Daily Papers

Most benchmarks for studying surgical interventions focus on a specific challenge instead of leveraging the intrinsic complementarity among different tasks. In this work, we present a new experimental framework towards holistic surgical scene understanding. First, we introduce the Phase, Step, Instrument, and Atomic Visual Action recognition (PSI-AVA) Dataset. PSI-AVA includes annotations for both long-term (Phase and Step recognition) and short-term reasoning (Instrument detection and novel Atomic Action recognition) in robot-assisted radical prostatectomy videos. Second, we present Transformers for Action, Phase, Instrument, and steps Recognition (TAPIR) as a strong baseline for surgical scene understanding. TAPIR leverages our dataset's multi-level annotations as it benefits from the learned representation on the instrument detection task to improve its classification capacity. Our experimental results in both PSI-AVA and other publicly available databases demonstrate the adequacy of our framework to spur future research on holistic surgical scene understanding.

This paper presents the Holistic and Multi-Granular Surgical Scene Understanding of Prostatectomies (GraSP) dataset, a curated benchmark that models surgical scene understanding as a hierarchy of complementary tasks with varying levels of granularity. Our approach encompasses long-term tasks, such as surgical phase and step recognition, and short-term tasks, including surgical instrument segmentation and atomic visual actions detection. To exploit our proposed benchmark, we introduce the Transformers for Actions, Phases, Steps, and Instrument Segmentation (TAPIS) model, a general architecture that combines a global video feature extractor with localized region proposals from an instrument segmentation model to tackle the multi-granularity of our benchmark. Through extensive experimentation in ours and alternative benchmarks, we demonstrate TAPIS's versatility and state-of-the-art performance across different tasks. This work represents a foundational step forward in Endoscopic Vision, offering a novel framework for future research towards holistic surgical scene understanding.

Surgical video-language pretraining (VLP) faces unique challenges due to the knowledge domain gap and the scarcity of multi-modal data. This study aims to bridge the gap by addressing issues regarding textual information loss in surgical lecture videos and the spatial-temporal challenges of surgical VLP. We propose a hierarchical knowledge augmentation approach and a novel Procedure-Encoded Surgical Knowledge-Augmented Video-Language Pretraining (PeskaVLP) framework to tackle these issues. The knowledge augmentation uses large language models (LLM) for refining and enriching surgical concepts, thus providing comprehensive language supervision and reducing the risk of overfitting. PeskaVLP combines language supervision with visual self-supervision, constructing hard negative samples and employing a Dynamic Time Warping (DTW) based loss function to effectively comprehend the cross-modal procedural alignment. Extensive experiments on multiple public surgical scene understanding and cross-modal retrieval datasets show that our proposed method significantly improves zero-shot transferring performance and offers a generalist visual representation for further advancements in surgical scene understanding.The code is available at https://github.com/CAMMA-public/SurgVLP

In recent years, the landscape of computer-assisted interventions and post-operative surgical video analysis has been dramatically reshaped by deep-learning techniques, resulting in significant advancements in surgeons' skills, operation room management, and overall surgical outcomes. However, the progression of deep-learning-powered surgical technologies is profoundly reliant on large-scale datasets and annotations. Particularly, surgical scene understanding and phase recognition stand as pivotal pillars within the realm of computer-assisted surgery and post-operative assessment of cataract surgery videos. In this context, we present the largest cataract surgery video dataset that addresses diverse requisites for constructing computerized surgical workflow analysis and detecting post-operative irregularities in cataract surgery. We validate the quality of annotations by benchmarking the performance of several state-of-the-art neural network architectures for phase recognition and surgical scene segmentation. Besides, we initiate the research on domain adaptation for instrument segmentation in cataract surgery by evaluating cross-domain instrument segmentation performance in cataract surgery videos. The dataset and annotations will be publicly available upon acceptance of the paper.

Surgical scene perception via videos are critical for advancing robotic surgery, telesurgery, and AI-assisted surgery, particularly in ophthalmology. However, the scarcity of diverse and richly annotated video datasets has hindered the development of intelligent systems for surgical workflow analysis. Existing datasets for surgical workflow analysis, which typically face challenges such as small scale, a lack of diversity in surgery and phase categories, and the absence of time-localized annotations, limit the requirements for action understanding and model generalization validation in complex and diverse real-world surgical scenarios. To address this gap, we introduce OphNet, a large-scale, expert-annotated video benchmark for ophthalmic surgical workflow understanding. OphNet features: 1) A diverse collection of 2,278 surgical videos spanning 66 types of cataract, glaucoma, and corneal surgeries, with detailed annotations for 102 unique surgical phases and 150 granular operations; 2) It offers sequential and hierarchical annotations for each surgery, phase, and operation, enabling comprehensive understanding and improved interpretability; 3) Moreover, OphNet provides time-localized annotations, facilitating temporal localization and prediction tasks within surgical workflows. With approximately 205 hours of surgical videos, OphNet is about 20 times larger than the largest existing surgical workflow analysis benchmark. Our dataset and code have been made available at: https://github.com/minghu0830/OphNet-benchmark.

Operating rooms (ORs) are complex, high-stakes environments requiring precise understanding of interactions among medical staff, tools, and equipment for enhancing surgical assistance, situational awareness, and patient safety. Current datasets fall short in scale, realism and do not capture the multimodal nature of OR scenes, limiting progress in OR modeling. To this end, we introduce MM-OR, a realistic and large-scale multimodal spatiotemporal OR dataset, and the first dataset to enable multimodal scene graph generation. MM-OR captures comprehensive OR scenes containing RGB-D data, detail views, audio, speech transcripts, robotic logs, and tracking data and is annotated with panoptic segmentations, semantic scene graphs, and downstream task labels. Further, we propose MM2SG, the first multimodal large vision-language model for scene graph generation, and through extensive experiments, demonstrate its ability to effectively leverage multimodal inputs. Together, MM-OR and MM2SG establish a new benchmark for holistic OR understanding, and open the path towards multimodal scene analysis in complex, high-stakes environments. Our code, and data is available at https://github.com/egeozsoy/MM-OR.

During surgical training, real-time feedback from trainers to trainees is important for preventing errors and enhancing long-term skill acquisition. Accurately predicting the effectiveness of this feedback, specifically whether it leads to a change in trainee behavior, is crucial for developing methods for improving surgical training and education. However, relying on human annotations to assess feedback effectiveness is laborious and prone to biases, underscoring the need for an automated, scalable, and objective method. Creating such an automated system poses challenges, as it requires an understanding of both the verbal feedback delivered by the trainer and the visual context of the real-time surgical scene. To address this, we propose a method that integrates information from transcribed verbal feedback and corresponding surgical video to predict feedback effectiveness. Our findings show that both transcribed feedback and surgical video are individually predictive of trainee behavior changes, and their combination achieves an AUROC of 0.70+/-0.02, improving prediction accuracy by up to 6.6%. Additionally, we introduce self-supervised fine-tuning as a strategy for enhancing surgical video representation learning, which is scalable and further enhances prediction performance. Our results demonstrate the potential of multi-modal learning to advance the automated assessment of surgical feedback.

Integration of Vision-Language Models (VLMs) in surgical intelligence is hindered by hallucinations, domain knowledge gaps, and limited understanding of task interdependencies within surgical scenes, undermining clinical reliability. While recent VLMs demonstrate strong general reasoning and thinking capabilities, they still lack the domain expertise and task-awareness required for precise surgical scene interpretation. Although Chain-of-Thought (CoT) can structure reasoning more effectively, current approaches rely on self-generated CoT steps, which often exacerbate inherent domain gaps and hallucinations. To overcome this, we present SurgRAW, a CoT-driven multi-agent framework that delivers transparent, interpretable insights for most tasks in robotic-assisted surgery. By employing specialized CoT prompts across five tasks: instrument recognition, action recognition, action prediction, patient data extraction, and outcome assessment, SurgRAW mitigates hallucinations through structured, domain-aware reasoning. Retrieval-Augmented Generation (RAG) is also integrated to external medical knowledge to bridge domain gaps and improve response reliability. Most importantly, a hierarchical agentic system ensures that CoT-embedded VLM agents collaborate effectively while understanding task interdependencies, with a panel discussion mechanism promotes logical consistency. To evaluate our method, we introduce SurgCoTBench, the first reasoning-based dataset with structured frame-level annotations. With comprehensive experiments, we demonstrate the effectiveness of proposed SurgRAW with 29.32% accuracy improvement over baseline VLMs on 12 robotic procedures, achieving the state-of-the-art performance and advancing explainable, trustworthy, and autonomous surgical assistance.

Modern operating room is becoming increasingly complex, requiring innovative intra-operative support systems. While the focus of surgical data science has largely been on video analysis, integrating surgical computer vision with language capabilities is emerging as a necessity. Our work aims to advance Visual Question Answering (VQA) in the surgical context with scene graph knowledge, addressing two main challenges in the current surgical VQA systems: removing question-condition bias in the surgical VQA dataset and incorporating scene-aware reasoning in the surgical VQA model design. First, we propose a Surgical Scene Graph-based dataset, SSG-QA, generated by employing segmentation and detection models on publicly available datasets. We build surgical scene graphs using spatial and action information of instruments and anatomies. These graphs are fed into a question engine, generating diverse QA pairs. Our SSG-QA dataset provides a more complex, diverse, geometrically grounded, unbiased, and surgical action-oriented dataset compared to existing surgical VQA datasets. We then propose SSG-QA-Net, a novel surgical VQA model incorporating a lightweight Scene-embedded Interaction Module (SIM), which integrates geometric scene knowledge in the VQA model design by employing cross-attention between the textual and the scene features. Our comprehensive analysis of the SSG-QA dataset shows that SSG-QA-Net outperforms existing methods across different question types and complexities. We highlight that the primary limitation in the current surgical VQA systems is the lack of scene knowledge to answer complex queries. We present a novel surgical VQA dataset and model and show that results can be significantly improved by incorporating geometric scene features in the VQA model design. The source code and the dataset will be made publicly available at: https://github.com/CAMMA-public/SSG-QA

Intra-operative recognition of surgical phases holds significant potential for enhancing real-time contextual awareness in the operating room. However, we argue that online recognition, while beneficial, primarily lends itself to post-operative video analysis due to its limited direct impact on the actual surgical decisions and actions during ongoing procedures. In contrast, we contend that the prediction and anticipation of surgical phases are inherently more valuable for intra-operative assistance, as they can meaningfully influence a surgeon's immediate and long-term planning by providing foresight into future steps. To address this gap, we propose a dual approach that simultaneously recognises the current surgical phase and predicts upcoming ones, thus offering comprehensive intra-operative assistance and guidance on the expected remaining workflow. Our novel method, Surgical Phase Recognition and Anticipation (SuPRA), leverages past and current information for accurate intra-operative phase recognition while using future segments for phase prediction. This unified approach challenges conventional frameworks that treat these objectives separately. We have validated SuPRA on two reputed datasets, Cholec80 and AutoLaparo21, where it demonstrated state-of-the-art performance with recognition accuracies of 91.8% and 79.3%, respectively. Additionally, we introduce and evaluate our model using new segment-level evaluation metrics, namely Edit and F1 Overlap scores, for a more temporal assessment of segment classification. In conclusion, SuPRA presents a new multi-task approach that paves the way for improved intra-operative assistance through surgical phase recognition and prediction of future events.

Understanding the workflow of surgical procedures in complex operating rooms requires a deep understanding of the interactions between clinicians and their environment. Surgical activity recognition (SAR) is a key computer vision task that detects activities or phases from multi-view camera recordings. Existing SAR models often fail to account for fine-grained clinician movements and multi-view knowledge, or they require calibrated multi-view camera setups and advanced point-cloud processing to obtain better results. In this work, we propose a novel calibration-free multi-view multi-modal pretraining framework called Multiview Pretraining for Video-Pose Surgical Activity Recognition PreViPS, which aligns 2D pose and vision embeddings across camera views. Our model follows CLIP-style dual-encoder architecture: one encoder processes visual features, while the other encodes human pose embeddings. To handle the continuous 2D human pose coordinates, we introduce a tokenized discrete representation to convert the continuous 2D pose coordinates into discrete pose embeddings, thereby enabling efficient integration within the dual-encoder framework. To bridge the gap between these two modalities, we propose several pretraining objectives using cross- and in-modality geometric constraints within the embedding space and incorporating masked pose token prediction strategy to enhance representation learning. Extensive experiments and ablation studies demonstrate improvements over the strong baselines, while data-efficiency experiments on two distinct operating room datasets further highlight the effectiveness of our approach. We highlight the benefits of our approach for surgical activity recognition in both multi-view and single-view settings, showcasing its practical applicability in complex surgical environments. Code will be made available at: https://github.com/CAMMA-public/PreViPS.

Every day, countless surgeries are performed worldwide, each within the distinct settings of operating rooms (ORs) that vary not only in their setups but also in the personnel, tools, and equipment used. This inherent diversity poses a substantial challenge for achieving a holistic understanding of the OR, as it requires models to generalize beyond their initial training datasets. To reduce this gap, we introduce ORacle, an advanced vision-language model designed for holistic OR domain modeling, which incorporates multi-view and temporal capabilities and can leverage external knowledge during inference, enabling it to adapt to previously unseen surgical scenarios. This capability is further enhanced by our novel data augmentation framework, which significantly diversifies the training dataset, ensuring ORacle's proficiency in applying the provided knowledge effectively. In rigorous testing, in scene graph generation, and downstream tasks on the 4D-OR dataset, ORacle not only demonstrates state-of-the-art performance but does so requiring less data than existing models. Furthermore, its adaptability is displayed through its ability to interpret unseen views, actions, and appearances of tools and equipment. This demonstrates ORacle's potential to significantly enhance the scalability and affordability of OR domain modeling and opens a pathway for future advancements in surgical data science. We will release our code and data upon acceptance.

Recent advancements in surgical computer vision have been driven by vision-only models, which lack language semantics, relying on manually annotated videos to predict fixed object categories. This limits their generalizability to unseen surgical procedures and tasks. We propose leveraging surgical video lectures from e-learning platforms to provide effective vision and language supervisory signals for multi-modal representation learning, bypassing manual annotations. We address surgery-specific linguistic challenges using multiple automatic speech recognition systems for text transcriptions. We introduce SurgVLP - Surgical Vision Language Pre-training - a novel method for multi-modal representation learning. SurgVLP employs a new contrastive learning objective, aligning video clip embeddings with corresponding multiple text embeddings in a joint latent space. We demonstrate the representational capability of this space through several vision-and-language surgical tasks and vision-only tasks specific to surgery. Unlike current fully supervised approaches, SurgVLP adapts to different surgical procedures and tasks without specific fine-tuning, achieving zero-shot adaptation to tasks such as surgical tool, phase, and triplet recognition without manual annotation. These results highlight the transferability and versatility of the learned multi-modal representations in surgical video analysis. The code is available at https://github.com/CAMMA-public/SurgVLP

The lack of labeled datasets in 3D vision for surgical scenes inhibits the development of robust 3D reconstruction algorithms in the medical domain. Despite the popularity of Neural Radiance Fields and 3D Gaussian Splatting in the general computer vision community, these systems have yet to find consistent success in surgical scenes due to challenges such as non-stationary lighting and non-Lambertian surfaces. As a result, the need for labeled surgical datasets continues to grow. In this work, we introduce a differentiable rendering framework for material and lighting estimation from endoscopic images and known geometry. Compared to previous approaches that model lighting and material jointly as radiance, we explicitly disentangle these scene properties for robust and photorealistic novel view synthesis. To disambiguate the training process, we formulate domain-specific properties inherent in surgical scenes. Specifically, we model the scene lighting as a simple spotlight and material properties as a bidirectional reflectance distribution function, parameterized by a neural network. By grounding color predictions in the rendering equation, we can generate photorealistic images at arbitrary camera poses. We evaluate our method with various sequences from the Colonoscopy 3D Video Dataset and show that our method produces competitive novel view synthesis results compared with other approaches. Furthermore, we demonstrate that synthetic data can be used to develop 3D vision algorithms by finetuning a depth estimation model with our rendered outputs. Overall, we see that the depth estimation performance is on par with fine-tuning with the original real images.

Surgical scene segmentation is critical in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, referring surgical segmentation is emerging, given its advantage of providing surgeons with an interactive experience to segment the target object. However, existing methods are limited by low efficiency and short-term tracking, hindering their applicability in complex real-world surgical scenarios. In this paper, we introduce ReSurgSAM2, a two-stage surgical referring segmentation framework that leverages Segment Anything Model 2 to perform text-referred target detection, followed by tracking with reliable initial frame identification and diversity-driven long-term memory. For the detection stage, we propose a cross-modal spatial-temporal Mamba to generate precise detection and segmentation results. Based on these results, our credible initial frame selection strategy identifies the reliable frame for the subsequent tracking. Upon selecting the initial frame, our method transitions to the tracking stage, where it incorporates a diversity-driven memory mechanism that maintains a credible and diverse memory bank, ensuring consistent long-term tracking. Extensive experiments demonstrate that ReSurgSAM2 achieves substantial improvements in accuracy and efficiency compared to existing methods, operating in real-time at 61.2 FPS. Our code and datasets will be available at https://github.com/jinlab-imvr/ReSurgSAM2.

Surgical robotics holds much promise for improving patient safety and clinician experience in the Operating Room (OR). However, it also comes with new challenges, requiring strong team coordination and effective OR management. Automatic detection of surgical activities is a key requirement for developing AI-based intelligent tools to tackle these challenges. The current state-of-the-art surgical activity recognition methods however operate on image-based representations and depend on large-scale labeled datasets whose collection is time-consuming and resource-expensive. This work proposes a new sample-efficient and object-based approach for surgical activity recognition in the OR. Our method focuses on the geometric arrangements between clinicians and surgical devices, thus utilizing the significant object interaction dynamics in the OR. We conduct experiments in a low-data regime study for long video activity recognition. We also benchmark our method againstother object-centric approaches on clip-level action classification and show superior performance.

Natural language could play an important role in developing generalist surgical models by providing a broad source of supervision from raw texts. This flexible form of supervision can enable the model's transferability across datasets and tasks as natural language can be used to reference learned visual concepts or describe new ones. In this work, we present HecVL, a novel hierarchical video-language pretraining approach for building a generalist surgical model. Specifically, we construct a hierarchical video-text paired dataset by pairing the surgical lecture video with three hierarchical levels of texts: at clip-level, atomic actions using transcribed audio texts; at phase-level, conceptual text summaries; and at video-level, overall abstract text of the surgical procedure. Then, we propose a novel fine-to-coarse contrastive learning framework that learns separate embedding spaces for the three video-text hierarchies using a single model. By disentangling embedding spaces of different hierarchical levels, the learned multi-modal representations encode short-term and long-term surgical concepts in the same model. Thanks to the injected textual semantics, we demonstrate that the HecVL approach can enable zero-shot surgical phase recognition without any human annotation. Furthermore, we show that the same HecVL model for surgical phase recognition can be transferred across different surgical procedures and medical centers. The code is available at https://github.com/CAMMA-public/SurgVLP

Surgical practice involves complex visual interpretation, procedural skills, and advanced medical knowledge, making surgical vision-language pretraining (VLP) particularly challenging due to this complexity and the limited availability of annotated data. To address the gap, we propose OphCLIP, a hierarchical retrieval-augmented vision-language pretraining framework specifically designed for ophthalmic surgical workflow understanding. OphCLIP leverages the OphVL dataset we constructed, a large-scale and comprehensive collection of over 375K hierarchically structured video-text pairs with tens of thousands of different combinations of attributes (surgeries, phases/operations/actions, instruments, medications, as well as more advanced aspects like the causes of eye diseases, surgical objectives, and postoperative recovery recommendations, etc). These hierarchical video-text correspondences enable OphCLIP to learn both fine-grained and long-term visual representations by aligning short video clips with detailed narrative descriptions and full videos with structured titles, capturing intricate surgical details and high-level procedural insights, respectively. Our OphCLIP also designs a retrieval-augmented pretraining framework to leverage the underexplored large-scale silent surgical procedure videos, automatically retrieving semantically relevant content to enhance the representation learning of narrative videos. Evaluation across 11 datasets for phase recognition and multi-instrument identification shows OphCLIP's robust generalization and superior performance.

Surgical workflow recognition has numerous potential medical applications, such as the automatic indexing of surgical video databases and the optimization of real-time operating room scheduling, among others. As a result, phase recognition has been studied in the context of several kinds of surgeries, such as cataract, neurological, and laparoscopic surgeries. In the literature, two types of features are typically used to perform this task: visual features and tool usage signals. However, the visual features used are mostly handcrafted. Furthermore, the tool usage signals are usually collected via a manual annotation process or by using additional equipment. In this paper, we propose a novel method for phase recognition that uses a convolutional neural network (CNN) to automatically learn features from cholecystectomy videos and that relies uniquely on visual information. In previous studies, it has been shown that the tool signals can provide valuable information in performing the phase recognition task. Thus, we present a novel CNN architecture, called EndoNet, that is designed to carry out the phase recognition and tool presence detection tasks in a multi-task manner. To the best of our knowledge, this is the first work proposing to use a CNN for multiple recognition tasks on laparoscopic videos. Extensive experimental comparisons to other methods show that EndoNet yields state-of-the-art results for both tasks.

In this paper, we propose a novel text promptable surgical instrument segmentation approach to overcome challenges associated with diversity and differentiation of surgical instruments in minimally invasive surgeries. We redefine the task as text promptable, thereby enabling a more nuanced comprehension of surgical instruments and adaptability to new instrument types. Inspired by recent advancements in vision-language models, we leverage pretrained image and text encoders as our model backbone and design a text promptable mask decoder consisting of attention- and convolution-based prompting schemes for surgical instrument segmentation prediction. Our model leverages multiple text prompts for each surgical instrument through a new mixture of prompts mechanism, resulting in enhanced segmentation performance. Additionally, we introduce a hard instrument area reinforcement module to improve image feature comprehension and segmentation precision. Extensive experiments on EndoVis2017 and EndoVis2018 datasets demonstrate our model's superior performance and promising generalization capability. To our knowledge, this is the first implementation of a promptable approach to surgical instrument segmentation, offering significant potential for practical application in the field of robotic-assisted surgery.

Advancements in computer-assisted surgical procedures heavily rely on accurate visual data interpretation from camera systems used during surgeries. Traditional open-access datasets focusing on surgical procedures are often limited by their small size, typically consisting of fewer than 100 videos with less than 100K images. To address these constraints, a new dataset called Surg-3M has been compiled using a novel aggregation pipeline that collects high-resolution videos from online sources. Featuring an extensive collection of over 4K surgical videos and more than 3 million high-quality images from multiple procedure types, Surg-3M offers a comprehensive resource surpassing existing alternatives in size and scope, including two novel tasks. To demonstrate the effectiveness of this dataset, we present SurgFM, a self-supervised foundation model pretrained on Surg-3M that achieves impressive results in downstream tasks such as surgical phase recognition, action recognition, and tool presence detection. Combining key components from ConvNeXt, DINO, and an innovative augmented distillation method, SurgFM exhibits exceptional performance compared to specialist architectures across various benchmarks. Our experimental results show that SurgFM outperforms state-of-the-art models in multiple downstream tasks, including significant gains in surgical phase recognition (+8.9pp, +4.7pp, and +3.9pp of Jaccard in AutoLaparo, M2CAI16, and Cholec80), action recognition (+3.1pp of mAP in CholecT50) and tool presence detection (+4.6pp of mAP in Cholec80). Moreover, even when using only half of the data, SurgFM outperforms state-of-the-art models in AutoLaparo and achieves state-of-the-art performance in Cholec80. Both Surg-3M and SurgFM have significant potential to accelerate progress towards developing autonomous robotic surgery systems.

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

Surgery video segmentation is an important topic in the surgical AI field. It allows the AI model to understand the spatial information of a surgical scene. Meanwhile, due to the lack of annotated surgical data, surgery segmentation models suffer from limited performance. With the emergence of SAM2 model, a large foundation model for video segmentation trained on natural videos, zero-shot surgical video segmentation became more realistic but meanwhile remains to be explored. In this paper, we systematically evaluate the performance of SAM2 model in zero-shot surgery video segmentation task. We conducted experiments under different configurations, including different prompting strategies, robustness, etc. Moreover, we conducted an empirical evaluation over the performance, including 9 datasets with 17 different types of surgeries.

Quantification of real-time informal feedback delivered by an experienced surgeon to a trainee during surgery is important for skill improvements in surgical training. Such feedback in the live operating room is inherently multimodal, consisting of verbal conversations (e.g., questions and answers) as well as non-verbal elements (e.g., through visual cues like pointing to anatomic elements). In this work, we leverage a clinically-validated five-category classification of surgical feedback: "Anatomic", "Technical", "Procedural", "Praise" and "Visual Aid". We then develop a multi-label machine learning model to classify these five categories of surgical feedback from inputs of text, audio, and video modalities. The ultimate goal of our work is to help automate the annotation of real-time contextual surgical feedback at scale. Our automated classification of surgical feedback achieves AUCs ranging from 71.5 to 77.6 with the fusion improving performance by 3.1%. We also show that high-quality manual transcriptions of feedback audio from experts improve AUCs to between 76.5 and 96.2, which demonstrates a clear path toward future improvements. Empirically, we find that the Staged training strategy, with first pre-training each modality separately and then training them jointly, is more effective than training different modalities altogether. We also present intuitive findings on the importance of modalities for different feedback categories. This work offers an important first look at the feasibility of automated classification of real-world live surgical feedback based on text, audio, and video modalities.

Foundation models have revolutionized computer vision by achieving vastly superior performance across diverse tasks through large-scale pretraining on extensive datasets. However, their application in surgical computer vision has been limited. This study addresses this gap by introducing SurgeNetXL, a novel surgical foundation model that sets a new benchmark in surgical computer vision. Trained on the largest reported surgical dataset to date, comprising over 4.7 million video frames, SurgeNetXL achieves consistent top-tier performance across six datasets spanning four surgical procedures and three tasks, including semantic segmentation, phase recognition, and critical view of safety (CVS) classification. Compared with the best-performing surgical foundation models, SurgeNetXL shows mean improvements of 2.4, 9.0, and 12.6 percent for semantic segmentation, phase recognition, and CVS classification, respectively. Additionally, SurgeNetXL outperforms the best-performing ImageNet-based variants by 14.4, 4.0, and 1.6 percent in the respective tasks. In addition to advancing model performance, this study provides key insights into scaling pretraining datasets, extending training durations, and optimizing model architectures specifically for surgical computer vision. These findings pave the way for improved generalizability and robustness in data-scarce scenarios, offering a comprehensive framework for future research in this domain. All models and a subset of the SurgeNetXL dataset, including over 2 million video frames, are publicly available at: https://github.com/TimJaspers0801/SurgeNet.

Segmentation of surgical instruments is crucial for enhancing surgeon performance and ensuring patient safety. Conventional techniques such as binary, semantic, and instance segmentation share a common drawback: they do not accommodate the parts of instruments obscured by tissues or other instruments. Precisely predicting the full extent of these occluded instruments can significantly improve laparoscopic surgeries by providing critical guidance during operations and assisting in the analysis of potential surgical errors, as well as serving educational purposes. In this paper, we introduce Amodal Segmentation to the realm of surgical instruments in the medical field. This technique identifies both the visible and occluded parts of an object. To achieve this, we introduce a new Amoal Instruments Segmentation (AIS) dataset, which was developed by reannotating each instrument with its complete mask, utilizing the 2017 MICCAI EndoVis Robotic Instrument Segmentation Challenge dataset. Additionally, we evaluate several leading amodal segmentation methods to establish a benchmark for this new dataset.

Purpose: Face detection is a needed component for the automatic analysis and assistance of human activities during surgical procedures. Efficient face detection algorithms can indeed help to detect and identify the persons present in the room, and also be used to automatically anonymize the data. However, current algorithms trained on natural images do not generalize well to the operating room (OR) images. In this work, we provide a comparison of state-of-the-art face detectors on OR data and also present an approach to train a face detector for the OR by exploiting non-annotated OR images. Methods: We propose a comparison of 6 state-of-the-art face detectors on clinical data using Multi-View Operating Room Faces (MVOR-Faces), a dataset of operating room images capturing real surgical activities. We then propose to use self-supervision, a domain adaptation method, for the task of face detection in the OR. The approach makes use of non-annotated images to fine-tune a state-of-the-art detector for the OR without using any human supervision. Results: The results show that the best model, namely the tiny face detector, yields an average precision of 0.536 at Intersection over Union (IoU) of 0.5. Our self-supervised model using non-annotated clinical data outperforms this result by 9.2%. Conclusion: We present the first comparison of state-of-the-art face detectors on operating room images and show that results can be significantly improved by using self-supervision on non-annotated data.

The ability to automatically detect and track surgical instruments in endoscopic videos can enable transformational interventions. Assessing surgical performance and efficiency, identifying skilled tool use and choreography, and planning operational and logistical aspects of OR resources are just a few of the applications that could benefit. Unfortunately, obtaining the annotations needed to train machine learning models to identify and localize surgical tools is a difficult task. Annotating bounding boxes frame-by-frame is tedious and time-consuming, yet large amounts of data with a wide variety of surgical tools and surgeries must be captured for robust training. Moreover, ongoing annotator training is needed to stay up to date with surgical instrument innovation. In robotic-assisted surgery, however, potentially informative data like timestamps of instrument installation and removal can be programmatically harvested. The ability to rely on tool installation data alone would significantly reduce the workload to train robust tool-tracking models. With this motivation in mind we invited the surgical data science community to participate in the challenge, SurgToolLoc 2022. The goal was to leverage tool presence data as weak labels for machine learning models trained to detect tools and localize them in video frames with bounding boxes. We present the results of this challenge along with many of the team's efforts. We conclude by discussing these results in the broader context of machine learning and surgical data science. The training data used for this challenge consisting of 24,695 video clips with tool presence labels is also being released publicly and can be accessed at https://console.cloud.google.com/storage/browser/isi-surgtoolloc-2022.

Purpose: Surgical performance depends not only on surgeons' technical skills but also on team communication within and across the different professional groups present during the operation. Therefore, automatically identifying team communication in the OR is crucial for patient safety and advances in the development of computer-assisted surgical workflow analysis and intra-operative support systems. To take the first step, we propose a new task of detecting communication briefings involving all OR team members, i.e. the team Time-out and the StOP?-protocol, by localizing their start and end times in video recordings of surgical operations. Methods: We generate an OR dataset of real surgeries, called Team-OR, with more than one hundred hours of surgical videos captured by the multi-view camera system in the OR. The dataset contains temporal annotations of 33 Time-out and 22 StOP?-protocol activities in total. We then propose a novel group activity detection approach, where we encode both scene context and action features, and use an efficient neural network model to output the results. Results: The experimental results on the Team-OR dataset show that our approach outperforms existing state-of-the-art temporal action detection approaches. It also demonstrates the lack of research on group activities in the OR, proving the significance of our dataset. Conclusion: We investigate the Team Time-Out and the StOP?-protocol in the OR, by presenting the first OR dataset with temporal annotations of group activities protocols, and introducing a novel group activity detection approach that outperforms existing approaches. Code is available at https://github.com/CAMMA-public/Team-OR.

Purpose: Surgical workflow analysis is crucial for improving surgical efficiency and safety. However, previous studies rely heavily on large-scale annotated datasets, posing challenges in cost, scalability, and reliance on expert annotations. To address this, we propose Surg-FTDA (Few-shot Text-driven Adaptation), designed to handle various surgical workflow analysis tasks with minimal paired image-label data. Methods: Our approach has two key components. First, Few-shot selection-based modality alignment selects a small subset of images and aligns their embeddings with text embeddings from the downstream task, bridging the modality gap. Second, Text-driven adaptation leverages only text data to train a decoder, eliminating the need for paired image-text data. This decoder is then applied to aligned image embeddings, enabling image-related tasks without explicit image-text pairs. Results: We evaluate our approach to generative tasks (image captioning) and discriminative tasks (triplet recognition and phase recognition). Results show that Surg-FTDA outperforms baselines and generalizes well across downstream tasks. Conclusion: We propose a text-driven adaptation approach that mitigates the modality gap and handles multiple downstream tasks in surgical workflow analysis, with minimal reliance on large annotated datasets. The code and dataset will be released in https://github.com/CAMMA-public/Surg-FTDA

In recent years, the application of machine learning to minimally invasive surgery (MIS) has attracted considerable interest. Datasets are critical to the use of such techniques. This paper presents a unique dataset recorded during ex vivo pseudo-cholecystectomy procedures on pig livers using the da Vinci Research Kit (dVRK). Unlike existing datasets, it addresses a critical gap by providing comprehensive kinematic data, recordings of all pedal inputs, and offers a time-stamped record of the endoscope's movements. This expanded version also includes segmentation and keypoint annotations of images, enhancing its utility for computer vision applications. Contributed by seven surgeons with varied backgrounds and experience levels that are provided as a part of this expanded version, the dataset is an important new resource for surgical robotics research. It enables the development of advanced methods for evaluating surgeon skills, tools for providing better context awareness, and automation of surgical tasks. Our work overcomes the limitations of incomplete recordings and imprecise kinematic data found in other datasets. To demonstrate the potential of the dataset for advancing automation in surgical robotics, we introduce two models that predict clutch usage and camera activation, a 3D scene reconstruction example, and the results from our keypoint and segmentation models.

Recent advancements in prompt-based medical image segmentation have enabled clinicians to identify tumors using simple input like bounding boxes or text prompts. However, existing methods face challenges when doctors need to interact through natural language or when position reasoning is required - understanding spatial relationships between anatomical structures and pathologies. We present PRS-Med, a framework that integrates vision-language models with segmentation capabilities to generate both accurate segmentation masks and corresponding spatial reasoning outputs. Additionally, we introduce the MMRS dataset (Multimodal Medical in Positional Reasoning Segmentation), which provides diverse, spatially-grounded question-answer pairs to address the lack of position reasoning data in medical imaging. PRS-Med demonstrates superior performance across six imaging modalities (CT, MRI, X-ray, ultrasound, endoscopy, RGB), significantly outperforming state-of-the-art methods in both segmentation accuracy and position reasoning. Our approach enables intuitive doctor-system interaction through natural language, facilitating more efficient diagnoses. Our dataset pipeline, model, and codebase will be released to foster further research in spatially-aware multimodal reasoning for medical applications.

The ability to interpret and intervene model decisions is important for the adoption of computer-aided diagnosis methods in clinical workflows. Recent concept-based methods link the model predictions with interpretable concepts and modify their activation scores to interact with the model. However, these concepts are at the image level, which hinders the model from pinpointing the exact patches the concepts are activated. Alternatively, prototype-based methods learn representations from training image patches and compare these with test image patches, using the similarity scores for final class prediction. However, interpreting the underlying concepts of these patches can be challenging and often necessitates post-hoc guesswork. To address this issue, this paper introduces the novel Concept-based Similarity Reasoning network (CSR), which offers (i) patch-level prototype with intrinsic concept interpretation, and (ii) spatial interactivity. First, the proposed CSR provides localized explanation by grounding prototypes of each concept on image regions. Second, our model introduces novel spatial-level interaction, allowing doctors to engage directly with specific image areas, making it an intuitive and transparent tool for medical imaging. CSR improves upon prior state-of-the-art interpretable methods by up to 4.5\% across three biomedical datasets. Our code is released at https://github.com/tadeephuy/InteractCSR.

Medical Visual Language Models have shown great potential in various healthcare applications, including medical image captioning and diagnostic assistance. However, most existing models rely on text-based instructions, limiting their usability in real-world clinical environments especially in scenarios such as surgery, text-based interaction is often impractical for physicians. In addition, current medical image analysis models typically lack comprehensive reasoning behind their predictions, which reduces their reliability for clinical decision-making. Given that medical diagnosis errors can have life-changing consequences, there is a critical need for interpretable and rational medical assistance. To address these challenges, we introduce an end-to-end speech-driven medical VLM, SilVar-Med, a multimodal medical image assistant that integrates speech interaction with VLMs, pioneering the task of voice-based communication for medical image analysis. In addition, we focus on the interpretation of the reasoning behind each prediction of medical abnormalities with a proposed reasoning dataset. Through extensive experiments, we demonstrate a proof-of-concept study for reasoning-driven medical image interpretation with end-to-end speech interaction. We believe this work will advance the field of medical AI by fostering more transparent, interactive, and clinically viable diagnostic support systems. Our code and dataset are publicly available at SiVar-Med.

Purpose: General consensus amongst researchers and industry points to a lack of large, representative annotated datasets as the biggest obstacle to progress in the field of surgical data science. Self-supervised learning represents a solution to part of this problem, removing the reliance on annotations. However, the robustness of current self-supervised learning methods to domain shifts remains unclear, limiting our understanding of its utility for leveraging diverse sources of surgical data. Methods: In this work, we employ self-supervised learning to flexibly leverage diverse surgical datasets, thereby learning taskagnostic representations that can be used for various surgical downstream tasks. Based on this approach, to elucidate the impact of pre-training on downstream task performance, we explore 22 different pre-training dataset combinations by modulating three variables: source hospital, type of surgical procedure, and pre-training scale (number of videos). We then finetune the resulting model initializations on three diverse downstream tasks: namely, phase recognition and critical view of safety in laparoscopic cholecystectomy and phase recognition in laparoscopic hysterectomy. Results: Controlled experimentation highlights sizable boosts in performance across various tasks, datasets, and labeling budgets. However, this performance is intricately linked to the composition of the pre-training dataset, robustly proven through several study stages. Conclusion: The composition of pre-training datasets can severely affect the effectiveness of SSL methods for various downstream tasks and should critically inform future data collection efforts to scale the application of SSL methodologies. Keywords: Self-Supervised Learning, Transfer Learning, Surgical Computer Vision, Endoscopic Videos, Critical View of Safety, Phase Recognition

The field of surgical computer vision has undergone considerable breakthroughs in recent years with the rising popularity of deep neural network-based methods. However, standard fully-supervised approaches for training such models require vast amounts of annotated data, imposing a prohibitively high cost; especially in the clinical domain. Self-Supervised Learning (SSL) methods, which have begun to gain traction in the general computer vision community, represent a potential solution to these annotation costs, allowing to learn useful representations from only unlabeled data. Still, the effectiveness of SSL methods in more complex and impactful domains, such as medicine and surgery, remains limited and unexplored. In this work, we address this critical need by investigating four state-of-the-art SSL methods (MoCo v2, SimCLR, DINO, SwAV) in the context of surgical computer vision. We present an extensive analysis of the performance of these methods on the Cholec80 dataset for two fundamental and popular tasks in surgical context understanding, phase recognition and tool presence detection. We examine their parameterization, then their behavior with respect to training data quantities in semi-supervised settings. Correct transfer of these methods to surgery, as described and conducted in this work, leads to substantial performance gains over generic uses of SSL - up to 7.4% on phase recognition and 20% on tool presence detection - as well as state-of-the-art semi-supervised phase recognition approaches by up to 14%. Further results obtained on a highly diverse selection of surgical datasets exhibit strong generalization properties. The code is available at https://github.com/CAMMA-public/SelfSupSurg.

Over the past decade, computer vision applications in minimally invasive surgery have rapidly increased. Despite this growth, the impact of surgical computer vision remains limited compared to other medical fields like pathology and radiology, primarily due to the scarcity of representative annotated data. Whereas transfer learning from large annotated datasets such as ImageNet has been conventionally the norm to achieve high-performing models, recent advancements in self-supervised learning (SSL) have demonstrated superior performance. In medical image analysis, in-domain SSL pretraining has already been shown to outperform ImageNet-based initialization. Although unlabeled data in the field of surgical computer vision is abundant, the diversity within this data is limited. This study investigates the role of dataset diversity in SSL for surgical computer vision, comparing procedure-specific datasets against a more heterogeneous general surgical dataset across three different downstream surgical applications. The obtained results show that using solely procedure-specific data can lead to substantial improvements of 13.8%, 9.5%, and 36.8% compared to ImageNet pretraining. However, extending this data with more heterogeneous surgical data further increases performance by an additional 5.0%, 5.2%, and 2.5%, suggesting that increasing diversity within SSL data is beneficial for model performance. The code and pretrained model weights are made publicly available at https://github.com/TimJaspers0801/SurgeNet.

In this work, we take aim towards increasing the effectiveness of surgical assistant robots. We intended to make assistant robots safer by making them aware about the actions of surgeon, so it can take appropriate assisting actions. In other words, we aim to solve the problem of surgeon action detection in endoscopic videos. To this, we introduce a challenging dataset for surgeon action detection in real-world endoscopic videos. Action classes are picked based on the feedback of surgeons and annotated by medical professional. Given a video frame, we draw bounding box around surgical tool which is performing action and label it with action label. Finally, we presenta frame-level action detection baseline model based on recent advances in ob-ject detection. Results on our new dataset show that our presented dataset provides enough interesting challenges for future method and it can serveas strong benchmark corresponding research in surgeon action detection in endoscopic videos.

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data-features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

Automated surgical instrument localization is an important technology to understand the surgical process and in order to analyze them to provide meaningful guidance during surgery or surgical index after surgery to the surgeon. We introduce a new dataset that reflects the kinematic characteristics of surgical instruments for automated surgical instrument localization of surgical videos. The hSDB(hutom Surgery DataBase)-instrument dataset consists of instrument localization information from 24 cases of laparoscopic cholecystecomy and 24 cases of robotic gastrectomy. Localization information for all instruments is provided in the form of a bounding box for object detection. To handle class imbalance problem between instruments, synthesized instruments modeled in Unity for 3D models are included as training data. Besides, for 3D instrument data, a polygon annotation is provided to enable instance segmentation of the tool. To reflect the kinematic characteristics of all instruments, they are annotated with head and body parts for laparoscopic instruments, and with head, wrist, and body parts for robotic instruments separately. Annotation data of assistive tools (specimen bag, needle, etc.) that are frequently used for surgery are also included. Moreover, we provide statistical information on the hSDB-instrument dataset and the baseline localization performances of the object detection networks trained by the MMDetection library and resulting analyses.

Visual Language Models (VLMs) have demonstrated impressive capabilities in visual grounding tasks. However, their effectiveness in the medical domain, particularly for abnormality detection and localization within medical images, remains underexplored. A major challenge is the complex and abstract nature of medical terminology, which makes it difficult to directly associate pathological anomaly terms with their corresponding visual features. In this work, we introduce a novel approach to enhance VLM performance in medical abnormality detection and localization by leveraging decomposed medical knowledge. Instead of directly prompting models to recognize specific abnormalities, we focus on breaking down medical concepts into fundamental attributes and common visual patterns. This strategy promotes a stronger alignment between textual descriptions and visual features, improving both the recognition and localization of abnormalities in medical images.We evaluate our method on the 0.23B Florence-2 base model and demonstrate that it achieves comparable performance in abnormality grounding to significantly larger 7B LLaVA-based medical VLMs, despite being trained on only 1.5% of the data used for such models. Experimental results also demonstrate the effectiveness of our approach in both known and previously unseen abnormalities, suggesting its strong generalization capabilities.

Medical vision-and-language pre-training (Med-VLP) has received considerable attention owing to its applicability to extracting generic vision-and-language representations from medical images and texts. Most existing methods mainly contain three elements: uni-modal encoders (i.e., a vision encoder and a language encoder), a multi-modal fusion module, and pretext tasks, with few studies considering the importance of medical domain expert knowledge and explicitly exploiting such knowledge to facilitate Med-VLP. Although there exist knowledge-enhanced vision-and-language pre-training (VLP) methods in the general domain, most require off-the-shelf toolkits (e.g., object detectors and scene graph parsers), which are unavailable in the medical domain. In this paper, we propose a systematic and effective approach to enhance Med-VLP by structured medical knowledge from three perspectives. First, considering knowledge can be regarded as the intermediate medium between vision and language, we align the representations of the vision encoder and the language encoder through knowledge. Second, we inject knowledge into the multi-modal fusion model to enable the model to perform reasoning using knowledge as the supplementation of the input image and text. Third, we guide the model to put emphasis on the most critical information in images and texts by designing knowledge-induced pretext tasks. To perform a comprehensive evaluation and facilitate further research, we construct a medical vision-and-language benchmark including three tasks. Experimental results illustrate the effectiveness of our approach, where state-of-the-art performance is achieved on all downstream tasks. Further analyses explore the effects of different components of our approach and various settings of pre-training.

Multi-organ medical segmentation is a crucial component of medical image processing, essential for doctors to make accurate diagnoses and develop effective treatment plans. Despite significant progress in this field, current multi-organ segmentation models often suffer from inaccurate details, dependence on geometric prompts and loss of spatial information. Addressing these challenges, we introduce a novel model named CRISP-SAM2 with CRoss-modal Interaction and Semantic Prompting based on SAM2. This model represents a promising approach to multi-organ medical segmentation guided by textual descriptions of organs. Our method begins by converting visual and textual inputs into cross-modal contextualized semantics using a progressive cross-attention interaction mechanism. These semantics are then injected into the image encoder to enhance the detailed understanding of visual information. To eliminate reliance on geometric prompts, we use a semantic prompting strategy, replacing the original prompt encoder to sharpen the perception of challenging targets. In addition, a similarity-sorting self-updating strategy for memory and a mask-refining process is applied to further adapt to medical imaging and enhance localized details. Comparative experiments conducted on seven public datasets indicate that CRISP-SAM2 outperforms existing models. Extensive analysis also demonstrates the effectiveness of our method, thereby confirming its superior performance, especially in addressing the limitations mentioned earlier. Our code is available at: https://github.com/YU-deep/CRISP\_SAM2.git.

Dynamic reconstruction of deformable tissues in endoscopic video is a key technology for robot-assisted surgery. Recent reconstruction methods based on neural radiance fields (NeRFs) have achieved remarkable results in the reconstruction of surgical scenes. However, based on implicit representation, NeRFs struggle to capture the intricate details of objects in the scene and cannot achieve real-time rendering. In addition, restricted single view perception and occluded instruments also propose special challenges in surgical scene reconstruction. To address these issues, we develop SurgicalGaussian, a deformable 3D Gaussian Splatting method to model dynamic surgical scenes. Our approach models the spatio-temporal features of soft tissues at each time stamp via a forward-mapping deformation MLP and regularization to constrain local 3D Gaussians to comply with consistent movement. With the depth initialization strategy and tool mask-guided training, our method can remove surgical instruments and reconstruct high-fidelity surgical scenes. Through experiments on various surgical videos, our network outperforms existing method on many aspects, including rendering quality, rendering speed and GPU usage. The project page can be found at https://surgicalgaussian.github.io.

Purpose: Foundation models, trained on multitudes of public datasets, often require additional fine-tuning or re-prompting mechanisms to be applied to visually distinct target domains such as surgical videos. Further, without domain knowledge, they cannot model the specific semantics of the target domain. Hence, when applied to surgical video segmentation, they fail to generalise to sections where previously tracked objects leave the scene or new objects enter. Methods: We propose SASVi, a novel re-prompting mechanism based on a frame-wise Mask R-CNN Overseer model, which is trained on a minimal amount of scarcely available annotations for the target domain. This model automatically re-prompts the foundation model SAM2 when the scene constellation changes, allowing for temporally smooth and complete segmentation of full surgical videos. Results: Re-prompting based on our Overseer model significantly improves the temporal consistency of surgical video segmentation compared to similar prompting techniques and especially frame-wise segmentation, which neglects temporal information, by at least 1.5%. Our proposed approach allows us to successfully deploy SAM2 to surgical videos, which we quantitatively and qualitatively demonstrate for three different cholecystectomy and cataract surgery datasets. Conclusion: SASVi can serve as a new baseline for smooth and temporally consistent segmentation of surgical videos with scarcely available annotation data. Our method allows us to leverage scarce annotations and obtain complete annotations for full videos of the large-scale counterpart datasets. We make those annotations publicly available, providing extensive annotation data for the future development of surgical data science models.

The fine-grained localization of clinicians in the operating room (OR) is a key component to design the new generation of OR support systems. Computer vision models for person pixel-based segmentation and body-keypoints detection are needed to better understand the clinical activities and the spatial layout of the OR. This is challenging, not only because OR images are very different from traditional vision datasets, but also because data and annotations are hard to collect and generate in the OR due to privacy concerns. To address these concerns, we first study how joint person pose estimation and instance segmentation can be performed on low resolutions images with downsampling factors from 1x to 12x. Second, to address the domain shift and the lack of annotations, we propose a novel unsupervised domain adaptation method, called AdaptOR, to adapt a model from an in-the-wild labeled source domain to a statistically different unlabeled target domain. We propose to exploit explicit geometric constraints on the different augmentations of the unlabeled target domain image to generate accurate pseudo labels and use these pseudo labels to train the model on high- and low-resolution OR images in a self-training framework. Furthermore, we propose disentangled feature normalization to handle the statistically different source and target domain data. Extensive experimental results with detailed ablation studies on the two OR datasets MVOR+ and TUM-OR-test show the effectiveness of our approach against strongly constructed baselines, especially on the low-resolution privacy-preserving OR images. Finally, we show the generality of our method as a semi-supervised learning (SSL) method on the large-scale COCO dataset, where we achieve comparable results with as few as 1% of labeled supervision against a model trained with 100% labeled supervision.

Person detection and pose estimation is a key requirement to develop intelligent context-aware assistance systems. To foster the development of human pose estimation methods and their applications in the Operating Room (OR), we release the Multi-View Operating Room (MVOR) dataset, the first public dataset recorded during real clinical interventions. It consists of 732 synchronized multi-view frames recorded by three RGB-D cameras in a hybrid OR. It also includes the visual challenges present in such environments, such as occlusions and clutter. We provide camera calibration parameters, color and depth frames, human bounding boxes, and 2D/3D pose annotations. In this paper, we present the dataset, its annotations, as well as baseline results from several recent person detection and 2D/3D pose estimation methods. Since we need to blur some parts of the images to hide identity and nudity in the released dataset, we also present a comparative study of how the baselines have been impacted by the blurring. Results show a large margin for improvement and suggest that the MVOR dataset can be useful to compare the performance of the different methods.

Trustworthiness is essential for the precise and interpretable application of artificial intelligence (AI) in medical imaging. Traditionally, precision and interpretability have been addressed as separate tasks, namely medical image analysis and explainable AI, each developing its own models independently. In this study, for the first time, we investigate the development of a unified medical vision-language pre-training model that can achieve both accurate analysis and interpretable understanding of medical images across various modalities. To build the model, we construct MedConcept-23M, a large-scale dataset comprising 23 million medical image-text pairs extracted from 6.2 million scientific articles, enriched with concepts from the Unified Medical Language System (UMLS). Based on MedConcept-23M, we introduce ConceptCLIP, a medical AI model utilizing concept-enhanced contrastive language-image pre-training. The pre-training of ConceptCLIP involves two primary components: image-text alignment learning (IT-Align) and patch-concept alignment learning (PC-Align). This dual alignment strategy enhances the model's capability to associate specific image regions with relevant concepts, thereby improving both the precision of analysis and the interpretability of the AI system. We conducted extensive experiments on 5 diverse types of medical image analysis tasks, spanning 51 subtasks across 10 image modalities, with the broadest range of downstream tasks. The results demonstrate the effectiveness of the proposed vision-language pre-training model. Further explainability analysis across 6 modalities reveals that ConceptCLIP achieves superior performance, underscoring its robust ability to advance explainable AI in medical imaging. These findings highlight ConceptCLIP's capability in promoting trustworthy AI in the field of medicine.

Colonoscopy is currently one of the most sensitive screening methods for colorectal cancer. This study investigates the frontiers of intelligent colonoscopy techniques and their prospective implications for multimodal medical applications. With this goal, we begin by assessing the current data-centric and model-centric landscapes through four tasks for colonoscopic scene perception, including classification, detection, segmentation, and vision-language understanding. This assessment enables us to identify domain-specific challenges and reveals that multimodal research in colonoscopy remains open for further exploration. To embrace the coming multimodal era, we establish three foundational initiatives: a large-scale multimodal instruction tuning dataset ColonINST, a colonoscopy-designed multimodal language model ColonGPT, and a multimodal benchmark. To facilitate ongoing monitoring of this rapidly evolving field, we provide a public website for the latest updates: https://github.com/ai4colonoscopy/IntelliScope.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

Humans can develop internal world models that encode common sense knowledge, telling them how the world works and predicting the consequences of their actions. This concept has emerged as a promising direction for establishing general-purpose machine-learning models in recent preliminary works, e.g., for visual representation learning. In this paper, we present CheXWorld, the first effort towards a self-supervised world model for radiographic images. Specifically, our work develops a unified framework that simultaneously models three aspects of medical knowledge essential for qualified radiologists, including 1) local anatomical structures describing the fine-grained characteristics of local tissues (e.g., architectures, shapes, and textures); 2) global anatomical layouts describing the global organization of the human body (e.g., layouts of organs and skeletons); and 3) domain variations that encourage CheXWorld to model the transitions across different appearance domains of radiographs (e.g., varying clarity, contrast, and exposure caused by collecting radiographs from different hospitals, devices, or patients). Empirically, we design tailored qualitative and quantitative analyses, revealing that CheXWorld successfully captures these three dimensions of medical knowledge. Furthermore, transfer learning experiments across eight medical image classification and segmentation benchmarks showcase that CheXWorld significantly outperforms existing SSL methods and large-scale medical foundation models. Code & pre-trained models are available at https://github.com/LeapLabTHU/CheXWorld.

Purpose: Surgical video is an important data stream for gesture recognition. Thus, robust visual encoders for those data-streams is similarly important. Methods: Leveraging the Bridge-Prompt framework, we fine-tune a pre-trained vision-text model (CLIP) for gesture recognition in surgical videos. This can utilize extensive outside video data such as text, but also make use of label meta-data and weakly supervised contrastive losses. Results: Our experiments show that prompt-based video encoder outperforms standard encoders in surgical gesture recognition tasks. Notably, it displays strong performance in zero-shot scenarios, where gestures/tasks that were not provided during the encoder training phase are included in the prediction phase. Additionally, we measure the benefit of inclusion text descriptions in the feature extractor training schema. Conclusion: Bridge-Prompt and similar pre-trained+fine-tuned video encoder models present significant visual representation for surgical robotics, especially in gesture recognition tasks. Given the diverse range of surgical tasks (gestures), the ability of these models to zero-shot transfer without the need for any task (gesture) specific retraining makes them invaluable.

3D scene understanding is a long-standing challenge in computer vision and a key component in enabling mixed reality, wearable computing, and embodied AI. Providing a solution to these applications requires a multifaceted approach that covers scene-centric, object-centric, as well as interaction-centric capabilities. While there exist numerous datasets approaching the former two problems, the task of understanding interactable and articulated objects is underrepresented and only partly covered by current works. In this work, we address this shortcoming and introduce (1) an expertly curated dataset in the Universal Scene Description (USD) format, featuring high-quality manual annotations, for instance, segmentation and articulation on 280 indoor scenes; (2) a learning-based model together with a novel baseline capable of predicting part segmentation along with a full specification of motion attributes, including motion type, articulated and interactable parts, and motion parameters; (3) a benchmark serving to compare upcoming methods for the task at hand. Overall, our dataset provides 8 types of annotations - object and part segmentations, motion types, movable and interactable parts, motion parameters, connectivity, and object mass annotations. With its broad and high-quality annotations, the data provides the basis for holistic 3D scene understanding models. All data is provided in the USD format, allowing interoperability and easy integration with downstream tasks. We provide open access to our dataset, benchmark, and method's source code.

Conventional medical image segmentation methods have been found inadequate in facilitating physicians with the identification of specific lesions for diagnosis and treatment. Given the utility of text as an instructional format, we introduce a novel task termed Medical Image Referring Segmentation (MIRS), which requires segmenting specified lesions in images based on the given language expressions. Due to the varying object scales in medical images, MIRS demands robust vision-language modeling and comprehensive multi-scale interaction for precise localization and segmentation under linguistic guidance. However, existing medical image segmentation methods fall short in meeting these demands, resulting in insufficient segmentation accuracy. In response, we propose an approach named Language-guided Scale-aware MedSegmentor (LSMS), incorporating two appealing designs: (1)~a Scale-aware Vision-Language Attention module that leverages diverse convolutional kernels to acquire rich visual knowledge and interact closely with linguistic features, thereby enhancing lesion localization capability; (2)~a Full-Scale Decoder that globally models multi-modal features across various scales, capturing complementary information between scales to accurately outline lesion boundaries. Addressing the lack of suitable datasets for MIRS, we constructed a vision-language medical dataset called Reference Hepatic Lesion Segmentation (RefHL-Seg). This dataset comprises 2,283 abdominal CT slices from 231 cases, with corresponding textual annotations and segmentation masks for various liver lesions in images. We validated the performance of LSMS for MIRS and conventional medical image segmentation tasks across various datasets. Our LSMS consistently outperforms on all datasets with lower computational costs. The code and datasets will be released.

The high cure rate of cancer is inextricably linked to physicians' accuracy in diagnosis and treatment, therefore a model that can accomplish high-precision tumor segmentation has become a necessity in many applications of the medical industry. It can effectively lower the rate of misdiagnosis while considerably lessening the burden on clinicians. However, fully automated target organ segmentation is problematic due to the irregular stereo structure of 3D volume organs. As a basic model for this class of real applications, U-Net excels. It can learn certain global and local features, but still lacks the capacity to grasp spatial long-range relationships and contextual information at multiple scales. This paper proposes a tumor segmentation model MPU-Net for patient volume CT images, which is inspired by Transformer with a global attention mechanism. By combining image serialization with the Position Attention Module, the model attempts to comprehend deeper contextual dependencies and accomplish precise positioning. Each layer of the decoder is also equipped with a multi-scale module and a cross-attention mechanism. The capability of feature extraction and integration at different levels has been enhanced, and the hybrid loss function developed in this study can better exploit high-resolution characteristic information. Moreover, the suggested architecture is tested and evaluated on the Liver Tumor Segmentation Challenge 2017 (LiTS 2017) dataset. Compared with the benchmark model U-Net, MPU-Net shows excellent segmentation results. The dice, accuracy, precision, specificity, IOU, and MCC metrics for the best model segmentation results are 92.17%, 99.08%, 91.91%, 99.52%, 85.91%, and 91.74%, respectively. Outstanding indicators in various aspects illustrate the exceptional performance of this framework in automatic medical image segmentation.

Visual scene understanding is the core task in making any crucial decision in any computer vision system. Although popular computer vision datasets like Cityscapes, MS-COCO, PASCAL provide good benchmarks for several tasks (e.g. image classification, segmentation, object detection), these datasets are hardly suitable for post disaster damage assessments. On the other hand, existing natural disaster datasets include mainly satellite imagery which have low spatial resolution and a high revisit period. Therefore, they do not have a scope to provide quick and efficient damage assessment tasks. Unmanned Aerial Vehicle(UAV) can effortlessly access difficult places during any disaster and collect high resolution imagery that is required for aforementioned tasks of computer vision. To address these issues we present a high resolution UAV imagery, FloodNet, captured after the hurricane Harvey. This dataset demonstrates the post flooded damages of the affected areas. The images are labeled pixel-wise for semantic segmentation task and questions are produced for the task of visual question answering. FloodNet poses several challenges including detection of flooded roads and buildings and distinguishing between natural water and flooded water. With the advancement of deep learning algorithms, we can analyze the impact of any disaster which can make a precise understanding of the affected areas. In this paper, we compare and contrast the performances of baseline methods for image classification, semantic segmentation, and visual question answering on our dataset.

Automatic radiology report generation is booming due to its huge application potential for the healthcare industry. However, existing computer vision and natural language processing approaches to tackle this problem are limited in two aspects. First, when extracting image features, most of them neglect multi-view reasoning in vision and model single-view structure of medical images, such as space-view or channel-view. However, clinicians rely on multi-view imaging information for comprehensive judgment in daily clinical diagnosis. Second, when generating reports, they overlook context reasoning with multi-modal information and focus on pure textual optimization utilizing retrieval-based methods. We aim to address these two issues by proposing a model that better simulates clinicians' perspectives and generates more accurate reports. Given the above limitation in feature extraction, we propose a Globally-intensive Attention (GIA) module in the medical image encoder to simulate and integrate multi-view vision perception. GIA aims to learn three types of vision perception: depth view, space view, and pixel view. On the other hand, to address the above problem in report generation, we explore how to involve multi-modal signals to generate precisely matched reports, i.e., how to integrate previously predicted words with region-aware visual content in next word prediction. Specifically, we design a Visual Knowledge-guided Decoder (VKGD), which can adaptively consider how much the model needs to rely on visual information and previously predicted text to assist next word prediction. Hence, our final Intensive Vision-guided Network (IVGN) framework includes a GIA-guided Visual Encoder and the VKGD. Experiments on two commonly-used datasets IU X-Ray and MIMIC-CXR demonstrate the superior ability of our method compared with other state-of-the-art approaches.

Identifying, tracking, and predicting wound heal-stage progression is a fundamental task towards proper diagnosis, effective treatment, facilitating healing, and reducing pain. Traditionally, a medical expert might observe a wound to determine the current healing state and recommend treatment. However, sourcing experts who can produce such a diagnosis solely from visual indicators can be difficult, time-consuming and expensive. In addition, lesions may take several weeks to undergo the healing process, demanding resources to monitor and diagnose continually. Automating this task can be challenging; datasets that follow wound progression from onset to maturation are small, rare, and often collected without computer vision in mind. To tackle these challenges, we introduce a self-supervised learning scheme composed of (a) learning embeddings of wound's temporal dynamics, (b) clustering for automatic stage discovery, and (c) fine-tuned classification. The proposed self-supervised and flexible learning framework is biologically inspired and trained on a small dataset with zero human labeling. The HealNet framework achieved high pre-text and downstream classification accuracy; when evaluated on held-out test data, HealNet achieved 97.7% pre-text accuracy and 90.62% heal-stage classification accuracy.

In the realm of robot-assisted minimally invasive surgery, dynamic scene reconstruction can significantly enhance downstream tasks and improve surgical outcomes. Neural Radiance Fields (NeRF)-based methods have recently risen to prominence for their exceptional ability to reconstruct scenes but are hampered by slow inference speed, prolonged training, and inconsistent depth estimation. Some previous work utilizes ground truth depth for optimization but is hard to acquire in the surgical domain. To overcome these obstacles, we present Endo-4DGS, a real-time endoscopic dynamic reconstruction approach that utilizes 3D Gaussian Splatting (GS) for 3D representation. Specifically, we propose lightweight MLPs to capture temporal dynamics with Gaussian deformation fields. To obtain a satisfactory Gaussian Initialization, we exploit a powerful depth estimation foundation model, Depth-Anything, to generate pseudo-depth maps as a geometry prior. We additionally propose confidence-guided learning to tackle the ill-pose problems in monocular depth estimation and enhance the depth-guided reconstruction with surface normal constraints and depth regularization. Our approach has been validated on two surgical datasets, where it can effectively render in real-time, compute efficiently, and reconstruct with remarkable accuracy.

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.

The surgical usage of Mixed Reality (MR) has received growing attention in areas such as surgical navigation systems, skill assessment, and robot-assisted surgeries. For such applications, pose estimation for hand and surgical instruments from an egocentric perspective is a fundamental task and has been studied extensively in the computer vision field in recent years. However, the development of this field has been impeded by a lack of datasets, especially in the surgical field, where bloody gloves and reflective metallic tools make it hard to obtain 3D pose annotations for hands and objects using conventional methods. To address this issue, we propose POV-Surgery, a large-scale, synthetic, egocentric dataset focusing on pose estimation for hands with different surgical gloves and three orthopedic surgical instruments, namely scalpel, friem, and diskplacer. Our dataset consists of 53 sequences and 88,329 frames, featuring high-resolution RGB-D video streams with activity annotations, accurate 3D and 2D annotations for hand-object pose, and 2D hand-object segmentation masks. We fine-tune the current SOTA methods on POV-Surgery and further show the generalizability when applying to real-life cases with surgical gloves and tools by extensive evaluations. The code and the dataset are publicly available at batfacewayne.github.io/POV_Surgery_io/.

As deep learning models gain attraction in medical data, ensuring transparent and trustworthy decision-making is essential. In skin cancer diagnosis, while advancements in lesion detection and classification have improved accuracy, the black-box nature of these methods poses challenges in understanding their decision processes, leading to trust issues among physicians. This study leverages the CLIP (Contrastive Language-Image Pretraining) model, trained on different skin lesion datasets, to capture meaningful relationships between visual features and diagnostic criteria terms. To further enhance transparency, we propose a method called MedGrad E-CLIP, which builds on gradient-based E-CLIP by incorporating a weighted entropy mechanism designed for complex medical imaging like skin lesions. This approach highlights critical image regions linked to specific diagnostic descriptions. The developed integrated pipeline not only classifies skin lesions by matching corresponding descriptions but also adds an essential layer of explainability developed especially for medical data. By visually explaining how different features in an image relates to diagnostic criteria, this approach demonstrates the potential of advanced vision-language models in medical image analysis, ultimately improving transparency, robustness, and trust in AI-driven diagnostic systems.

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 37 open-access, mostly categorical fundus imaging datasets from various sources, with up to 97 different target conditions and 284,660 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a large margin more generalist, larger-scale image-language models, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.

Predicting in-hospital mortality for intensive care unit (ICU) patients is key to final clinical outcomes. AI has shown advantaged accuracy but suffers from the lack of explainability. To address this issue, this paper proposes an eXplainable Multimodal Mortality Predictor (X-MMP) approaching an efficient, explainable AI solution for predicting in-hospital mortality via multimodal ICU data. We employ multimodal learning in our framework, which can receive heterogeneous inputs from clinical data and make decisions. Furthermore, we introduce an explainable method, namely Layer-Wise Propagation to Transformer, as a proper extension of the LRP method to Transformers, producing explanations over multimodal inputs and revealing the salient features attributed to prediction. Moreover, the contribution of each modality to clinical outcomes can be visualized, assisting clinicians in understanding the reasoning behind decision-making. We construct a multimodal dataset based on MIMIC-III and MIMIC-III Waveform Database Matched Subset. Comprehensive experiments on benchmark datasets demonstrate that our proposed framework can achieve reasonable interpretation with competitive prediction accuracy. In particular, our framework can be easily transferred to other clinical tasks, which facilitates the discovery of crucial factors in healthcare research.

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

Following the impressive development of LLMs, vision-language alignment in LLMs is actively being researched to enable multimodal reasoning and visual IO. This direction of research is particularly relevant to medical imaging because medical image analysis and generation consist of reasoning based on a combination of visual features and prior knowledge. Many recent works have focused on training adapter networks that serve as an information bridge between image processing networks and LLMs; but presumably, in order to achieve maximum reasoning potential of LLMs on visual information as well, visual and language features should be allowed to interact more freely. This is especially important in the medical domain because understanding and generating medical images such as chest X-rays (CXR) require not only accurate visual and language-based reasoning but also a more intimate mapping between the two modalities. Thus, taking inspiration from previous work on the transformer and VQ-GAN combination for bidirectional image and text generation, we build upon this approach and develop a method for instruction-tuning an LLM pre-trained only on text to gain vision-language capabilities for medical images. Specifically, we leverage a pretrained LLM's existing question-answering and instruction-following abilities to teach it to understand visual inputs by instructing it to answer questions about image inputs and, symmetrically, output both text and image responses appropriate to a given query by tuning the LLM with diverse tasks that encompass image-based text-generation and text-based image-generation. We show that our model, LLM-CXR, trained in this approach shows better image-text alignment in both CXR understanding and generation tasks while being smaller in size compared to previously developed models that perform a narrower range of tasks. The code is at https://github.com/hyn2028/llm-cxr.

Surgical tool detection is a fundamental task for understanding egocentric open surgery videos. However, detecting surgical tools presents significant challenges due to their highly imbalanced class distribution, similar shapes and similar textures, and heavy occlusion. The lack of a comprehensive large-scale dataset compounds these challenges. In this paper, we introduce EgoSurgery-Tool, an extension of the existing EgoSurgery-Phase dataset, which contains real open surgery videos captured using an egocentric camera attached to the surgeon's head, along with phase annotations. EgoSurgery-Tool has been densely annotated with surgical tools and comprises over 49K surgical tool bounding boxes across 15 categories, constituting a large-scale surgical tool detection dataset. EgoSurgery-Tool also provides annotations for hand detection with over 46K hand-bounding boxes, capturing hand-object interactions that are crucial for understanding activities in egocentric open surgery. EgoSurgery-Tool is superior to existing datasets due to its larger scale, greater variety of surgical tools, more annotations, and denser scenes. We conduct a comprehensive analysis of EgoSurgery-Tool using nine popular object detectors to assess their effectiveness in both surgical tool and hand detection. The dataset will be released at https://github.com/Fujiry0/EgoSurgery.

The rapid increase in the number of Computed Tomography (CT) scan examinations has created an urgent need for automated tools, such as organ segmentation, anomaly classification, and report generation, to assist radiologists with their growing workload. Multi-label classification of Three-Dimensional (3D) CT scans is a challenging task due to the volumetric nature of the data and the variety of anomalies to be detected. Existing deep learning methods based on Convolutional Neural Networks (CNNs) struggle to capture long-range dependencies effectively, while Vision Transformers require extensive pre-training, posing challenges for practical use. Additionally, these existing methods do not explicitly model the radiologist's navigational behavior while scrolling through CT scan slices, which requires both global context understanding and local detail awareness. In this study, we present CT-Scroll, a novel global-local attention model specifically designed to emulate the scrolling behavior of radiologists during the analysis of 3D CT scans. Our approach is evaluated on two public datasets, demonstrating its efficacy through comprehensive experiments and an ablation study that highlights the contribution of each model component.

The Segment Anything Model 2 (SAM 2) is the latest generation foundation model for image and video segmentation. Trained on the expansive Segment Anything Video (SA-V) dataset, which comprises 35.5 million masks across 50.9K videos, SAM 2 advances its predecessor's capabilities by supporting zero-shot segmentation through various prompts (e.g., points, boxes, and masks). Its robust zero-shot performance and efficient memory usage make SAM 2 particularly appealing for surgical tool segmentation in videos, especially given the scarcity of labeled data and the diversity of surgical procedures. In this study, we evaluate the zero-shot video segmentation performance of the SAM 2 model across different types of surgeries, including endoscopy and microscopy. We also assess its performance on videos featuring single and multiple tools of varying lengths to demonstrate SAM 2's applicability and effectiveness in the surgical domain. We found that: 1) SAM 2 demonstrates a strong capability for segmenting various surgical videos; 2) When new tools enter the scene, additional prompts are necessary to maintain segmentation accuracy; and 3) Specific challenges inherent to surgical videos can impact the robustness of SAM 2.

We investigate fine-tuning Vision-Language Models (VLMs) for multi-task medical image understanding, focusing on detection, localization, and counting of findings in medical images. Our objective is to evaluate whether instruction-tuned VLMs can simultaneously improve these tasks, with the goal of enhancing diagnostic accuracy and efficiency. Using MedMultiPoints, a multimodal dataset with annotations from endoscopy (polyps and instruments) and microscopy (sperm cells), we reformulate each task into instruction-based prompts suitable for vision-language reasoning. We fine-tune Qwen2.5-VL-7B-Instruct using Low-Rank Adaptation (LoRA) across multiple task combinations. Results show that multi-task training improves robustness and accuracy. For example, it reduces the Count Mean Absolute Error (MAE) and increases Matching Accuracy in the Counting + Pointing task. However, trade-offs emerge, such as more zero-case point predictions, indicating reduced reliability in edge cases despite overall performance gains. Our study highlights the potential of adapting general-purpose VLMs to specialized medical tasks via prompt-driven fine-tuning. This approach mirrors clinical workflows, where radiologists simultaneously localize, count, and describe findings - demonstrating how VLMs can learn composite diagnostic reasoning patterns. The model produces interpretable, structured outputs, offering a promising step toward explainable and versatile medical AI. Code, model weights, and scripts will be released for reproducibility at https://github.com/simula/PointDetectCount.

Computer-assisted surgery has been developed to enhance surgery correctness and safety. However, researchers and engineers suffer from limited annotated data to develop and train better algorithms. Consequently, the development of fundamental algorithms such as Simultaneous Localization and Mapping (SLAM) is limited. This article elaborates on the efforts of preparing the dataset for semantic segmentation, which is the foundation of many computer-assisted surgery mechanisms. Based on the Cholec80 dataset [3], we extracted 8,080 laparoscopic cholecystectomy image frames from 17 video clips in Cholec80 and annotated the images. The dataset is named CholecSeg8K and its total size is 3GB. Each of these images is annotated at pixel-level for thirteen classes, which are commonly founded in laparoscopic cholecystectomy surgery. CholecSeg8k is released under the license CC BY- NC-SA 4.0.

Training Large Multimodality Models (LMMs) relies on descriptive image caption that connects image and language. Existing methods either distill the caption from the LMM models or construct the captions from the internet images or by human. We propose to leverage off-the-shelf visual specialists, which were trained from annotated images initially not for image captioning, for enhancing the image caption. Our approach, named DCE, explores object low-level and fine-grained attributes (e.g., depth, emotion and fine-grained categories) and object relations (e.g., relative location and human-object-interaction (HOI)), and combine the attributes into the descriptive caption. Experiments demonstrate that such visual specialists are able to improve the performance for visual understanding tasks as well as reasoning that benefits from more accurate visual understanding. We will release the source code and the pipeline so that other visual specialists are easily combined into the pipeline. The complete source code of DCE pipeline and datasets will be available at https://github.com/syp2ysy/DCE.

Medical image classification in radiology faces significant challenges, particularly in generalizing to unseen pathologies. In contrast, CLIP offers a promising solution by leveraging multimodal learning to improve zero-shot classification performance. However, in the medical domain, lesions can be small and might not be well represented in the embedding space. Therefore, in this paper, we explore the potential of visual prompt engineering to enhance the capabilities of Vision Language Models (VLMs) in radiology. Leveraging BiomedCLIP, trained on extensive biomedical image-text pairs, we investigate the impact of embedding visual markers directly within radiological images to guide the model's attention to critical regions. Our evaluation on the JSRT dataset, focusing on lung nodule malignancy classification, demonstrates that incorporating visual prompts x2013 such as arrows, circles, and contours x2013 significantly improves classification metrics including AUROC, AUPRC, F1 score, and accuracy. Moreover, the study provides attention maps, showcasing enhanced model interpretability and focus on clinically relevant areas. These findings underscore the efficacy of visual prompt engineering as a straightforward yet powerful approach to advance VLM performance in medical image analysis.

The previous advancements in pathology image understanding primarily involved developing models tailored to specific tasks. Recent studies has demonstrated that the large vision-language model can enhance the performance of various downstream tasks in medical image understanding. In this study, we developed a domain-specific large language-vision assistant (PA-LLaVA) for pathology image understanding. Specifically, (1) we first construct a human pathology image-text dataset by cleaning the public medical image-text data for domain-specific alignment; (2) Using the proposed image-text data, we first train a pathology language-image pretraining (PLIP) model as the specialized visual encoder for pathology image, and then we developed scale-invariant connector to avoid the information loss caused by image scaling; (3) We adopt two-stage learning to train PA-LLaVA, first stage for domain alignment, and second stage for end to end visual question \& answering (VQA) task. In experiments, we evaluate our PA-LLaVA on both supervised and zero-shot VQA datasets, our model achieved the best overall performance among multimodal models of similar scale. The ablation experiments also confirmed the effectiveness of our design. We posit that our PA-LLaVA model and the datasets presented in this work can promote research in field of computational pathology. All codes are available at: https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA}{https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA

Medical image segmentation allows quantifying target structure size and shape, aiding in disease diagnosis, prognosis, surgery planning, and comprehension.Building upon recent advancements in foundation Vision-Language Models (VLMs) from natural image-text pairs, several studies have proposed adapting them to Vision-Language Segmentation Models (VLSMs) that allow using language text as an additional input to segmentation models. Introducing auxiliary information via text with human-in-the-loop prompting during inference opens up unique opportunities, such as open vocabulary segmentation and potentially more robust segmentation models against out-of-distribution data. Although transfer learning from natural to medical images has been explored for image-only segmentation models, the joint representation of vision-language in segmentation problems remains underexplored. This study introduces the first systematic study on transferring VLSMs to 2D medical images, using carefully curated 11 datasets encompassing diverse modalities and insightful language prompts and experiments. Our findings demonstrate that although VLSMs show competitive performance compared to image-only models for segmentation after finetuning in limited medical image datasets, not all VLSMs utilize the additional information from language prompts, with image features playing a dominant role. While VLSMs exhibit enhanced performance in handling pooled datasets with diverse modalities and show potential robustness to domain shifts compared to conventional segmentation models, our results suggest that novel approaches are required to enable VLSMs to leverage the various auxiliary information available through language prompts. The code and datasets are available at https://github.com/naamiinepal/medvlsm.

In 2015 we began a sub-challenge at the EndoVis workshop at MICCAI in Munich using endoscope images of ex-vivo tissue with automatically generated annotations from robot forward kinematics and instrument CAD models. However, the limited background variation and simple motion rendered the dataset uninformative in learning about which techniques would be suitable for segmentation in real surgery. In 2017, at the same workshop in Quebec we introduced the robotic instrument segmentation dataset with 10 teams participating in the challenge to perform binary, articulating parts and type segmentation of da Vinci instruments. This challenge included realistic instrument motion and more complex porcine tissue as background and was widely addressed with modifications on U-Nets and other popular CNN architectures. In 2018 we added to the complexity by introducing a set of anatomical objects and medical devices to the segmented classes. To avoid over-complicating the challenge, we continued with porcine data which is dramatically simpler than human tissue due to the lack of fatty tissue occluding many organs.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Human perception of the world is shaped by a multitude of viewpoints and modalities. While many existing datasets focus on scene understanding from a certain perspective (e.g. egocentric or third-person views), our dataset offers a panoptic perspective (i.e. multiple viewpoints with multiple data modalities). Specifically, we encapsulate third-person panoramic and front views, as well as egocentric monocular/binocular views with rich modalities including video, multi-channel audio, directional binaural delay, location data and textual scene descriptions within each scene captured, presenting comprehensive observation of the world. Figure 1 offers a glimpse of all 28 scene categories of our 360+x dataset. To the best of our knowledge, this is the first database that covers multiple viewpoints with multiple data modalities to mimic how daily information is accessed in the real world. Through our benchmark analysis, we presented 5 different scene understanding tasks on the proposed 360+x dataset to evaluate the impact and benefit of each data modality and perspective in panoptic scene understanding. We hope this unique dataset could broaden the scope of comprehensive scene understanding and encourage the community to approach these problems from more diverse perspectives.

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

Large Multimodal Models (LMMs) have shown remarkable progress in the field of medical Visual Question Answering (Med-VQA), achieving high accuracy on existing benchmarks. However, their reliability under robust evaluation is questionable. This study reveals that state-of-the-art models, when subjected to simple probing evaluation, perform worse than random guessing on medical diagnosis questions. To address this critical evaluation problem, we introduce the Probing Evaluation for Medical Diagnosis (ProbMed) dataset to rigorously assess LMM performance in medical imaging through probing evaluation and procedural diagnosis. Particularly, probing evaluation features pairing original questions with negation questions with hallucinated attributes, while procedural diagnosis requires reasoning across various diagnostic dimensions for each image, including modality recognition, organ identification, clinical findings, abnormalities, and positional grounding. Our evaluation reveals that top-performing models like GPT-4V and Gemini Pro perform worse than random guessing on specialized diagnostic questions, indicating significant limitations in handling fine-grained medical inquiries. Besides, models like LLaVA-Med struggle even with more general questions, and results from CheXagent demonstrate the transferability of expertise across different modalities of the same organ, showing that specialized domain knowledge is still crucial for improving performance. This study underscores the urgent need for more robust evaluation to ensure the reliability of LMMs in critical fields like medical diagnosis, and current LMMs are still far from applicable to those fields.

The application of deep learning to nursing procedure activity understanding has the potential to greatly enhance the quality and safety of nurse-patient interactions. By utilizing the technique, we can facilitate training and education, improve quality control, and enable operational compliance monitoring. However, the development of automatic recognition systems in this field is currently hindered by the scarcity of appropriately labeled datasets. The existing video datasets pose several limitations: 1) these datasets are small-scale in size to support comprehensive investigations of nursing activity; 2) they primarily focus on single procedures, lacking expert-level annotations for various nursing procedures and action steps; and 3) they lack temporally localized annotations, which prevents the effective localization of targeted actions within longer video sequences. To mitigate these limitations, we propose NurViD, a large video dataset with expert-level annotation for nursing procedure activity understanding. NurViD consists of over 1.5k videos totaling 144 hours, making it approximately four times longer than the existing largest nursing activity datasets. Notably, it encompasses 51 distinct nursing procedures and 177 action steps, providing a much more comprehensive coverage compared to existing datasets that primarily focus on limited procedures. To evaluate the efficacy of current deep learning methods on nursing activity understanding, we establish three benchmarks on NurViD: procedure recognition on untrimmed videos, procedure and action recognition on trimmed videos, and action detection. Our benchmark and code will be available at https://github.com/minghu0830/NurViD-benchmark.

Accurate 3D scene reconstruction is essential for numerous medical tasks. Given the challenges in obtaining ground truth data, there has been an increasing focus on self-supervised learning (SSL) for endoscopic depth estimation as a basis for scene reconstruction. While foundation models have shown remarkable progress in visual tasks, their direct application to the medical domain often leads to suboptimal results. However, the visual features from these models can still enhance endoscopic tasks, emphasizing the need for efficient adaptation strategies, which still lack exploration currently. In this paper, we introduce Endo3DAC, a unified framework for endoscopic scene reconstruction that efficiently adapts foundation models. We design an integrated network capable of simultaneously estimating depth maps, relative poses, and camera intrinsic parameters. By freezing the backbone foundation model and training only the specially designed Gated Dynamic Vector-Based Low-Rank Adaptation (GDV-LoRA) with separate decoder heads, Endo3DAC achieves superior depth and pose estimation while maintaining training efficiency. Additionally, we propose a 3D scene reconstruction pipeline that optimizes depth maps' scales, shifts, and a few parameters based on our integrated network. Extensive experiments across four endoscopic datasets demonstrate that Endo3DAC significantly outperforms other state-of-the-art methods while requiring fewer trainable parameters. To our knowledge, we are the first to utilize a single network that only requires surgical videos to perform both SSL depth estimation and scene reconstruction tasks. The code will be released upon acceptance.

2D/3D human pose estimation is needed to develop novel intelligent tools for the operating room that can analyze and support the clinical activities. The lack of annotated data and the complexity of state-of-the-art pose estimation approaches limit, however, the deployment of such techniques inside the OR. In this work, we propose to use knowledge distillation in a teacher/student framework to harness the knowledge present in a large-scale non-annotated dataset and in an accurate but complex multi-stage teacher network to train a lightweight network for joint 2D/3D pose estimation. The teacher network also exploits the unlabeled data to generate both hard and soft labels useful in improving the student predictions. The easily deployable network trained using this effective self-supervision strategy performs on par with the teacher network on MVOR+, an extension of the public MVOR dataset where all persons have been fully annotated, thus providing a viable solution for real-time 2D/3D human pose estimation in the OR.

Scene understanding is an active research area. Commercial depth sensors, such as Kinect, have enabled the release of several RGB-D datasets over the past few years which spawned novel methods in 3D scene understanding. More recently with the launch of the LiDAR sensor in Apple's iPads and iPhones, high quality RGB-D data is accessible to millions of people on a device they commonly use. This opens a whole new era in scene understanding for the Computer Vision community as well as app developers. The fundamental research in scene understanding together with the advances in machine learning can now impact people's everyday experiences. However, transforming these scene understanding methods to real-world experiences requires additional innovation and development. In this paper we introduce ARKitScenes. It is not only the first RGB-D dataset that is captured with a now widely available depth sensor, but to our best knowledge, it also is the largest indoor scene understanding data released. In addition to the raw and processed data from the mobile device, ARKitScenes includes high resolution depth maps captured using a stationary laser scanner, as well as manually labeled 3D oriented bounding boxes for a large taxonomy of furniture. We further analyze the usefulness of the data for two downstream tasks: 3D object detection and color-guided depth upsampling. We demonstrate that our dataset can help push the boundaries of existing state-of-the-art methods and it introduces new challenges that better represent real-world scenarios.

Open-vocabulary scene understanding aims to localize and recognize unseen categories beyond the annotated label space. The recent breakthrough of 2D open-vocabulary perception is largely driven by Internet-scale paired image-text data with rich vocabulary concepts. However, this success cannot be directly transferred to 3D scenarios due to the inaccessibility of large-scale 3D-text pairs. To this end, we propose to distill knowledge encoded in pre-trained vision-language (VL) foundation models through captioning multi-view images from 3D, which allows explicitly associating 3D and semantic-rich captions. Further, to foster coarse-to-fine visual-semantic representation learning from captions, we design hierarchical 3D-caption pairs, leveraging geometric constraints between 3D scenes and multi-view images. Finally, by employing contrastive learning, the model learns language-aware embeddings that connect 3D and text for open-vocabulary tasks. Our method not only remarkably outperforms baseline methods by 25.8% sim 44.7% hIoU and 14.5% sim 50.4% hAP_{50} in open-vocabulary semantic and instance segmentation, but also shows robust transferability on challenging zero-shot domain transfer tasks. See the project website at https://dingry.github.io/projects/PLA.

Medical vision-and-language models (MVLMs) have attracted substantial interest due to their capability to offer a natural language interface for interpreting complex medical data. Their applications are versatile and have the potential to improve diagnostic accuracy and decision-making for individual patients while also contributing to enhanced public health monitoring, disease surveillance, and policy-making through more efficient analysis of large data sets. MVLMS integrate natural language processing with medical images to enable a more comprehensive and contextual understanding of medical images alongside their corresponding textual information. Unlike general vision-and-language models trained on diverse, non-specialized datasets, MVLMs are purpose-built for the medical domain, automatically extracting and interpreting critical information from medical images and textual reports to support clinical decision-making. Popular clinical applications of MVLMs include automated medical report generation, medical visual question answering, medical multimodal segmentation, diagnosis and prognosis and medical image-text retrieval. Here, we provide a comprehensive overview of MVLMs and the various medical tasks to which they have been applied. We conduct a detailed analysis of various vision-and-language model architectures, focusing on their distinct strategies for cross-modal integration/exploitation of medical visual and textual features. We also examine the datasets used for these tasks and compare the performance of different models based on standardized evaluation metrics. Furthermore, we highlight potential challenges and summarize future research trends and directions. The full collection of papers and codes is available at: https://github.com/YtongXie/Medical-Vision-and-Language-Tasks-and-Methodologies-A-Survey.

Comprehending 3D environments is vital for intelligent systems in domains like robotics and autonomous navigation. Voxel grids offer a structured representation of 3D space, but extracting high-level semantic meaning remains challenging. This paper proposes a novel approach utilizing a Vision-Language Model (VLM) to extract "voxel semantics"-object identity, color, and location-from voxel data. Critically, instead of employing complex 3D networks, our method processes the voxel space by systematically slicing it along a primary axis (e.g., the Z-axis, analogous to CT scan slices). These 2D slices are then formatted and sequentially fed into the image encoder of a standard VLM. The model learns to aggregate information across slices and correlate spatial patterns with semantic concepts provided by the language component. This slice-based strategy aims to leverage the power of pre-trained 2D VLMs for efficient 3D semantic understanding directly from voxel representations.

Effectively representing medical images, especially retinal images, presents a considerable challenge due to variations in appearance, size, and contextual information of pathological signs called lesions. Precise discrimination of these lesions is crucial for diagnosing vision-threatening issues such as diabetic retinopathy. While visual attention-based neural networks have been introduced to learn spatial context and channel correlations from retinal images, they often fall short in capturing localized lesion context. Addressing this limitation, we propose a novel attention mechanism called Guided Context Gating, an unique approach that integrates Context Formulation, Channel Correlation, and Guided Gating to learn global context, spatial correlations, and localized lesion context. Our qualitative evaluation against existing attention mechanisms emphasize the superiority of Guided Context Gating in terms of explainability. Notably, experiments on the Zenodo-DR-7 dataset reveal a substantial 2.63% accuracy boost over advanced attention mechanisms & an impressive 6.53% improvement over the state-of-the-art Vision Transformer for assessing the severity grade of retinopathy, even with imbalanced and limited training samples for each class.

Multimodal large language models (MLLMs) hold significant potential in the medical field, but their capabilities are often limited by insufficient data in certain medical domains, highlighting the need for understanding what kinds of images can be used by MLLMs for generalization. Current research suggests that multi-task training outperforms single-task as different tasks can benefit each other, but they often overlook the internal relationships within these tasks, providing limited guidance on selecting datasets to enhance specific tasks. To analyze this phenomenon, we attempted to employ compositional generalization (CG)-the ability of models to understand novel combinations by recombining learned elements-as a guiding framework. Since medical images can be precisely defined by Modality, Anatomical area, and Task, naturally providing an environment for exploring CG. Therefore, we assembled 106 medical datasets to create Med-MAT for comprehensive experiments. The experiments confirmed that MLLMs can use CG to understand unseen medical images and identified CG as one of the main drivers of the generalization observed in multi-task training. Additionally, further studies demonstrated that CG effectively supports datasets with limited data and delivers consistent performance across different backbones, highlighting its versatility and broad applicability. Med-MAT is publicly available at https://github.com/FreedomIntelligence/Med-MAT.

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.

Recent advances in vision language models (VLMs) have enabled broad progress in the general medical field. However, pathology still remains a more challenging subdomain, with current pathology specific VLMs exhibiting limitations in both diagnostic accuracy and reasoning plausibility. Such shortcomings are largely attributable to the nature of current pathology datasets, which are primarily composed of image description pairs that lack the depth and structured diagnostic paradigms employed by real world pathologists. In this study, we leverage pathology textbooks and real world pathology experts to construct high-quality, reasoning-oriented datasets. Building on this, we introduce Patho-R1, a multimodal RL-based pathology Reasoner, trained through a three-stage pipeline: (1) continued pretraining on 3.5 million image-text pairs for knowledge infusion; (2) supervised fine-tuning on 500k high-quality Chain-of-Thought samples for reasoning incentivizing; (3) reinforcement learning using Group Relative Policy Optimization and Decoupled Clip and Dynamic sAmpling Policy Optimization strategies for multimodal reasoning quality refinement. To further assess the alignment quality of our dataset, we propose PathoCLIP, trained on the same figure-caption corpus used for continued pretraining. Comprehensive experimental results demonstrate that both PathoCLIP and Patho-R1 achieve robust performance across a wide range of pathology-related tasks, including zero-shot classification, cross-modal retrieval, Visual Question Answering, and Multiple Choice Question. Our project is available at the Patho-R1 repository: https://github.com/Wenchuan-Zhang/Patho-R1.

Vision-language models (VLMs) have advanced reasoning in natural scenes, but their role in medical imaging remains underexplored. Medical reasoning tasks demand robust image analysis and well-justified answers, posing challenges due to the complexity of medical images. Transparency and trustworthiness are essential for clinical adoption and regulatory compliance. We introduce Med-R1, a framework exploring reinforcement learning (RL) to enhance VLMs' generalizability and trustworthiness in medical reasoning. Leveraging the DeepSeek strategy, we employ Group Relative Policy Optimization (GRPO) to guide reasoning paths via reward signals. Unlike supervised fine-tuning (SFT), which often overfits and lacks generalization, RL fosters robust and diverse reasoning. Med-R1 is evaluated across eight medical imaging modalities: CT, MRI, Ultrasound, Dermoscopy, Fundus Photography, Optical Coherence Tomography (OCT), Microscopy, and X-ray Imaging. Compared to its base model, Qwen2-VL-2B, Med-R1 achieves a 29.94% accuracy improvement and outperforms Qwen2-VL-72B, which has 36 times more parameters. Testing across five question types-modality recognition, anatomy identification, disease diagnosis, lesion grading, and biological attribute analysis Med-R1 demonstrates superior generalization, exceeding Qwen2-VL-2B by 32.06% and surpassing Qwen2-VL-72B in question-type generalization. These findings show that RL improves medical reasoning and enables parameter-efficient models to outperform significantly larger ones. With interpretable reasoning outputs, Med-R1 represents a promising step toward generalizable, trustworthy, and clinically viable medical VLMs.

Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of high clinical relevance because diagnostic decisions often depend on rating of objects rather than e.g. pixels. For this task, the cumbersome and iterative process of method configuration constitutes a major research bottleneck. Recently, nnU-Net has tackled this challenge for the task of image segmentation with great success. Following nnU-Net's agenda, in this work we systematize and automate the configuration process for medical object detection. The resulting self-configuring method, nnDetection, adapts itself without any manual intervention to arbitrary medical detection problems while achieving results en par with or superior to the state-of-the-art. We demonstrate the effectiveness of nnDetection on two public benchmarks, ADAM and LUNA16, and propose 11 further medical object detection tasks on public data sets for comprehensive method evaluation. Code is at https://github.com/MIC-DKFZ/nnDetection .

Increasing numbers of patients with disabilities or elderly people with mobility issues often suffer from a pressure ulcer. The affected areas need regular checks, but they have a difficulty in accessing a hospital. Some remote diagnosis systems are being used for them, but there are limitations in checking a patient's status regularly. In this paper, we present a remote medical assistant that can help pressure ulcer management with image processing techniques. The proposed system includes a mobile application with a deep learning model for wound segmentation and analysis. As there are not enough data to train the deep learning model, we make use of a pretrained model from a relevant domain and data augmentation that is appropriate for this task. First of all, an image preprocessing method using bilinear interpolation is used to resize images and normalize the images. Second, for data augmentation, we use rotation, reflection, and a watershed algorithm. Third, we use a pretrained deep learning model generated from skin wound images similar to pressure ulcer images. Finally, we added an attention module that can provide hints on the pressure ulcer image features. The resulting model provides an accuracy of 99.0%, an intersection over union (IoU) of 99.99%, and a dice similarity coefficient (DSC) of 93.4% for pressure ulcer segmentation, which is better than existing results.

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at https://github.com/sinAshish/Multi-Scale-Attention

Surgical video segmentation is a critical task in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, the Segment Anything Model 2 (SAM2) framework has shown superior advancements in image and video segmentation. However, SAM2 struggles with efficiency due to the high computational demands of processing high-resolution images and complex and long-range temporal dynamics in surgical videos. To address these challenges, we introduce Surgical SAM 2 (SurgSAM-2), an advanced model to utilize SAM2 with an Efficient Frame Pruning (EFP) mechanism, to facilitate real-time surgical video segmentation. The EFP mechanism dynamically manages the memory bank by selectively retaining only the most informative frames, reducing memory usage and computational cost while maintaining high segmentation accuracy. Our extensive experiments demonstrate that SurgSAM-2 significantly improves both efficiency and segmentation accuracy compared to the vanilla SAM2. Remarkably, SurgSAM-2 achieves a 3times FPS compared with SAM2, while also delivering state-of-the-art performance after fine-tuning with lower-resolution data. These advancements establish SurgSAM-2 as a leading model for surgical video analysis, making real-time surgical video segmentation in resource-constrained environments a feasible reality.

Vision-Language Models (VLMs) have demonstrated impressive capabilities in understanding visual content, but their reliability in safety-critical contexts remains under-explored. We introduce VERI (Visual Emergency Recognition Dataset), a carefully designed diagnostic benchmark of 200 images (100 contrastive pairs). Each emergency scene is matched with a visually similar but safe counterpart through multi-stage human verification and iterative refinement. Using a two-stage protocol - risk identification and emergency response - we evaluate 14 VLMs (2B-124B parameters) across medical emergencies, accidents, and natural disasters. Our analysis reveals a systematic overreaction problem: models excel at identifying real emergencies (70-100 percent success rate) but suffer from an alarming rate of false alarms, misidentifying 31-96 percent of safe situations as dangerous, with 10 scenarios failed by all models regardless of scale. This "better-safe-than-sorry" bias manifests primarily through contextual overinterpretation (88-93 percent of errors), challenging VLMs' reliability for safety applications. These findings highlight persistent limitations that are not resolved by increasing model scale, motivating targeted approaches for improving contextual safety assessment in visually misleading scenarios.

The integration of artificial intelligence in image-guided interventions holds transformative potential, promising to extract 3D geometric and quantitative information from conventional 2D imaging modalities during complex procedures. Achieving this requires the rapid and precise alignment of 2D intraoperative images (e.g., X-ray) with 3D preoperative volumes (e.g., CT, MRI). However, current 2D/3D registration methods fail across the broad spectrum of procedures dependent on X-ray guidance: traditional optimization techniques require custom parameter tuning for each subject, whereas neural networks trained on small datasets do not generalize to new patients or require labor-intensive manual annotations, increasing clinical burden and precluding application to new anatomical targets. To address these challenges, we present xvr, a fully automated framework for training patient-specific neural networks for 2D/3D registration. xvr uses physics-based simulation to generate abundant high-quality training data from a patient's own preoperative volumetric imaging, thereby overcoming the inherently limited ability of supervised models to generalize to new patients and procedures. Furthermore, xvr requires only 5 minutes of training per patient, making it suitable for emergency interventions as well as planned procedures. We perform the largest evaluation of a 2D/3D registration algorithm on real X-ray data to date and find that xvr robustly generalizes across a diverse dataset comprising multiple anatomical structures, imaging modalities, and hospitals. Across surgical tasks, xvr achieves submillimeter-accurate registration at intraoperative speeds, improving upon existing methods by an order of magnitude. xvr is released as open-source software freely available at https://github.com/eigenvivek/xvr.

In recent years, the potential applications of machine learning to Minimally Invasive Surgery (MIS) have spurred interest in data sets that can be used to develop data-driven tools. This paper introduces a novel dataset recorded during ex vivo pseudo-cholecystectomy procedures on pig livers, utilizing the da Vinci Research Kit (dVRK). Unlike current datasets, ours bridges a critical gap by offering not only full kinematic data but also capturing all pedal inputs used during the procedure and providing a time-stamped record of the endoscope's movements. Contributed by seven surgeons, this data set introduces a new dimension to surgical robotics research, allowing the creation of advanced models for automating console functionalities. Our work addresses the existing limitation of incomplete recordings and imprecise kinematic data, common in other datasets. By introducing two models, dedicated to predicting clutch usage and camera activation, we highlight the dataset's potential for advancing automation in surgical robotics. The comparison of methodologies and time windows provides insights into the models' boundaries and limitations.

Automated segmentation of brain tumors from 3D magnetic resonance images (MRIs) is necessary for the diagnosis, monitoring, and treatment planning of the disease. Manual delineation practices require anatomical knowledge, are expensive, time consuming and can be inaccurate due to human error. Here, we describe a semantic segmentation network for tumor subregion segmentation from 3D MRIs based on encoder-decoder architecture. Due to a limited training dataset size, a variational auto-encoder branch is added to reconstruct the input image itself in order to regularize the shared decoder and impose additional constraints on its layers. The current approach won 1st place in the BraTS 2018 challenge.

Pathological diagnosis remains the definitive standard for identifying tumors. The rise of multimodal large models has simplified the process of integrating image analysis with textual descriptions. Despite this advancement, the substantial costs associated with training and deploying these complex multimodal models, together with a scarcity of high-quality training datasets, create a significant divide between cutting-edge technology and its application in the clinical setting. We had meticulously compiled a dataset of approximately 45,000 cases, covering over 6 different tasks, including the classification of organ tissues, generating pathology report descriptions, and addressing pathology-related questions and answers. We have fine-tuned multimodal large models, specifically LLaVA, Qwen-VL, InternLM, with this dataset to enhance instruction-based performance. We conducted a qualitative assessment of the capabilities of the base model and the fine-tuned model in performing image captioning and classification tasks on the specific dataset. The evaluation results demonstrate that the fine-tuned model exhibits proficiency in addressing typical pathological questions. We hope that by making both our models and datasets publicly available, they can be valuable to the medical and research communities.

Several medical Multimodal Large Languange Models (MLLMs) have been developed to address tasks involving visual images with textual instructions across various medical modalities, achieving impressive results. Most current medical generalist models are region-agnostic, treating the entire image as a holistic representation. However, they struggle to identify which specific regions they are focusing on when generating a sentence. To mimic the behavior of doctors, who typically begin by reviewing the entire image before concentrating on specific regions for a thorough evaluation, we aim to enhance the capability of medical MLLMs in understanding anatomical regions within entire medical scans. To achieve it, we first formulate Region-Centric tasks and construct a large-scale dataset, MedRegInstruct, to incorporate regional information into training. Combining our collected dataset with other medical multimodal corpora for training, we propose a Region-Aware medical MLLM, MedRegA, which is the first bilingual generalist medical AI system to simultaneously handle image-level and region-level medical vision-language tasks across a broad range of modalities. Our MedRegA not only enables three region-centric tasks, but also achieves the best performance for visual question answering, report generation and medical image classification over 8 modalities, showcasing significant versatility. Experiments demonstrate that our model can not only accomplish powerful performance across various medical vision-language tasks in bilingual settings, but also recognize and detect structures in multimodal medical scans, boosting the interpretability and user interactivity of medical MLLMs. Our project page is https://medrega.github.io.

In this work, we develop an open-source surgical simulation environment that includes a realistic model obtained by MRI-scanning a physical phantom, for the purpose of training and evaluating a Learning from Demonstration (LfD) algorithm for autonomous suturing. The LfD algorithm utilizes Dynamic Movement Primitives (DMP) and Locally Weighted Regression (LWR), but focuses on the needle trajectory, rather than the instruments, to obtain better generality with respect to needle grasps. We conduct a user study to collect multiple suturing demonstrations and perform a comprehensive analysis of the ability of the LfD algorithm to generalize from a demonstration at one location in one phantom to different locations in the same phantom and to a different phantom. Our results indicate good generalization, on the order of 91.5%, when learning from more experienced subjects, indicating the need to integrate skill assessment in the future.

A comprehensive semantic understanding of a scene is important for many applications - but in what space should diverse semantic information (e.g., objects, scene categories, material types, texture, etc.) be grounded and what should be its structure? Aspiring to have one unified structure that hosts diverse types of semantics, we follow the Scene Graph paradigm in 3D, generating a 3D Scene Graph. Given a 3D mesh and registered panoramic images, we construct a graph that spans the entire building and includes semantics on objects (e.g., class, material, and other attributes), rooms (e.g., scene category, volume, etc.) and cameras (e.g., location, etc.), as well as the relationships among these entities. However, this process is prohibitively labor heavy if done manually. To alleviate this we devise a semi-automatic framework that employs existing detection methods and enhances them using two main constraints: I. framing of query images sampled on panoramas to maximize the performance of 2D detectors, and II. multi-view consistency enforcement across 2D detections that originate in different camera locations.

Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the accuracy and reliability of cancer diagnosis and treatment. There can be disease-related information that is too subtle for humans or existing technological tools to discern visually. Traditional methods typically focus on partial or unimodal information about biological systems at individual scales and fail to encapsulate the complete spectrum of the heterogeneous nature of data. Deep neural networks have facilitated the development of sophisticated multimodal data fusion approaches that can extract and integrate relevant information from multiple sources. Recent deep learning frameworks such as Graph Neural Networks (GNNs) and Transformers have shown remarkable success in multimodal learning. This review article provides an in-depth analysis of the state-of-the-art in GNNs and Transformers for multimodal data fusion in oncology settings, highlighting notable research studies and their findings. We also discuss the foundations of multimodal learning, inherent challenges, and opportunities for integrative learning in oncology. By examining the current state and potential future developments of multimodal data integration in oncology, we aim to demonstrate the promising role that multimodal neural networks can play in cancer prevention, early detection, and treatment through informed oncology practices in personalized settings.

Understanding functionalities in 3D scenes involves interpreting natural language descriptions to locate functional interactive objects, such as handles and buttons, in a 3D environment. Functionality understanding is highly challenging, as it requires both world knowledge to interpret language and spatial perception to identify fine-grained objects. For example, given a task like 'turn on the ceiling light', an embodied AI agent must infer that it needs to locate the light switch, even though the switch is not explicitly mentioned in the task description. To date, no dedicated methods have been developed for this problem. In this paper, we introduce Fun3DU, the first approach designed for functionality understanding in 3D scenes. Fun3DU uses a language model to parse the task description through Chain-of-Thought reasoning in order to identify the object of interest. The identified object is segmented across multiple views of the captured scene by using a vision and language model. The segmentation results from each view are lifted in 3D and aggregated into the point cloud using geometric information. Fun3DU is training-free, relying entirely on pre-trained models. We evaluate Fun3DU on SceneFun3D, the most recent and only dataset to benchmark this task, which comprises over 3000 task descriptions on 230 scenes. Our method significantly outperforms state-of-the-art open-vocabulary 3D segmentation approaches. Project page: https://jcorsetti.github.io/fun3du

Single-view depth estimation can be remarkably effective if there is enough ground-truth depth data for supervised training. However, there are scenarios, especially in medicine in the case of endoscopies, where such data cannot be obtained. In such cases, multi-view self-supervision and synthetic-to-real transfer serve as alternative approaches, however, with a considerable performance reduction in comparison to supervised case. Instead, we propose a single-view self-supervised method that achieves a performance similar to the supervised case. In some medical devices, such as endoscopes, the camera and light sources are co-located at a small distance from the target surfaces. Thus, we can exploit that, for any given albedo and surface orientation, pixel brightness is inversely proportional to the square of the distance to the surface, providing a strong single-view self-supervisory signal. In our experiments, our self-supervised models deliver accuracies comparable to those of fully supervised ones, while being applicable without depth ground-truth data.