UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image Segmentation

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.

SmartScan: An AI-based Interactive Framework for Automated Region Extraction from Satellite Images

The deployment of a continuous methane monitoring system requires determining the optimal number and placement of fixed sensors. However, planning is labor-intensive, requiring extensive site setup and iteration to meet client restrictions. This challenge is amplified when evaluating multiple sites, limiting scalability. To address this, we introduce SmartScan, an AI framework that automates data extraction for optimal sensor placement. SmartScan identifies subspaces of interest from satellite images using an interactive tool to create facility-specific constraint sets efficiently. SmartScan leverages the Segment Anything Model (SAM), a prompt-based transformer for zero-shot segmentation, enabling subspace extraction without explicit training. It operates in two modes: (1) Data Curation Mode, where satellite images are processed to extract high-quality subspaces using an interactive prompting system for SAM, and (2) Autonomous Mode, where user-curated prompts train a deep learning network to replace manual prompting, fully automating subspace extraction. The interactive tool also serves for quality control, allowing users to refine AI-generated outputs and generate additional constraint sets as needed. With its AI-driven prompting mechanism, SmartScan delivers high-throughput, high-quality subspace extraction with minimal human intervention, enhancing scalability and efficiency. Notably, its adaptable design makes it suitable for extracting regions of interest from ultra-high-resolution satellite imagery across various domains.

AdaViT: Adaptive Vision Transformer for Flexible Pretrain and Finetune with Variable 3D Medical Image Modalities

Pretrain techniques, whether supervised or self-supervised, are widely used in deep learning to enhance model performance. In real-world clinical scenarios, different sets of magnetic resonance (MR) contrasts are often acquired for different subjects/cases, creating challenges for deep learning models assuming consistent input modalities among all the cases and between pretrain and finetune. Existing methods struggle to maintain performance when there is an input modality/contrast set mismatch with the pretrained model, often resulting in degraded accuracy. We propose an adaptive Vision Transformer (AdaViT) framework capable of handling variable set of input modalities for each case. We utilize a dynamic tokenizer to encode different input image modalities to tokens and take advantage of the characteristics of the transformer to build attention mechanism across variable length of tokens. Through extensive experiments, we demonstrate that this architecture effectively transfers supervised pretrained models to new datasets with different input modality/contrast sets, resulting in superior performance on zero-shot testing, few-shot finetuning, and backward transferring in brain infarct and brain tumor segmentation tasks. Additionally, for self-supervised pretrain, the proposed method is able to maximize the pretrain data and facilitate transferring to diverse downstream tasks with variable sets of input modalities.

Zero-shot Domain Generalization of Foundational Models for 3D Medical Image Segmentation: An Experimental Study

Domain shift, caused by variations in imaging modalities and acquisition protocols, limits model generalization in medical image segmentation. While foundation models (FMs) trained on diverse large-scale data hold promise for zero-shot generalization, their application to volumetric medical data remains underexplored. In this study, we examine their ability towards domain generalization (DG), by conducting a comprehensive experimental study encompassing 6 medical segmentation FMs and 12 public datasets spanning multiple modalities and anatomies. Our findings reveal the potential of promptable FMs in bridging the domain gap via smart prompting techniques. Additionally, by probing into multiple facets of zero-shot DG, we offer valuable insights into the viability of FMs for DG and identify promising avenues for future research.

AI-Assisted Colonoscopy: Polyp Detection and Segmentation using Foundation Models

In colonoscopy, 80% of the missed polyps could be detected with the help of Deep Learning models. In the search for algorithms capable of addressing this challenge, foundation models emerge as promising candidates. Their zero-shot or few-shot learning capabilities, facilitate generalization to new data or tasks without extensive fine-tuning. A concept that is particularly advantageous in the medical imaging domain, where large annotated datasets for traditional training are scarce. In this context, a comprehensive evaluation of foundation models for polyp segmentation was conducted, assessing both detection and delimitation. For the study, three different colonoscopy datasets have been employed to compare the performance of five different foundation models, DINOv2, YOLO-World, GroundingDINO, SAM and MedSAM, against two benchmark networks, YOLOv8 and Mask R-CNN. Results show that the success of foundation models in polyp characterization is highly dependent on domain specialization. For optimal performance in medical applications, domain-specific models are essential, and generic models require fine-tuning to achieve effective results. Through this specialization, foundation models demonstrated superior performance compared to state-of-the-art detection and segmentation models, with some models even excelling in zero-shot evaluation; outperforming fine-tuned models on unseen data.

SALT: A Flexible Semi-Automatic Labeling Tool for General LiDAR Point Clouds with Cross-Scene Adaptability and 4D Consistency

We propose a flexible Semi-Automatic Labeling Tool (SALT) for general LiDAR point clouds with cross-scene adaptability and 4D consistency. Unlike recent approaches that rely on camera distillation, SALT operates directly on raw LiDAR data, automatically generating pre-segmentation results. To achieve this, we propose a novel zero-shot learning paradigm, termed data alignment, which transforms LiDAR data into pseudo-images by aligning with the training distribution of vision foundation models. Additionally, we design a 4D-consistent prompting strategy and 4D non-maximum suppression module to enhance SAM2, ensuring high-quality, temporally consistent presegmentation. SALT surpasses the latest zero-shot methods by 18.4% PQ on SemanticKITTI and achieves nearly 40-50% of human annotator performance on our newly collected low-resolution LiDAR data and on combined data from three LiDAR types, significantly boosting annotation efficiency. We anticipate that SALT's open-sourcing will catalyze substantial expansion of current LiDAR datasets and lay the groundwork for the future development of LiDAR foundation models. Code is available at https://github.com/Cavendish518/SALT.

Delineate Anything: Resolution-Agnostic Field Boundary Delineation on Satellite Imagery

The accurate delineation of agricultural field boundaries from satellite imagery is vital for land management and crop monitoring. However, current methods face challenges due to limited dataset sizes, resolution discrepancies, and diverse environmental conditions. We address this by reformulating the task as instance segmentation and introducing the Field Boundary Instance Segmentation - 22M dataset (FBIS-22M), a large-scale, multi-resolution dataset comprising 672,909 high-resolution satellite image patches (ranging from 0.25 m to 10 m) and 22,926,427 instance masks of individual fields, significantly narrowing the gap between agricultural datasets and those in other computer vision domains. We further propose Delineate Anything, an instance segmentation model trained on our new FBIS-22M dataset. Our proposed model sets a new state-of-the-art, achieving a substantial improvement of 88.5% in mAP@0.5 and 103% in mAP@0.5:0.95 over existing methods, while also demonstrating significantly faster inference and strong zero-shot generalization across diverse image resolutions and unseen geographic regions. Code, pre-trained models, and the FBIS-22M dataset are available at https://lavreniuk.github.io/Delineate-Anything.

Semantic Segmentation of Transparent and Opaque Drinking Glasses with the Help of Zero-shot Learning

Segmenting transparent structures in images is challenging since they are difficult to distinguish from the background. Common examples are drinking glasses, which are a ubiquitous part of our lives and appear in many different shapes and sizes. In this work we propose TransCaGNet, a modified version of the zero-shot model CaGNet. We exchange the segmentation backbone with the architecture of Trans4Trans to be capable of segmenting transparent objects. Since some glasses are rarely captured, we use zeroshot learning to be able to create semantic segmentations of glass categories not given during training. We propose a novel synthetic dataset covering a diverse set of different environmental conditions. Additionally we capture a real-world evaluation dataset since most applications take place in the real world. Comparing our model with Zeg-Clip we are able to show that TransCaGNet produces better mean IoU and accuracy values while ZegClip outperforms it mostly for unseen classes. To improve the segmentation results, we combine the semantic segmentation of the models with the segmentation results of SAM 2. Our evaluation emphasizes that distinguishing between different classes is challenging for the models due to similarity, points of view, or coverings. Taking this behavior into account, we assign glasses multiple possible categories. The modification leads to an improvement up to 13.68% for the mean IoU and up to 17.88% for the mean accuracy values on the synthetic dataset. Using our difficult synthetic dataset for training, the models produce even better results on the real-world dataset. The mean IoU is improved up to 5.55% and the mean accuracy up to 5.72% on the real-world dataset.

Extracting Patient History from Clinical Text: A Comparative Study of Clinical Large Language Models

Extracting medical history entities (MHEs) related to a patient's chief complaint (CC), history of present illness (HPI), and past, family, and social history (PFSH) helps structure free-text clinical notes into standardized EHRs, streamlining downstream tasks like continuity of care, medical coding, and quality metrics. Fine-tuned clinical large language models (cLLMs) can assist in this process while ensuring the protection of sensitive data via on-premises deployment. This study evaluates the performance of cLLMs in recognizing CC/HPI/PFSH-related MHEs and examines how note characteristics impact model accuracy. We annotated 1,449 MHEs across 61 outpatient-related clinical notes from the MTSamples repository. To recognize these entities, we fine-tuned seven state-of-the-art cLLMs. Additionally, we assessed the models' performance when enhanced by integrating, problems, tests, treatments, and other basic medical entities (BMEs). We compared the performance of these models against GPT-4o in a zero-shot setting. To further understand the textual characteristics affecting model accuracy, we conducted an error analysis focused on note length, entity length, and segmentation. The cLLMs showed potential in reducing the time required for extracting MHEs by over 20%. However, detecting many types of MHEs remained challenging due to their polysemous nature and the frequent involvement of non-medical vocabulary. Fine-tuned GatorTron and GatorTronS, two of the most extensively trained cLLMs, demonstrated the highest performance. Integrating pre-identified BME information improved model performance for certain entities. Regarding the impact of textual characteristics on model performance, we found that longer entities were harder to identify, note length did not correlate with a higher error rate, and well-organized segments with headings are beneficial for the extraction.

SPNeRF: Open Vocabulary 3D Neural Scene Segmentation with Superpoints

Open-vocabulary segmentation, powered by large visual-language models like CLIP, has expanded 2D segmentation capabilities beyond fixed classes predefined by the dataset, enabling zero-shot understanding across diverse scenes. Extending these capabilities to 3D segmentation introduces challenges, as CLIP's image-based embeddings often lack the geometric detail necessary for 3D scene segmentation. Recent methods tend to address this by introducing additional segmentation models or replacing CLIP with variations trained on segmentation data, which lead to redundancy or loss on CLIP's general language capabilities. To overcome this limitation, we introduce SPNeRF, a NeRF based zero-shot 3D segmentation approach that leverages geometric priors. We integrate geometric primitives derived from the 3D scene into NeRF training to produce primitive-wise CLIP features, avoiding the ambiguity of point-wise features. Additionally, we propose a primitive-based merging mechanism enhanced with affinity scores. Without relying on additional segmentation models, our method further explores CLIP's capability for 3D segmentation and achieves notable improvements over original LERF.