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May 09, 2024
The paper introduces a novel autonomous robot ultrasound (US) system targeting liver follow-up scans for outpatients in local communities. Given a computed tomography (CT) image with specific target regions of interest, the proposed system carries out the autonomous follow-up scan in three steps: (i) initial robot contact to surface, (ii) coordinate mapping between CT image and robot, and (iii) target US scan. Utilizing 3D US-CT registration and deep learning-based segmentation networks, we can achieve precise imaging of 3D hepatic veins, facilitating accurate coordinate mapping between CT and the robot. This enables the automatic localization of follow-up targets within the CT image, allowing the robot to navigate precisely to the target's surface. Evaluation of the ultrasound phantom confirms the quality of the US-CT registration and shows the robot reliably locates the targets in repeated trials. The proposed framework holds the potential to significantly reduce time and costs for healthcare providers, clinicians, and follow-up patients, thereby addressing the increasing healthcare burden associated with chronic disease in local communities.
Prompt-driven Universal Model for View-Agnostic Echocardiography Analysis
Apr 09, 2024Echocardiography segmentation for cardiac analysis is time-consuming and resource-intensive due to the variability in image quality and the necessity to process scans from various standard views. While current automated segmentation methods in echocardiography show promising performance, they are trained on specific scan views to analyze corresponding data. However, this solution has a limitation as the number of required models increases with the number of standard views. To address this, in this paper, we present a prompt-driven universal method for view-agnostic echocardiography analysis. Considering the domain shift between standard views, we first introduce a method called prompt matching, aimed at learning prompts specific to different views by matching prompts and querying input embeddings using a pre-trained vision model. Then, we utilized a pre-trained medical language model to align textual information with pixel data for accurate segmentation. Extensive experiments on three standard views showed that our approach significantly outperforms the state-of-the-art universal methods and achieves comparable or even better performances over the segmentation model trained and tested on same views.
Cardiac Magnetic Resonance 2D+T Short- and Long-axis Segmentation via Spatio-temporal SAM Adaptation
Mar 15, 2024
Accurate 2D+T myocardium segmentation in cine cardiac magnetic resonance (CMR) scans is essential to analyze LV motion throughout the cardiac cycle comprehensively. The Segment Anything Model (SAM), known for its accurate segmentation and zero-shot generalization, has not yet been tailored for CMR 2D+T segmentation. We therefore introduce CMR2D+T-SAM, a novel approach to adapt SAM for CMR 2D+T segmentation using spatio-temporal adaption. This approach also incorporates a U-Net framework for multi-scale feature extraction, as well as text prompts for accurate segmentation on both short-axis (SAX) and long-axis (LAX) views using a single model. CMR2D+T-SAM outperforms existing deep learning methods on the STACOM2011 dataset, achieving a myocardium Dice score of 0.885 and a Hausdorff distance (HD) of 2.900 pixels. It also demonstrates superior zero-shot generalization on the ACDC dataset with a Dice score of 0.840 and a HD of 4.076 pixels.
MediViSTA-SAM: Zero-shot Medical Video Analysis with Spatio-temporal SAM Adaptation
Sep 24, 2023
In recent years, the Segmentation Anything Model (SAM) has attracted considerable attention as a foundational model well-known for its robust generalization capabilities across various downstream tasks. However, SAM does not exhibit satisfactory performance in the realm of medical image analysis. In this study, we introduce the first study on adapting SAM on video segmentation, called MediViSTA-SAM, a novel approach designed for medical video segmentation. Given video data, MediViSTA, spatio-temporal adapter captures long and short range temporal attention with cross-frame attention mechanism effectively constraining it to consider the immediately preceding video frame as a reference, while also considering spatial information effectively. Additionally, it incorporates multi-scale fusion by employing a U-shaped encoder and a modified mask decoder to handle objects of varying sizes. To evaluate our approach, extensive experiments were conducted using state-of-the-art (SOTA) methods, assessing its generalization abilities on multi-vendor in-house echocardiography datasets. The results highlight the accuracy and effectiveness of our network in medical video segmentation.
MA-SAM: Modality-agnostic SAM Adaptation for 3D Medical Image Segmentation
Sep 16, 2023
The Segment Anything Model (SAM), a foundation model for general image segmentation, has demonstrated impressive zero-shot performance across numerous natural image segmentation tasks. However, SAM's performance significantly declines when applied to medical images, primarily due to the substantial disparity between natural and medical image domains. To effectively adapt SAM to medical images, it is important to incorporate critical third-dimensional information, i.e., volumetric or temporal knowledge, during fine-tuning. Simultaneously, we aim to harness SAM's pre-trained weights within its original 2D backbone to the fullest extent. In this paper, we introduce a modality-agnostic SAM adaptation framework, named as MA-SAM, that is applicable to various volumetric and video medical data. Our method roots in the parameter-efficient fine-tuning strategy to update only a small portion of weight increments while preserving the majority of SAM's pre-trained weights. By injecting a series of 3D adapters into the transformer blocks of the image encoder, our method enables the pre-trained 2D backbone to extract third-dimensional information from input data. The effectiveness of our method has been comprehensively evaluated on four medical image segmentation tasks, by using 10 public datasets across CT, MRI, and surgical video data. Remarkably, without using any prompt, our method consistently outperforms various state-of-the-art 3D approaches, surpassing nnU-Net by 0.9%, 2.6%, and 9.9% in Dice for CT multi-organ segmentation, MRI prostate segmentation, and surgical scene segmentation respectively. Our model also demonstrates strong generalization, and excels in challenging tumor segmentation when prompts are used. Our code is available at: https://github.com/cchen-cc/MA-SAM.
Radiology-Llama2: Best-in-Class Large Language Model for Radiology
Aug 29, 2023
This paper introduces Radiology-Llama2, a large language model specialized for radiology through a process known as instruction tuning. Radiology-Llama2 is based on the Llama2 architecture and further trained on a large dataset of radiology reports to generate coherent and clinically useful impressions from radiological findings. Quantitative evaluations using ROUGE metrics on the MIMIC-CXR and OpenI datasets demonstrate that Radiology-Llama2 achieves state-of-the-art performance compared to other generative language models, with a Rouge-1 score of 0.4834 on MIMIC-CXR and 0.4185 on OpenI. Additional assessments by radiology experts highlight the model's strengths in understandability, coherence, relevance, conciseness, and clinical utility. The work illustrates the potential of localized language models designed and tuned for specialized domains like radiology. When properly evaluated and deployed, such models can transform fields like radiology by automating rote tasks and enhancing human expertise.
Radiology-GPT: A Large Language Model for Radiology
Jun 14, 2023
We introduce Radiology-GPT, a large language model for radiology. Using an instruction tuning approach on an extensive dataset of radiology domain knowledge, Radiology-GPT demonstrates superior performance compared to general language models such as StableLM, Dolly and LLaMA. It exhibits significant versatility in radiological diagnosis, research, and communication. This work serves as a catalyst for future developments in clinical NLP. The successful implementation of Radiology-GPT is indicative of the potential of localizing generative large language models, specifically tailored for distinctive medical specialties, while ensuring adherence to privacy standards such as HIPAA. The prospect of developing individualized, large-scale language models that cater to specific needs of various hospitals presents a promising direction. The fusion of conversational competence and domain-specific knowledge in these models is set to foster future development in healthcare AI. A demo of Radiology-GPT is available at https://huggingface.co/spaces/allen-eric/radiology-gpt.
Bayesian approaches for Quantifying Clinicians' Variability in Medical Image Quantification
Jul 06, 2022
Medical imaging, including MRI, CT, and Ultrasound, plays a vital role in clinical decisions. Accurate segmentation is essential to measure the structure of interest from the image. However, manual segmentation is highly operator-dependent, which leads to high inter and intra-variability of quantitative measurements. In this paper, we explore the feasibility that Bayesian predictive distribution parameterized by deep neural networks can capture the clinicians' inter-intra variability. By exploring and analyzing recently emerged approximate inference schemes, we evaluate whether approximate Bayesian deep learning with the posterior over segmentations can learn inter-intra rater variability both in segmentation and clinical measurements. The experiments are performed with two different imaging modalities: MRI and ultrasound. We empirically demonstrated that Bayesian predictive distribution parameterized by deep neural networks could approximate the clinicians' inter-intra variability. We show a new perspective in analyzing medical images quantitatively by providing clinical measurement uncertainty.