arXiv subjects

Ron Kikinis

Publications and source records attributed to Ron Kikinis.

At least 19 recordsLinked to original sources

arXiv2026

Annotating anatomy and pathology in the National Lung Screening Trial computed tomography images

Large-scale public medical imaging datasets contribute critically to translational research. When accompanied by rich clinical and multi-omics data, they can stimulate exploratory research and enable secondary analyses. Expert annotations of such imaging collections can support the development of new image analysis tools. Continuous enrichment of images with image-derived data makes them more usable for researchers without expertise in image analysis or access to large-scale computational resources. The National Lung Screening Trial (NLST) released a rich longitudinal dataset that includes Computed Tomography (CT) images for over 26,000 patients. We introduce three Digital Imaging and Communications in Medicine (DICOM) formatted datasets, complementing NLST CT images, shared as analysis results in the National Cancer Institute Imaging Data Commons (IDC). Two of those (IDC NLSTSeg and IDC NLSTSybil) contain DICOM-harmonized annotations and extracted measurements (for 581 and 601 NLST patients, respectively) shared earlier using research formats (Sybil and NLSTseg). The third one (TotalSegmentator-CT-Segmentations) contains volumetric segmentations generated using TotalSegmentator and radiomics features for each segment for 26,194 NLST patients.

eess.IV↗

arXiv2026

Final Report, Center for Computer-Integrated Computer-Integrated Surgical Systems and Technology, NSF ERC Cooperative Agreement EEC9731748, Volume 1

In the last ten years, medical robotics has moved from the margins to the mainstream. Since the Engineering Research Center for Computer-Integrated Surgical Systems and Technology was Launched in 1998 with National Science Foundation funding, medical robots have been promoted from handling routine tasks to performing highly sophisticated interventions and related assignments. The CISST ERC has played a significant role in this transformation. And thanks to NSF support, the ERC has built the professional infrastructure that will continue our mission: bringing data and technology together in clinical systems that will dramatically change how surgery and other procedures are done. The enhancements we envision touch virtually every aspect of the delivery of care: - More accurate procedures - More consistent, predictable results from one patient to the next - Improved clinical outcomes - Greater patient safety - Reduced liability for healthcare providers - Lower costs for everyone - patients, facilities, insurers, government - Easier, faster recovery for patients - Effective new ways to treat health problems - Healthier patients, and a healthier system The basic science and engineering the ERC is developing now will yield profound benefits for all concerned about health care - from government agencies to insurers, from clinicians to patients to the general public. All will experience the healing touch of medical robotics, thanks in no small part to the work of the CISST ERC and its successors.

cs.RO↗

arXiv2026

MHub.ai: A Simple, Standardized, and Reproducible Platform for AI Models in Medical Imaging

Artificial intelligence (AI) has the potential to transform medical imaging by automating image analysis and accelerating clinical research. However, research and clinical use are limited by the wide variety of AI implementations and architectures, inconsistent documentation, and reproducibility issues. Here, we introduce MHub$.$ai, an open-source, container-based platform that standardizes access to AI models with minimal configuration, promoting accessibility and reproducibility in medical imaging. MHub$.$ai packages models from peer-reviewed publications into standardized containers that support direct processing of DICOM and other formats, provide a unified application interface, and embed structured metadata. Each model is accompanied by publicly available reference data that can be used to confirm model operation. MHub$.$ai includes an initial set of state-of-the-art segmentation, prediction, and feature extraction models for different modalities. The modular framework enables adaptation of any model and supports community contributions. We demonstrate the utility of the platform in a clinical use case through comparative evaluation of lung segmentation models. To further strengthen transparency and reproducibility, we publicly release the generated segmentations and evaluation metrics and provide interactive dashboards that allow readers to inspect individual cases and reproduce or extend our analysis. By simplifying model use, MHub$.$ai enables side-by-side benchmarking with identical execution commands and standardized outputs, and lowers the barrier to clinical translation.

cs.AI↗

arXiv2025

In search of truth: Evaluating concordance of AI-based anatomy segmentation models

Purpose AI-based methods for anatomy segmentation can help automate characterization of large imaging datasets. The growing number of similar in functionality models raises the challenge of evaluating them on datasets that do not contain ground truth annotations. We introduce a practical framework to assist in this task. Approach We harmonize the segmentation results into a standard, interoperable representation, which enables consistent, terminology-based labeling of the structures. We extend 3D Slicer to streamline loading and comparison of these harmonized segmentations, and demonstrate how standard representation simplifies review of the results using interactive summary plots and browser-based visualization using OHIF Viewer. To demonstrate the utility of the approach we apply it to evaluating segmentation of 31 anatomical structures (lungs, vertebrae, ribs, and heart) by six open-source models - TotalSegmentator 1.5 and 2.6, Auto3DSeg, MOOSE, MultiTalent, and CADS - for a sample of Computed Tomography (CT) scans from the publicly available National Lung Screening Trial (NLST) dataset. Results We demonstrate the utility of the framework in enabling automating loading, structure-wise inspection and comparison across models. Preliminary results ascertain practical utility of the approach in allowing quick detection and review of problematic results. The comparison shows excellent agreement segmenting some (e.g., lung) but not all structures (e.g., some models produce invalid vertebrae or rib segmentations). Conclusions The resources developed are linked from https://imagingdatacommons.github.io/segmentation-comparison/ including segmentation harmonization scripts, summary plots, and visualization tools. This work assists in model evaluation in absence of ground truth, ultimately enabling informed model selection.

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arXiv2025

SurgiATM: A Physics-Guided Plug-and-Play Model for Deep Learning-Based Smoke Removal in Laparoscopic Surgery

During laparoscopic surgery, smoke generated by tissue cauterization can significantly degrade the visual quality of endoscopic frames, increasing the risk of surgical errors and hindering both clinical decision-making and computer-assisted visual analysis. Consequently, removing surgical smoke is critical to ensuring patient safety and maintaining operative efficiency. In this study, we propose the Surgical Atmospheric Model (SurgiATM) for surgical smoke removal. SurgiATM statistically bridges a physics-based atmospheric model and data-driven deep learning models, combining the superior generalizability of the former with the high accuracy of the latter. Furthermore, SurgiATM is designed as a lightweight module that can be easily integrated into existing surgical desmoking architectures with minimal modification, aiming to enhance their accuracy and stability. The proposed method is derived via statistically optimizing a Mixture-of-Experts (MoE) model at the output end of arbitrary deep learning methods, with a Laplacian-like error distribution specifically leveraged to model surgical smoke. The output-stage MoE ensures minimal modification to the architecture of the original methods, while the Laplacian-like distribution characteristic of surgical smoke enables a lightweight reconstruction formulation with minimal parameters. Therefore, SurgiATM introduces only two hyperparameters and no additional trainable weights, preserving the original network architecture with minimal computational and modification overhead. We conduct extensive experiments on three public surgical datasets with ten desmoking methods, involving multiple network architectures and covering diverse procedures, including cholecystectomy, partial nephrectomy, and diaphragm dissection.

cs.CV↗

arXiv2025

CADS: A Comprehensive Anatomical Dataset and Segmentation for Whole-Body Anatomy in Computed Tomography

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.

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arXiv2025

Benchmarking of Deep Learning Methods for Generic MRI Multi-Organ Abdominal Segmentation

Recent advances in deep learning have led to robust automated tools for segmentation of abdominal computed tomography (CT). Meanwhile, segmentation of magnetic resonance imaging (MRI) is substantially more challenging due to the inherent signal variability and the increased effort required for annotating training datasets. Hence, existing approaches are trained on limited sets of MRI sequences, which might limit their generalizability. To characterize the landscape of MRI abdominal segmentation tools, we present here a comprehensive benchmarking of the three state-of-the-art and open-source models: MRSegmentator, MRISegmentator-Abdomen, and TotalSegmentator MRI. Since these models are trained using labor-intensive manual annotation cycles, we also introduce and evaluate ABDSynth, a SynthSeg-based model purely trained on widely available CT segmentations (no real images). More generally, we assess accuracy and generalizability by leveraging three public datasets (not seen by any of the evaluated methods during their training), which span all major manufacturers, five MRI sequences, as well as a variety of subject conditions, voxel resolutions, and fields-of-view. Our results reveal that MRSegmentator achieves the best performance and is most generalizable. In contrast, ABDSynth yields slightly less accurate results, but its relaxed requirements in training data make it an alternative when the annotation budget is limited. The evaluation code and datasets are given for future benchmarking at https://github.com/deepakri201/AbdoBench, along with inference code and weights for ABDSynth.

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arXiv2025

MultiCo3D: Multi-Label Voxel Contrast for One-Shot Incremental Segmentation of 3D Neuroimages

3D neuroimages provide a comprehensive view of brain structure and function, aiding in precise localization and functional connectivity analysis. Segmentation of white matter (WM) tracts using 3D neuroimages is vital for understanding the brain's structural connectivity in both healthy and diseased states. One-shot Class Incremental Semantic Segmentation (OCIS) refers to effectively segmenting new (novel) classes using only a single sample while retaining knowledge of old (base) classes without forgetting. Voxel-contrastive OCIS methods adjust the feature space to alleviate the feature overlap problem between the base and novel classes. However, since WM tract segmentation is a multi-label segmentation task, existing single-label voxel contrastive-based methods may cause inherent contradictions. To address this, we propose a new multi-label voxel contrast framework called MultiCo3D for one-shot class incremental tract segmentation. Our method utilizes uncertainty distillation to preserve base tract segmentation knowledge while adjusting the feature space with multi-label voxel contrast to alleviate feature overlap when learning novel tracts and dynamically weighting multi losses to balance overall loss. We compare our method against several state-of-the-art (SOTA) approaches. The experimental results show that our method significantly enhances one-shot class incremental tract segmentation accuracy across five different experimental setups on HCP and Preto datasets.

cs.CV↗

arXiv2025

Medical Image Registration Meets Vision Foundation Model: Prototype Learning and Contour Awareness

Medical image registration is a fundamental task in medical image analysis, aiming to establish spatial correspondences between paired images. However, existing unsupervised deformable registration methods rely solely on intensity-based similarity metrics, lacking explicit anatomical knowledge, which limits their accuracy and robustness. Vision foundation models, such as the Segment Anything Model (SAM), can generate high-quality segmentation masks that provide explicit anatomical structure knowledge, addressing the limitations of traditional methods that depend only on intensity similarity. Based on this, we propose a novel SAM-assisted registration framework incorporating prototype learning and contour awareness. The framework includes: (1) Explicit anatomical information injection, where SAM-generated segmentation masks are used as auxiliary inputs throughout training and testing to ensure the consistency of anatomical information; (2) Prototype learning, which leverages segmentation masks to extract prototype features and aligns prototypes to optimize semantic correspondences between images; and (3) Contour-aware loss, a contour-aware loss is designed that leverages the edges of segmentation masks to improve the model's performance in fine-grained deformation fields. Extensive experiments demonstrate that the proposed framework significantly outperforms existing methods across multiple datasets, particularly in challenging scenarios with complex anatomical structures and ambiguous boundaries. Our code is available at https://github.com/HaoXu0507/IPMI25-SAM-Assisted-Registration.

cs.CV↗

arXiv2025

Tab2Visual: Overcoming Limited Data in Tabular Data Classification Using Deep Learning with Visual Representations

This research addresses the challenge of limited data in tabular data classification, particularly prevalent in domains with constraints like healthcare. We propose Tab2Visual, a novel approach that transforms heterogeneous tabular data into visual representations, enabling the application of powerful deep learning models. Tab2Visual effectively addresses data scarcity by incorporating novel image augmentation techniques and facilitating transfer learning. We extensively evaluate the proposed approach on diverse tabular datasets, comparing its performance against a wide range of machine learning algorithms, including classical methods, tree-based ensembles, and state-of-the-art deep learning models specifically designed for tabular data. We also perform an in-depth analysis of factors influencing Tab2Visual's performance. Our experimental results demonstrate that Tab2Visual outperforms other methods in classification problems with limited tabular data.

cs.LG↗

arXiv2024

AMNCutter: Affinity-Attention-Guided Multi-View Normalized Cutter for Unsupervised Surgical Instrument Segmentation

Surgical instrument segmentation (SIS) is pivotal for robotic-assisted minimally invasive surgery, assisting surgeons by identifying surgical instruments in endoscopic video frames. Recent unsupervised surgical instrument segmentation (USIS) methods primarily rely on pseudo-labels derived from low-level features such as color and optical flow, but these methods show limited effectiveness and generalizability in complex and unseen endoscopic scenarios. In this work, we propose a label-free unsupervised model featuring a novel module named Multi-View Normalized Cutter (m-NCutter). Different from previous USIS works, our model is trained using a graph-cutting loss function that leverages patch affinities for supervision, eliminating the need for pseudo-labels. The framework adaptively determines which affinities from which levels should be prioritized. Therefore, the low- and high-level features and their affinities are effectively integrated to train a label-free unsupervised model, showing superior effectiveness and generalization ability. We conduct comprehensive experiments across multiple SIS datasets to validate our approach's state-of-the-art (SOTA) performance, robustness, and exceptional potential as a pre-trained model. Our code is released at https://github.com/MingyuShengSMY/AMNCutter.

cs.CV↗

arXiv2024

Revisiting Surgical Instrument Segmentation Without Human Intervention: A Graph Partitioning View

Surgical instrument segmentation (SIS) on endoscopic images stands as a long-standing and essential task in the context of computer-assisted interventions for boosting minimally invasive surgery. Given the recent surge of deep learning methodologies and their data-hungry nature, training a neural predictive model based on massive expert-curated annotations has been dominating and served as an off-the-shelf approach in the field, which could, however, impose prohibitive burden to clinicians for preparing fine-grained pixel-wise labels corresponding to the collected surgical video frames. In this work, we propose an unsupervised method by reframing the video frame segmentation as a graph partitioning problem and regarding image pixels as graph nodes, which is significantly different from the previous efforts. A self-supervised pre-trained model is firstly leveraged as a feature extractor to capture high-level semantic features. Then, Laplacian matrixs are computed from the features and are eigendecomposed for graph partitioning. On the "deep" eigenvectors, a surgical video frame is meaningfully segmented into different modules such as tools and tissues, providing distinguishable semantic information like locations, classes, and relations. The segmentation problem can then be naturally tackled by applying clustering or threshold on the eigenvectors. Extensive experiments are conducted on various datasets (e.g., EndoVis2017, EndoVis2018, UCL, etc.) for different clinical endpoints. Across all the challenging scenarios, our method demonstrates outstanding performance and robustness higher than unsupervised state-of-the-art (SOTA) methods. The code is released at https://github.com/MingyuShengSMY/GraphClusteringSIS.git.

cs.CV↗

arXiv2024

LNQ 2023 challenge: Benchmark of weakly-supervised techniques for mediastinal lymph node quantification

Accurate assessment of lymph node size in 3D CT scans is crucial for cancer staging, therapeutic management, and monitoring treatment response. Existing state-of-the-art segmentation frameworks in medical imaging often rely on fully annotated datasets. However, for lymph node segmentation, these datasets are typically small due to the extensive time and expertise required to annotate the numerous lymph nodes in 3D CT scans. Weakly-supervised learning, which leverages incomplete or noisy annotations, has recently gained interest in the medical imaging community as a potential solution. Despite the variety of weakly-supervised techniques proposed, most have been validated only on private datasets or small publicly available datasets. To address this limitation, the Mediastinal Lymph Node Quantification (LNQ) challenge was organized in conjunction with the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023). This challenge aimed to advance weakly-supervised segmentation methods by providing a new, partially annotated dataset and a robust evaluation framework. A total of 16 teams from 5 countries submitted predictions to the validation leaderboard, and 6 teams from 3 countries participated in the evaluation phase. The results highlighted both the potential and the current limitations of weakly-supervised approaches. On one hand, weakly-supervised approaches obtained relatively good performance with a median Dice score of $61.0\%$. On the other hand, top-ranked teams, with a median Dice score exceeding $70\%$, boosted their performance by leveraging smaller but fully annotated datasets to combine weak supervision and full supervision. This highlights both the promise of weakly-supervised methods and the ongoing need for high-quality, fully annotated data to achieve higher segmentation performance.

cs.CV↗

arXiv2024

Rule-based outlier detection of AI-generated anatomy segmentations

There is a dire need for medical imaging datasets with accompanying annotations to perform downstream patient analysis. However, it is difficult to manually generate these annotations, due to the time-consuming nature, and the variability in clinical conventions. Artificial intelligence has been adopted in the field as a potential method to annotate these large datasets, however, a lack of expert annotations or ground truth can inhibit the adoption of these annotations. We recently made a dataset publicly available including annotations and extracted features of up to 104 organs for the National Lung Screening Trial using the TotalSegmentator method. However, the released dataset does not include expert-derived annotations or an assessment of the accuracy of the segmentations, limiting its usefulness. We propose the development of heuristics to assess the quality of the segmentations, providing methods to measure the consistency of the annotations and a comparison of results to the literature. We make our code and related materials publicly available at https://github.com/ImagingDataCommons/CloudSegmentatorResults and interactive tools at https://huggingface.co/spaces/ImagingDataCommons/CloudSegmentatorResults.

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arXiv2024

Towards Automatic Abdominal MRI Organ Segmentation: Leveraging Synthesized Data Generated From CT Labels

Deep learning has shown great promise in the ability to automatically annotate organs in magnetic resonance imaging (MRI) scans, for example, of the brain. However, despite advancements in the field, the ability to accurately segment abdominal organs remains difficult across MR. In part, this may be explained by the much greater variability in image appearance and severely limited availability of training labels. The inherent nature of computed tomography (CT) scans makes it easier to annotate, resulting in a larger availability of expert annotations for the latter. We leverage a modality-agnostic domain randomization approach, utilizing CT label maps to generate synthetic images on-the-fly during training, further used to train a U-Net segmentation network for abdominal organs segmentation. Our approach shows comparable results compared to fully-supervised segmentation methods trained on MR data. Our method results in Dice scores of 0.90 (0.08) and 0.91 (0.08) for the right and left kidney respectively, compared to a pretrained nnU-Net model yielding 0.87 (0.20) and 0.91 (0.03). We will make our code publicly available.

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arXiv2023

Real-Time Dynamic Data Driven Deformable Registration for Image-Guided Neurosurgery: Computational Aspects

Current neurosurgical procedures utilize medical images of various modalities to enable the precise location of tumors and critical brain structures to plan accurate brain tumor resection. The difficulty of using preoperative images during the surgery is caused by the intra-operative deformation of the brain tissue (brain shift), which introduces discrepancies concerning the preoperative configuration. Intra-operative imaging allows tracking such deformations but cannot fully substitute for the quality of the pre-operative data. Dynamic Data Driven Deformable Non-Rigid Registration (D4NRR) is a complex and time-consuming image processing operation that allows the dynamic adjustment of the pre-operative image data to account for intra-operative brain shift during the surgery. This paper summarizes the computational aspects of a specific adaptive numerical approximation method and its variations for registering brain MRIs. It outlines its evolution over the last 15 years and identifies new directions for the computational aspects of the technique.

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arXiv2023

Advancing Intra-operative Precision: Dynamic Data-Driven Non-Rigid Registration for Enhanced Brain Tumor Resection in Image-Guided Neurosurgery

During neurosurgery, medical images of the brain are used to locate tumors and critical structures, but brain tissue shifts make pre-operative images unreliable for accurate removal of tumors. Intra-operative imaging can track these deformations but is not a substitute for pre-operative data. To address this, we use Dynamic Data-Driven Non-Rigid Registration (NRR), a complex and time-consuming image processing operation that adjusts the pre-operative image data to account for intra-operative brain shift. Our review explores a specific NRR method for registering brain MRI during image-guided neurosurgery and examines various strategies for improving the accuracy and speed of the NRR method. We demonstrate that our implementation enables NRR results to be delivered within clinical time constraints while leveraging Distributed Computing and Machine Learning to enhance registration accuracy by identifying optimal parameters for the NRR method. Additionally, we highlight challenges associated with its use in the operating room.

eess.IV↗

arXiv2023

Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods

The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body. Diffusion MRI tractography is the only method that enables the study of the anatomy and variability of the CST pathway in human health. In this work, we explored the performance of six widely used tractography methods for reconstructing the CST and its somatotopic organization. We perform experiments using diffusion MRI data from the Human Connectome Project. Four quantitative measurements including reconstruction rate, the WM-GM interface coverage, anatomical distribution of streamlines, and correlation with cortical volumes to assess the advantages and limitations of each method. Overall, we conclude that while current tractography methods have made progress toward the well-known challenge of improving the reconstruction of the lateral projections of the CST, the overall problem of performing a comprehensive CST reconstruction, including clinically important projections in the lateral (hand and face area) and medial portions (leg area), remains an important challenge for diffusion MRI tractography.

cs.CV↗