localise 377 million, 900K and 2.1 million nuclei, glands and lumina, respectively and make the results available to the community for downstream analysis.

Teeth segmentation and recognition are critical in various dental applications and dental diagnosis. Automatic and accurate segmentation approaches have been made possible by integrating deep learning models. Although teeth segmentation has been studied in the past, only some techniques were able to effectively classify and segment teeth simultaneously. This article offers a pipeline of two deep learning models, U-Net and YOLOv8, which results in BB-UNet, a new architecture for the classification and segmentation of teeth on panoramic X-rays that is efficient and reliable. We have improved the quality and reliability of teeth segmentation by utilising the YOLOv8 and U-Net capabilities. The proposed networks have been evaluated using the mean average precision (mAP) and dice coefficient for YOLOv8 and BB-UNet, respectively. We have achieved a 3\% increase in mAP score for teeth classification compared to existing methods, and a 10-15\% increase in dice coefficient for teeth segmentation compared to U-Net across different categories of teeth. A new Dental dataset was created based on UFBA-UESC dataset with Bounding-Box and Polygon annotations of 425 dental panoramic X-rays. The findings of this research pave the way for a wider adoption of object detection models in the field of dental diagnosis.

Segmentation of crop fields is essential for enhancing agricultural productivity, monitoring crop health, and promoting sustainable practices. Deep learning models adopted for this task must ensure accurate and reliable predictions to avoid economic losses and environmental impact. The newly proposed Kolmogorov-Arnold networks (KANs) offer promising advancements in the performance of neural networks. This paper analyzes the integration of KAN layers into the U-Net architecture (U-KAN) to segment crop fields using Sentinel-2 and Sentinel-1 satellite images and provides an analysis of the performance and explainability of these networks. Our findings indicate a 2\% improvement in IoU compared to the traditional full-convolutional U-Net model in fewer GFLOPs. Furthermore, gradient-based explanation techniques show that U-KAN predictions are highly plausible and that the network has a very high ability to focus on the boundaries of cultivated areas rather than on the areas themselves. The per-channel relevance analysis also reveals that some channels are irrelevant to this task.

In this study, we develop a novel methodology for annotating the brain vasculature using dynamic 4D-CTA head scans. By using multiple time points from dynamic CTA acquisitions, we subtract bone and soft tissue to enhance the visualization of arteries and veins, reducing the effort required to obtain manual annotations of brain vessels. We then train deep learning models on our ground truth annotations by using the same segmentation for multiple phases from the dynamic 4D-CTA collection, effectively enlarging our dataset by 4 to 5 times and inducing robustness to contrast phases. In total, our dataset comprises 110 training images from 25 patients and 165 test images from 14 patients. In comparison with two similarly-sized datasets for CTA-based brain vessel segmentation, a nnUNet model trained on our dataset can achieve significantly better segmentations across all vascular regions, with an average mDC of 0.846 for arteries and 0.957 for veins in the TopBrain dataset. Furthermore, metrics such as average directed Hausdorff distance (adHD) and topology sensitivity (tSens) reflected similar trends: using our dataset resulted in low error margins (adHD of 0.304 mm for arteries and 0.078 for veins) and high sensitivity (tSens of 0.877 for arteries and 0.974 for veins), indicating excellent accuracy in capturing vessel morphology. Our code and model weights are available online at https://github.com/alceballosa/robust-vessel-segmentation

Modern cars are incorporating an increasing number of driver assist features, among which automatic lane keeping. The latter allows the car to properly position itself within the road lanes, which is also crucial for any subsequent lane departure or trajectory planning decision in fully autonomous cars. Traditional lane detection methods rely on a combination of highly-specialized, hand-crafted features and heuristics, usually followed by post-processing techniques, that are computationally expensive and prone to scalability due to road scene variations. More recent approaches leverage deep learning models, trained for pixel-wise lane segmentation, even when no markings are present in the image due to their big receptive field. Despite their advantages, these methods are limited to detecting a pre-defined, fixed number of lanes, e.g. ego-lanes, and can not cope with lane changes. In this paper, we go beyond the aforementioned limitations and propose to cast the lane detection problem as an instance segmentation problem - in which each lane forms its own instance - that can be trained end-to-end. To parametrize the segmented lane instances before fitting the lane, we further propose to apply a learned perspective transformation, conditioned on the image, in contrast to a fixed "bird's-eye view" transformation. By doing so, we ensure a lane fitting which is robust against road plane changes, unlike existing approaches that rely on a fixed, pre-defined transformation. In summary, we propose a fast lane detection algorithm, running at 50 fps, which can handle a variable number of lanes and cope with lane changes. We verify our method on the tuSimple dataset and achieve competitive results.

Mangroves are dynamic coastal ecosystems that are crucial to environmental health, economic stability, and climate resilience. The monitoring and preservation of mangroves are of global importance, with remote sensing technologies playing a pivotal role in these efforts. The integration of cutting-edge artificial intelligence with satellite data opens new avenues for ecological monitoring, potentially revolutionizing conservation strategies at a time when the protection of natural resources is more crucial than ever. The objective of this work is to provide a comprehensive evaluation of recent deep-learning models on the task of mangrove segmentation. We first introduce and make available a novel open-source dataset, MagSet-2, incorporating mangrove annotations from the Global Mangrove Watch and satellite images from Sentinel-2, from mangrove positions all over the world. We then benchmark three architectural groups, namely convolutional, transformer, and mamba models, using the created dataset. The experimental outcomes further validate the deep learning community's interest in the Mamba model, which surpasses other architectures in all metrics.

There are two major types of uncertainty one can model. Aleatoric uncertainty captures noise inherent in the observations. On the other hand, epistemic uncertainty accounts for uncertainty in the model -- uncertainty which can be explained away given enough data. Traditionally it has been difficult to model epistemic uncertainty in computer vision, but with new Bayesian deep learning tools this is now possible. We study the benefits of modeling epistemic vs. aleatoric uncertainty in Bayesian deep learning models for vision tasks. For this we present a Bayesian deep learning framework combining input-dependent aleatoric uncertainty together with epistemic uncertainty. We study models under the framework with per-pixel semantic segmentation and depth regression tasks. Further, our explicit uncertainty formulation leads to new loss functions for these tasks, which can be interpreted as learned attenuation. This makes the loss more robust to noisy data, also giving new state-of-the-art results on segmentation and depth regression benchmarks.

Esophageal cancer is among the most common types of cancer worldwide. It is traditionally treated using open esophagectomy, but in recent years, robot-assisted minimally invasive esophagectomy (RAMIE) has emerged as a promising alternative. However, robot-assisted surgery can be challenging for novice surgeons, as they often suffer from a loss of spatial orientation. Computer-aided anatomy recognition holds promise for improving surgical navigation, but research in this area remains limited. In this study, we developed a comprehensive dataset for semantic segmentation in RAMIE, featuring the largest collection of vital anatomical structures and surgical instruments to date. Handling this diverse set of classes presents challenges, including class imbalance and the recognition of complex structures such as nerves. This study aims to understand the challenges and limitations of current state-of-the-art algorithms on this novel dataset and problem. Therefore, we benchmarked eight real-time deep learning models using two pretraining datasets. We assessed both traditional and attention-based networks, hypothesizing that attention-based networks better capture global patterns and address challenges such as occlusion caused by blood or other tissues. The benchmark includes our RAMIE dataset and the publicly available CholecSeg8k dataset, enabling a thorough assessment of surgical segmentation tasks. Our findings indicate that pretraining on ADE20k, a dataset for semantic segmentation, is more effective than pretraining on ImageNet. Furthermore, attention-based models outperform traditional convolutional neural networks, with SegNeXt and Mask2Former achieving higher Dice scores, and Mask2Former additionally excelling in average symmetric surface distance.

Despite the success of deep learning models on instance segmentation, current methods still suffer from catastrophic forgetting in continual learning scenarios. In this paper, our contributions for continual instance segmentation are threefold. First, we propose the Y-knowledge distillation (Y-KD), a technique that shares a common feature extractor between the teacher and student networks. As the teacher is also updated with new data in Y-KD, the increased plasticity results in new modules that are specialized on new classes. Second, our Y-KD approach is supported by a dynamic architecture method that trains task-specific modules with a unique instance segmentation head, thereby significantly reducing forgetting. Third, we complete our approach by leveraging checkpoint averaging as a simple method to manually balance the trade-off between performance on the various sets of classes, thus increasing control over the model's behavior without any additional cost. These contributions are united in our model that we name the Dynamic Y-KD network. We perform extensive experiments on several single-step and multi-steps incremental learning scenarios, and we show that our approach outperforms previous methods both on past and new classes. For instance, compared to recent work, our method obtains +2.1% mAP on old classes in 15-1, +7.6% mAP on new classes in 19-1 and reaches 91.5% of the mAP obtained by joint-training on all classes in 15-5.

Vision transformers are effective deep learning models for vision tasks, including medical image segmentation. However, they lack efficiency and translational invariance, unlike convolutional neural networks (CNNs). To model long-range interactions in 3D brain lesion segmentation, we propose an all-convolutional transformer block variant of the U-Net architecture. We demonstrate that our model provides the greatest compromise in three factors: performance competitive with the state-of-the-art; parameter efficiency of a CNN; and the favourable inductive biases of a transformer. Our public implementation is available at https://github.com/liamchalcroft/MDUNet .

Deep learning for medical imaging is hampered by task-specific models that lack generalizability and prognostic capabilities, while existing 'universal' approaches suffer from simplistic conditioning and poor medical semantic understanding. To address these limitations, we introduce DuPLUS, a deep learning framework for efficient multi-modal medical image analysis. DuPLUS introduces a novel vision-language framework that leverages hierarchical semantic prompts for fine-grained control over the analysis task, a capability absent in prior universal models. To enable extensibility to other medical tasks, it includes a hierarchical, text-controlled architecture driven by a unique dual-prompt mechanism. For segmentation, DuPLUS is able to generalize across three imaging modalities, ten different anatomically various medical datasets, encompassing more than 30 organs and tumor types. It outperforms the state-of-the-art task specific and universal models on 8 out of 10 datasets. We demonstrate extensibility of its text-controlled architecture by seamless integration of electronic health record (EHR) data for prognosis prediction, and on a head and neck cancer dataset, DuPLUS achieved a Concordance Index (CI) of 0.69. Parameter-efficient fine-tuning enables rapid adaptation to new tasks and modalities from varying centers, establishing DuPLUS as a versatile and clinically relevant solution for medical image analysis. The code for this work is made available at: https://anonymous.4open.science/r/DuPLUS-6C52

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

Zero-shot point cloud segmentation aims to make deep models capable of recognizing novel objects in point cloud that are unseen in the training phase. Recent trends favor the pipeline which transfers knowledge from seen classes with labels to unseen classes without labels. They typically align visual features with semantic features obtained from word embedding by the supervision of seen classes' annotations. However, point cloud contains limited information to fully match with semantic features. In fact, the rich appearance information of images is a natural complement to the textureless point cloud, which is not well explored in previous literature. Motivated by this, we propose a novel multi-modal zero-shot learning method to better utilize the complementary information of point clouds and images for more accurate visual-semantic alignment. Extensive experiments are performed in two popular benchmarks, i.e., SemanticKITTI and nuScenes, and our method outperforms current SOTA methods with 52% and 49% improvement on average for unseen class mIoU, respectively.

Building on the success of deep learning models in cardiovascular structure segmentation, increasing attention has been focused on improving generalization and robustness, particularly in small, annotated datasets. Despite recent advancements, current approaches often face challenges such as overfitting and accuracy limitations, largely due to their reliance on large datasets and narrow optimization techniques. This paper introduces the UU-Mamba model, an extension of the U-Mamba architecture, designed to address these challenges in both cardiac and vascular segmentation. By incorporating Sharpness-Aware Minimization (SAM), the model enhances generalization by targeting flatter minima in the loss landscape. Additionally, we propose an uncertainty-aware loss function that combines region-based, distribution-based, and pixel-based components to improve segmentation accuracy by capturing both local and global features. While the UU-Mamba model has already demonstrated great performance, further testing is required to fully assess its generalization and robustness. We expand our evaluation by conducting new trials on the ImageCAS (coronary artery) and Aorta (aortic branches and zones) datasets, which present more complex segmentation challenges than the ACDC dataset (left and right ventricles) used in our previous work, showcasing the model's adaptability and resilience. We confirm UU-Mamba's superior performance over leading models such as TransUNet, Swin-Unet, nnUNet, and nnFormer. Moreover, we provide a more comprehensive evaluation of the model's robustness and segmentation accuracy, as demonstrated by extensive experiments.

Semantic segmentation of point clouds is an essential task for understanding the environment in autonomous driving and robotics. Recent range-based works achieve real-time efficiency, while point- and voxel-based methods produce better results but are affected by high computational complexity. Moreover, highly complex deep learning models are often not suited to efficiently learn from small datasets. Their generalization capabilities can easily be driven by the abundance of data rather than the architecture design. In this paper, we harness the information from the three-dimensional representation to proficiently capture local features, while introducing the range image representation to incorporate additional information and facilitate fast computation. A GPU-based KDTree allows for rapid building, querying, and enhancing projection with straightforward operations. Extensive experiments on SemanticKITTI and nuScenes datasets demonstrate the benefits of our modification in a ``small data'' setup, in which only one sequence of the dataset is used to train the models, but also in the conventional setup, where all sequences except one are used for training. We show that a reduced version of our model not only demonstrates strong competitiveness against full-scale state-of-the-art models but also operates in real-time, making it a viable choice for real-world case applications. The code of our method is available at https://github.com/Bender97/WaffleAndRange.

With the significantly increasing incidence and prevalence of abdominal diseases, there is a need to embrace greater use of new innovations and technology for the diagnosis and treatment of patients. Although deep-learning methods have notably been developed to assist radiologists in diagnosing abdominal diseases, existing models have the restricted ability to segment common lesions in the abdomen due to missing annotations for typical abdominal pathologies in their training datasets. To address the limitation, we introduce MSWAL, the first 3D Multi-class Segmentation of the Whole Abdominal Lesions dataset, which broadens the coverage of various common lesion types, such as gallstones, kidney stones, liver tumors, kidney tumors, pancreatic cancer, liver cysts, and kidney cysts. With CT scans collected from 694 patients (191,417 slices) of different genders across various scanning phases, MSWAL demonstrates strong robustness and generalizability. The transfer learning experiment from MSWAL to two public datasets, LiTS and KiTS, effectively demonstrates consistent improvements, with Dice Similarity Coefficient (DSC) increase of 3.00% for liver tumors and 0.89% for kidney tumors, demonstrating that the comprehensive annotations and diverse lesion types in MSWAL facilitate effective learning across different domains and data distributions. Furthermore, we propose Inception nnU-Net, a novel segmentation framework that effectively integrates an Inception module with the nnU-Net architecture to extract information from different receptive fields, achieving significant enhancement in both voxel-level DSC and region-level F1 compared to the cutting-edge public algorithms on MSWAL. Our dataset will be released after being accepted, and the code is publicly released at https://github.com/tiuxuxsh76075/MSWAL-.

The retinal vasculature provides important clues in the diagnosis and monitoring of systemic diseases including hypertension and diabetes. The microvascular system is of primary involvement in such conditions, and the retina is the only anatomical site where the microvasculature can be directly observed. The objective assessment of retinal vessels has long been considered a surrogate biomarker for systemic vascular diseases, and with recent advancements in retinal imaging and computer vision technologies, this topic has become the subject of renewed attention. In this paper, we present a novel dataset, dubbed RAVIR, for the semantic segmentation of Retinal Arteries and Veins in Infrared Reflectance (IR) imaging. It enables the creation of deep learning-based models that distinguish extracted vessel type without extensive post-processing. We propose a novel deep learning-based methodology, denoted as SegRAVIR, for the semantic segmentation of retinal arteries and veins and the quantitative measurement of the widths of segmented vessels. Our extensive experiments validate the effectiveness of SegRAVIR and demonstrate its superior performance in comparison to state-of-the-art models. Additionally, we propose a knowledge distillation framework for the domain adaptation of RAVIR pretrained networks on color images. We demonstrate that our pretraining procedure yields new state-of-the-art benchmarks on the DRIVE, STARE, and CHASE_DB1 datasets. Dataset link: https://ravirdataset.github.io/data/

Two challenges are presented when parsing road scenes in UAV images. First, the high resolution of UAV images makes processing difficult. Second, supervised deep learning methods require a large amount of manual annotations to train robust and accurate models. In this paper, an unsupervised road parsing framework that leverages recent advances in vision language models and fundamental computer vision model is introduced.Initially, a vision language model is employed to efficiently process ultra-large resolution UAV images to quickly detect road regions of interest in the images. Subsequently, the vision foundation model SAM is utilized to generate masks for the road regions without category information. Following that, a self-supervised representation learning network extracts feature representations from all masked regions. Finally, an unsupervised clustering algorithm is applied to cluster these feature representations and assign IDs to each cluster. The masked regions are combined with the corresponding IDs to generate initial pseudo-labels, which initiate an iterative self-training process for regular semantic segmentation. The proposed method achieves an impressive 89.96% mIoU on the development dataset without relying on any manual annotation. Particularly noteworthy is the extraordinary flexibility of the proposed method, which even goes beyond the limitations of human-defined categories and is able to acquire knowledge of new categories from the dataset itself.

Data diversity and volume are crucial to the success of training deep learning models, while in the medical imaging field, the difficulty and cost of data collection and annotation are especially huge. Specifically in robotic surgery, data scarcity and imbalance have heavily affected the model accuracy and limited the design and deployment of deep learning-based surgical applications such as surgical instrument segmentation. Considering this, we rethink the surgical instrument segmentation task and propose a one-to-many data generation solution that gets rid of the complicated and expensive process of data collection and annotation from robotic surgery. In our method, we only utilize a single surgical background tissue image and a few open-source instrument images as the seed images and apply multiple augmentations and blending techniques to synthesize amounts of image variations. In addition, we also introduce the chained augmentation mixing during training to further enhance the data diversities. The proposed approach is evaluated on the real datasets of the EndoVis-2018 and EndoVis-2017 surgical scene segmentation. Our empirical analysis suggests that without the high cost of data collection and annotation, we can achieve decent surgical instrument segmentation performance. Moreover, we also observe that our method can deal with novel instrument prediction in the deployment domain. We hope our inspiring results will encourage researchers to emphasize data-centric methods to overcome demanding deep learning limitations besides data shortage, such as class imbalance, domain adaptation, and incremental learning. Our code is available at https://github.com/lofrienger/Single_SurgicalScene_For_Segmentation.

Semantic medical image segmentation is a crucial part of both scientific research and clinical care. With enough labelled data, deep learning models can be trained to accurately automate specific medical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive. In this paper, we present ScribblePrompt, an interactive segmentation framework for medical imaging that enables human annotators to segment unseen structures using scribbles, clicks, and bounding boxes. Scribbles are an intuitive and effective form of user interaction for complex tasks, however most existing methods focus on click-based interactions. We introduce algorithms for simulating realistic scribbles that enable training models that are amenable to multiple types of interaction. To achieve generalization to new tasks, we train on a diverse collection of 65 open-access biomedical datasets -- using both real and synthetic labels. We test ScribblePrompt on multiple network architectures and unseen datasets, and demonstrate that it can be used in real-time on a single CPU. We evaluate ScribblePrompt using manually-collected scribbles, simulated interactions, and a user study. ScribblePrompt outperforms existing methods in all our evaluations. In the user study, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to existing methods. We showcase ScribblePrompt in an online demo and provide code at https://scribbleprompt.csail.mit.edu

Discussions of minimum parking requirement policies often include maps of parking lots, which are time consuming to construct manually. Open source datasets for such parking lots are scarce, particularly for US cities. This paper introduces the idea of using Near-Infrared (NIR) channels as input and several post-processing techniques to improve the prediction of off-street surface parking lots using satellite imagery. We constructed two datasets with 12,617 image-mask pairs each: one with 3-channel (RGB) and another with 4-channel (RGB + NIR). The datasets were used to train five deep learning models (OneFormer, Mask2Former, SegFormer, DeepLabV3, and FCN) for semantic segmentation, classifying images to differentiate between parking and non-parking pixels. Our results demonstrate that the NIR channel improved accuracy because parking lots are often surrounded by grass, even though the NIR channel needed to be upsampled from a lower resolution. Post-processing including eliminating erroneous holes, simplifying edges, and removing road and building footprints further improved the accuracy. Best model, OneFormer trained on 4-channel input and paired with post-processing techniques achieves a mean Intersection over Union (mIoU) of 84.9 percent and a pixel-wise accuracy of 96.3 percent.

Medical image segmentation is crucial for many healthcare tasks, including disease diagnosis and treatment planning. One key area is the segmentation of skin lesions, which is vital for diagnosing skin cancer and monitoring patients. In this context, this paper introduces SegDT, a new segmentation model based on diffusion transformer (DiT). SegDT is designed to work on low-cost hardware and incorporates Rectified Flow, which improves the generation quality at reduced inference steps and maintains the flexibility of standard diffusion models. Our method is evaluated on three benchmarking datasets and compared against several existing works, achieving state-of-the-art results while maintaining fast inference speeds. This makes the proposed model appealing for real-world medical applications. This work advances the performance and capabilities of deep learning models in medical image analysis, enabling faster, more accurate diagnostic tools for healthcare professionals. The code is made publicly available at https://github.com/Bekhouche/SegDT{GitHub}.

Deep learning plays an important role in crack segmentation, but most work utilize off-the-shelf or improved models that have not been specifically developed for this task. High-resolution convolution neural networks that are sensitive to objects' location and detail help improve the performance of crack segmentation, yet conflict with real-time detection. This paper describes HrSegNet, a high-resolution network with semantic guidance specifically designed for crack segmentation, which guarantees real-time inference speed while preserving crack details. After evaluation on the composite dataset CrackSeg9k and the scenario-specific datasets Asphalt3k and Concrete3k, HrSegNet obtains state-of-the-art segmentation performance and efficiencies that far exceed those of the compared models. This approach demonstrates that there is a trade-off between high-resolution modeling and real-time detection, which fosters the use of edge devices to analyze cracks in real-world applications.

Model calibration measures the agreement between the predicted probability estimates and the true correctness likelihood. Proper model calibration is vital for high-risk applications. Unfortunately, modern deep neural networks are poorly calibrated, compromising trustworthiness and reliability. Medical image segmentation particularly suffers from this due to the natural uncertainty of tissue boundaries. This is exasperated by their loss functions, which favor overconfidence in the majority classes. We address these challenges with DOMINO, a domain-aware model calibration method that leverages the semantic confusability and hierarchical similarity between class labels. Our experiments demonstrate that our DOMINO-calibrated deep neural networks outperform non-calibrated models and state-of-the-art morphometric methods in head image segmentation. Our results show that our method can consistently achieve better calibration, higher accuracy, and faster inference times than these methods, especially on rarer classes. This performance is attributed to our domain-aware regularization to inform semantic model calibration. These findings show the importance of semantic ties between class labels in building confidence in deep learning models. The framework has the potential to improve the trustworthiness and reliability of generic medical image segmentation models. The code for this article is available at: https://github.com/lab-smile/DOMINO.

Large-scale 2D datasets have been instrumental in advancing machine learning; however, progress in 3D vision tasks has been relatively slow. This disparity is largely due to the limited availability of 3D benchmarking datasets. In particular, creating real-world point cloud datasets for indoor scene semantic segmentation presents considerable challenges, including data collection within confined spaces and the costly, often inaccurate process of per-point labeling to generate ground truths. While synthetic datasets address some of these challenges, they often fail to replicate real-world conditions, particularly the occlusions that occur in point clouds collected from real environments. Existing 3D benchmarking datasets typically evaluate deep learning models under the assumption that training and test data are independently and identically distributed (IID), which affects the models' usability for real-world point cloud segmentation. To address these challenges, we introduce the BelHouse3D dataset, a new synthetic point cloud dataset designed for 3D indoor scene semantic segmentation. This dataset is constructed using real-world references from 32 houses in Belgium, ensuring that the synthetic data closely aligns with real-world conditions. Additionally, we include a test set with data occlusion to simulate out-of-distribution (OOD) scenarios, reflecting the occlusions commonly encountered in real-world point clouds. We evaluate popular point-based semantic segmentation methods using our OOD setting and present a benchmark. We believe that BelHouse3D and its OOD setting will advance research in 3D point cloud semantic segmentation for indoor scenes, providing valuable insights for the development of more generalizable models.

Rapid progress in 3D semantic segmentation is inseparable from the advances of deep network models, which highly rely on large-scale annotated data for training. To address the high cost and challenges of 3D point-level labeling, we present a method for semi-supervised point cloud semantic segmentation to adopt unlabeled point clouds in training to boost the model performance. Inspired by the recent contrastive loss in self-supervised tasks, we propose the guided point contrastive loss to enhance the feature representation and model generalization ability in semi-supervised setting. Semantic predictions on unlabeled point clouds serve as pseudo-label guidance in our loss to avoid negative pairs in the same category. Also, we design the confidence guidance to ensure high-quality feature learning. Besides, a category-balanced sampling strategy is proposed to collect positive and negative samples to mitigate the class imbalance problem. Extensive experiments on three datasets (ScanNet V2, S3DIS, and SemanticKITTI) show the effectiveness of our semi-supervised method to improve the prediction quality with unlabeled data.

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

Convolutional Neural Networks (CNNs) and Transformers have been the most popular architectures for biomedical image segmentation, but both of them have limited ability to handle long-range dependencies because of inherent locality or computational complexity. To address this challenge, we introduce U-Mamba, a general-purpose network for biomedical image segmentation. Inspired by the State Space Sequence Models (SSMs), a new family of deep sequence models known for their strong capability in handling long sequences, we design a hybrid CNN-SSM block that integrates the local feature extraction power of convolutional layers with the abilities of SSMs for capturing the long-range dependency. Moreover, U-Mamba enjoys a self-configuring mechanism, allowing it to automatically adapt to various datasets without manual intervention. We conduct extensive experiments on four diverse tasks, including the 3D abdominal organ segmentation in CT and MR images, instrument segmentation in endoscopy images, and cell segmentation in microscopy images. The results reveal that U-Mamba outperforms state-of-the-art CNN-based and Transformer-based segmentation networks across all tasks. This opens new avenues for efficient long-range dependency modeling in biomedical image analysis. The code, models, and data are publicly available at https://wanglab.ai/u-mamba.html.

Virtually all aspects of modern life depend on space technology. Thanks to the great advancement of computer vision in general and deep learning-based techniques in particular, over the decades, the world witnessed the growing use of deep learning in solving problems for space applications, such as self-driving robot, tracers, insect-like robot on cosmos and health monitoring of spacecraft. These are just some prominent examples that has advanced space industry with the help of deep learning. However, the success of deep learning models requires a lot of training data in order to have decent performance, while on the other hand, there are very limited amount of publicly available space datasets for the training of deep learning models. Currently, there is no public datasets for space-based object detection or instance segmentation, partly because manually annotating object segmentation masks is very time consuming as they require pixel-level labelling, not to mention the challenge of obtaining images from space. In this paper, we aim to fill this gap by releasing a dataset for spacecraft detection, instance segmentation and part recognition. The main contribution of this work is the development of the dataset using images of space stations and satellites, with rich annotations including bounding boxes of spacecrafts and masks to the level of object parts, which are obtained with a mixture of automatic processes and manual efforts. We also provide evaluations with state-of-the-art methods in object detection and instance segmentation as a benchmark for the dataset. The link for downloading the proposed dataset can be found on https://github.com/Yurushia1998/SatelliteDataset.

Coronavirus disease 2019 (COVID-19) has been diagnosed automatically using Machine Learning algorithms over chest X-ray (CXR) images. However, most of the earlier studies used Deep Learning models over scarce datasets bearing the risk of overfitting. Additionally, previous studies have revealed the fact that deep networks are not reliable for classification since their decisions may originate from irrelevant areas on the CXRs. Therefore, in this study, we propose Operational Segmentation Network (OSegNet) that performs detection by segmenting COVID-19 pneumonia for a reliable diagnosis. To address the data scarcity encountered in training and especially in evaluation, this study extends the largest COVID-19 CXR dataset: QaTa-COV19 with 121,378 CXRs including 9258 COVID-19 samples with their corresponding ground-truth segmentation masks that are publicly shared with the research community. Consequently, OSegNet has achieved a detection performance with the highest accuracy of 99.65% among the state-of-the-art deep models with 98.09% precision.

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.

Tooth segmentation in Cone-Beam Computed Tomography (CBCT) remains challenging, especially for fine structures like root apices, which is critical for assessing root resorption in orthodontics. We introduce GEPAR3D, a novel approach that unifies instance detection and multi-class segmentation into a single step tailored to improve root segmentation. Our method integrates a Statistical Shape Model of dentition as a geometric prior, capturing anatomical context and morphological consistency without enforcing restrictive adjacency constraints. We leverage a deep watershed method, modeling each tooth as a continuous 3D energy basin encoding voxel distances to boundaries. This instance-aware representation ensures accurate segmentation of narrow, complex root apices. Trained on publicly available CBCT scans from a single center, our method is evaluated on external test sets from two in-house and two public medical centers. GEPAR3D achieves the highest overall segmentation performance, averaging a Dice Similarity Coefficient (DSC) of 95.0% (+2.8% over the second-best method) and increasing recall to 95.2% (+9.5%) across all test sets. Qualitative analyses demonstrated substantial improvements in root segmentation quality, indicating significant potential for more accurate root resorption assessment and enhanced clinical decision-making in orthodontics. We provide the implementation and dataset at https://github.com/tomek1911/GEPAR3D.

Stroke is the basic element of Chinese character and stroke extraction has been an important and long-standing endeavor. Existing stroke extraction methods are often handcrafted and highly depend on domain expertise due to the limited training data. Moreover, there are no standardized benchmarks to provide a fair comparison between different stroke extraction methods, which, we believe, is a major impediment to the development of Chinese character stroke understanding and related tasks. In this work, we present the first public available Chinese Character Stroke Extraction (CCSE) benchmark, with two new large-scale datasets: Kaiti CCSE (CCSE-Kai) and Handwritten CCSE (CCSE-HW). With the large-scale datasets, we hope to leverage the representation power of deep models such as CNNs to solve the stroke extraction task, which, however, remains an open question. To this end, we turn the stroke extraction problem into a stroke instance segmentation problem. Using the proposed datasets to train a stroke instance segmentation model, we surpass previous methods by a large margin. Moreover, the models trained with the proposed datasets benefit the downstream font generation and handwritten aesthetic assessment tasks. We hope these benchmark results can facilitate further research. The source code and datasets are publicly available at: https://github.com/lizhaoliu-Lec/CCSE.

We present Point-Voxel CNN (PVCNN) for efficient, fast 3D deep learning. Previous work processes 3D data using either voxel-based or point-based NN models. However, both approaches are computationally inefficient. The computation cost and memory footprints of the voxel-based models grow cubically with the input resolution, making it memory-prohibitive to scale up the resolution. As for point-based networks, up to 80% of the time is wasted on structuring the sparse data which have rather poor memory locality, not on the actual feature extraction. In this paper, we propose PVCNN that represents the 3D input data in points to reduce the memory consumption, while performing the convolutions in voxels to reduce the irregular, sparse data access and improve the locality. Our PVCNN model is both memory and computation efficient. Evaluated on semantic and part segmentation datasets, it achieves much higher accuracy than the voxel-based baseline with 10x GPU memory reduction; it also outperforms the state-of-the-art point-based models with 7x measured speedup on average. Remarkably, the narrower version of PVCNN achieves 2x speedup over PointNet (an extremely efficient model) on part and scene segmentation benchmarks with much higher accuracy. We validate the general effectiveness of PVCNN on 3D object detection: by replacing the primitives in Frustrum PointNet with PVConv, it outperforms Frustrum PointNet++ by 2.4% mAP on average with 1.5x measured speedup and GPU memory reduction.

The Vines-DB dataset contains 1,218 original high-resolution RGB images of seven ornamental vine species collected under field conditions at the Utah Agricultural Experiment Station's Greenville Research Farm in Logan, Utah, USA. The dataset was generated from 168 individual vine plants that were transplanted in 2022 and photographed repeatedly across multiple months during the 2023 and 2024 growing seasons (July-October). Images were captured with an iPhone 16 Pro equipped with a 48 MP camera between 10:00 AM and 12:00 PM under daylight. Vines were grown on 1.2m x 2.4m trellises and photographed from a distance of 1m against black or white Styrofoam backdrops to improve contrast and reduce background noise. The dataset includes Akebia quinata, Campsis radicans, Hydrangea anomala petiolaris, Lonicera x heckrottii, Campsis x tagliabuana 'Madame Galen', Parthenocissus quinquefolia, and Wisteria floribunda. All original images were manually annotated in Roboflow by trained annotators to produce polygon-based instance segmentation masks for eight classes, including seven species and background. After preprocessing and data augmentation, the working dataset was expanded to 2,307 images for model development and evaluation. The augmented dataset was divided into 2,019 training images, 192 validation images, and 96 test images using stratified sampling to maintain balanced representation. Vines-DB supports the development and evaluation of deep learning models for multi-class instance segmentation in precision horticulture and urban ecology. The dataset enables applications such as automated canopy cover estimation, species identification, and scalable field phenotyping. In addition, repeated monthly imaging of the plants captures temporal variation in canopy development and plant appearance, increasing the dataset's utility for segmentation benchmarking under realistic field conditions.

In orchard automation, dense foliage during the canopy season severely occludes tree structures, minimizing visibility to various canopy parts such as trunks and branches, which limits the ability of a machine vision system. However, canopy structure is more open and visible during the dormant season when trees are defoliated. In this work, we present an information fusion framework that integrates multi-seasonal structural data to support robotic and automated crop load management during the entire growing season. The framework combines high-resolution RGB-D imagery from both dormant and canopy periods using YOLOv9-Seg for instance segmentation, Kinect Fusion for 3D reconstruction, and Fast Generalized Iterative Closest Point (Fast GICP) for model alignment. Segmentation outputs from YOLOv9-Seg were used to extract depth-informed masks, which enabled accurate 3D point cloud reconstruction via Kinect Fusion; these reconstructed models from each season were subsequently aligned using Fast GICP to achieve spatially coherent multi-season fusion. The YOLOv9-Seg model, trained on manually annotated images, achieved a mean squared error (MSE) of 0.0047 and segmentation mAP@50 scores up to 0.78 for trunks in dormant season dataset. Kinect Fusion enabled accurate reconstruction of tree geometry, validated with field measurements resulting in root mean square errors (RMSE) of 5.23 mm for trunk diameter, 4.50 mm for branch diameter, and 13.72 mm for branch spacing. Fast GICP achieved precise cross-seasonal registration with a minimum fitness score of 0.00197, allowing integrated, comprehensive tree structure modeling despite heavy occlusions during the growing season. This fused structural representation enables robotic systems to access otherwise obscured architectural information, improving the precision of pruning, thinning, and other automated orchard operations.

In computer vision, models must be able to adapt to changes in image resolution to effectively carry out tasks such as image segmentation; This is known as scale-equivariance. Recent works have made progress in developing scale-equivariant convolutional neural networks, e.g., through weight-sharing and kernel resizing. However, these networks are not truly scale-equivariant in practice. Specifically, they do not consider anti-aliasing as they formulate the down-scaling operation in the continuous domain. To address this shortcoming, we directly formulate down-scaling in the discrete domain with consideration of anti-aliasing. We then propose a novel architecture based on Fourier layers to achieve truly scale-equivariant deep nets, i.e., absolute zero equivariance-error. Following prior works, we test this model on MNIST-scale and STL-10 datasets. Our proposed model achieves competitive classification performance while maintaining zero equivariance-error.

Domain adaptation is to transfer the shared knowledge learned from the source domain to a new environment, i.e., target domain. One common practice is to train the model on both labeled source-domain data and unlabeled target-domain data. Yet the learned models are usually biased due to the strong supervision of the source domain. Most researchers adopt the early-stopping strategy to prevent over-fitting, but when to stop training remains a challenging problem since the lack of the target-domain validation set. In this paper, we propose one efficient bootstrapping method, called Adaboost Student, explicitly learning complementary models during training and liberating users from empirical early stopping. Adaboost Student combines the deep model learning with the conventional training strategy, i.e., adaptive boosting, and enables interactions between learned models and the data sampler. We adopt one adaptive data sampler to progressively facilitate learning on hard samples and aggregate "weak" models to prevent over-fitting. Extensive experiments show that (1) Without the need to worry about the stopping time, AdaBoost Student provides one robust solution by efficient complementary model learning during training. (2) AdaBoost Student is orthogonal to most domain adaptation methods, which can be combined with existing approaches to further improve the state-of-the-art performance. We have achieved competitive results on three widely-used scene segmentation domain adaptation benchmarks.