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Computer-aided diagnosis (CAD) for thyroid nodules has been studied for years, yet there are still reliability and interpretability challenges due to the lack of clinically-relevant evidence. To address this issue, inspired by Thyroid Imaging Reporting and Data System (TI-RADS), we propose a novel interpretable two-branch bi-coordinate network based on multi-grained domain knowledge. First, we transform the two types of domain knowledge provided by TI-RADS, namely region-based and boundary-based knowledge, into labels at multi-grained levels: coarse-grained classification labels, and fine-grained region segmentation masks and boundary localization vectors. We combine these two labels to form the Multi-grained Domain Knowledge Representation (MG-DKR) of TI-RADS. Then we design a Two-branch Bi-coordinate network (TB 2 C-net) which utilizes two branches to predict MG-DKR from both Cartesian and polar images, and uses an attention-based integration module to integrate the features of the two branches for benign-malignant classification. We validated our method on a large cohort containing 3245 patients (with 3558 nodules and 6466 ultrasound images). Results show that our method achieves competitive performance with AUC of 0.93 and ACC of 0.87 compared with other state-of-the-art methods. Ablation experiment results demonstrate the effectiveness of the TB 2 C-net and MG-DKR, and the knowledge attention map from the integration module provides the interpretability for benign-malignant classification., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The burgeoning field of brain health research increasingly leverages artificial intelligence (AI) to analyze and interpret neuroimaging data. Medical foundation models have shown promise of superior performance with better sample efficiency. This work introduces a novel approach towards creating 3-dimensional (3D) medical foundation models for multimodal neuroimage segmentation through self-supervised training. Our approach involves a novel two-stage pretraining approach using vision transformers. The first stage encodes anatomical structures in generally healthy brains from the large-scale unlabeled neuroimage dataset of multimodal brain magnetic resonance imaging (MRI) images from 41,400 participants. This stage of pertaining focuses on identifying key features such as shapes and sizes of different brain structures. The second pretraining stage identifies disease-specific attributes, such as geometric shapes of tumors and lesions and spatial placements within the brain. This dual-phase methodology significantly reduces the extensive data requirements usually necessary for AI model training in neuroimage segmentation with the flexibility to adapt to various imaging modalities. We rigorously evaluate our model, BrainSegFounder, using the Brain Tumor Segmentation (BraTS) challenge and Anatomical Tracings of Lesions After Stroke v2.0 (ATLAS v2.0) datasets. BrainSegFounder demonstrates a significant performance gain, surpassing the achievements of the previous winning solutions using fully supervised learning. Our findings underscore the impact of scaling up both the model complexity and the volume of unlabeled training data derived from generally healthy brains. Both of these factors enhance the accuracy and predictive capabilities of the model in neuroimage segmentation tasks. Our pretrained models and code are at https://github.com/lab-smile/BrainSegFounder., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Transformer-based models, capable of learning better global dependencies, have recently demonstrated exceptional representation learning capabilities in computer vision and medical image analysis. Transformer reformats the image into separate patches and realizes global communication via the self-attention mechanism. However, positional information between patches is hard to preserve in such 1D sequences, and loss of it can lead to sub-optimal performance when dealing with large amounts of heterogeneous tissues of various sizes in 3D medical image segmentation. Additionally, current methods are not robust and efficient for heavy-duty medical segmentation tasks such as predicting a large number of tissue classes or modeling globally inter-connected tissue structures. To address such challenges and inspired by the nested hierarchical structures in vision transformer, we proposed a novel 3D medical image segmentation method (UNesT), employing a simplified and faster-converging transformer encoder design that achieves local communication among spatially adjacent patch sequences by aggregating them hierarchically. We extensively validate our method on multiple challenging datasets, consisting of multiple modalities, anatomies, and a wide range of tissue classes, including 133 structures in the brain, 14 organs in the abdomen, 4 hierarchical components in the kidneys, inter-connected kidney tumors and brain tumors. We show that UNesT consistently achieves state-of-the-art performance and evaluate its generalizability and data efficiency. Particularly, the model achieves whole brain segmentation task complete ROI with 133 tissue classes in a single network, outperforming prior state-of-the-art method SLANT27 ensembled with 27 networks. Our model performance increases the mean DSC score of the publicly available Colin and CANDI dataset from 0.7264 to 0.7444 and from 0.6968 to 0.7025, respectively. Code, pre-trained models, and use case pipeline are available at: https://github.com/MASILab/UNesT., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Yucheng Tang reports financial support was provided by Vanderbilt University. Yucheng Tang reports a relationship with Vanderbilt University that includes: employment., (Copyright © 2023 Elsevier B.V. All rights reserved.)

An important challenge and limiting factor in deep learning methods for medical imaging segmentation is the lack of available of annotated data to properly train models. For the specific task of tumor segmentation, the process entails clinicians labeling every slice of volumetric scans for every patient, which becomes prohibitive at the scale of datasets required to train neural networks to optimal performance. To address this, we propose a novel semi-supervised framework that allows training any segmentation (encoder-decoder) model using only information readily available in radiological data, namely the presence of a tumor in the image, in addition to a few annotated images. Specifically, we conjecture that a generative model performing domain translation on this weak label - healthy vs diseased scans - helps achieve tumor segmentation. The proposed GenSeg method first disentangles tumoral tissue from healthy "background" tissue. The latent representation is separated into (1) the common background information across both domains, and (2) the unique tumoral information. GenSeg then achieves diseased-to-healthy image translation by decoding a healthy version of the image from just the common representation, as well as a residual image that allows adding back the tumors. The same decoder that produces this residual tumor image, also outputs a tumor segmentation. Implicit data augmentation is achieved by re-using the same framework for healthy-to-diseased image translation, where a residual tumor image is produced from a prior distribution. By performing both image translation and segmentation simultaneously, GenSeg allows training on only partially annotated datasets. To test the framework, we trained U-Net-like architectures using GenSeg and evaluated their performance on 3 variants of a synthetic task, as well as on 2 benchmark datasets: brain tumor segmentation in MRI (derived from BraTS) and liver metastasis segmentation in CT (derived from LiTS). Our method outperforms the baseline semi-supervised (autoencoder and mean teacher) and supervised segmentation methods, with improvements ranging between 8-14% Dice score on the brain task and 5-8% on the liver task, when only 1% of the training images were annotated. These results show the proposed framework is ideal at addressing the problem of training deep segmentation models when a large portion of the available data is unlabeled and unpaired, a common issue in tumor segmentation., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Eugene Vorontsov reports financial support was provided by NVIDIA Corp. Eugene Vorontsov, Pavlo Molchanov has patent pending to Nvidia., (Copyright © 2022 Elsevier B.V. All rights reserved.)

In the last decade, convolutional neural networks (ConvNets) have been a major focus of research in medical image analysis. However, the performances of ConvNets may be limited by a lack of explicit consideration of the long-range spatial relationships in an image. Recently, Vision Transformer architectures have been proposed to address the shortcomings of ConvNets and have produced state-of-the-art performances in many medical imaging applications. Transformers may be a strong candidate for image registration because their substantially larger receptive field enables a more precise comprehension of the spatial correspondence between moving and fixed images. Here, we present TransMorph, a hybrid Transformer-ConvNet model for volumetric medical image registration. This paper also presents diffeomorphic and Bayesian variants of TransMorph: the diffeomorphic variants ensure the topology-preserving deformations, and the Bayesian variant produces a well-calibrated registration uncertainty estimate. We extensively validated the proposed models using 3D medical images from three applications: inter-patient and atlas-to-patient brain MRI registration and phantom-to-CT registration. The proposed models are evaluated in comparison to a variety of existing registration methods and Transformer architectures. Qualitative and quantitative results demonstrate that the proposed Transformer-based model leads to a substantial performance improvement over the baseline methods, confirming the effectiveness of Transformers for medical image registration., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision support systems for diagnosis, surgery planning, and population-based analysis of spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms tackling the labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the results of this evaluation and further investigate the performance variation at the vertebra level, scan level, and different fields of view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top-performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The VerSe content and code can be accessed at: https://github.com/anjany/verse., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Purpose: To investigate the diagnostic performance of a deep convolutional neural network for differentiation of clear cell renal cell carcinoma (ccRCC) from renal oncocytoma., Methods: In this retrospective study, 74 patients (49 male, mean age 59.3) with 243 renal masses (203 ccRCC and 40 oncocytoma) that had undergone MR imaging 6 months prior to pathologic confirmation of the lesions were included. Segmentation using seed placement and bounding box selection was used to extract the lesion patches from T2-WI, and T1-WI pre-contrast, post-contrast arterial and venous phases. Then, a deep convolutional neural network (AlexNet) was fine-tuned to distinguish the ccRCC from oncocytoma. Five-fold cross validation was used to evaluate the AI algorithm performance. A subset of 80 lesions (40 ccRCC, 40 oncocytoma) were randomly selected to be classified by two radiologists and their performance was compared to the AI algorithm. Intra-class correlation coefficient was calculated using the Shrout-Fleiss method., Results: Overall accuracy of the AI system was 91% for differentiation of ccRCC from oncocytoma with an area under the curve of 0.9. For the observer study on 80 randomly selected lesions, there was moderate agreement between the two radiologists and AI algorithm. In the comparison sub-dataset, classification accuracies were 81%, 78%, and 70% for AI, radiologist 1, and radiologist 2, respectively., Conclusion: The developed AI system in this study showed high diagnostic performance in differentiation of ccRCC versus oncocytoma on multi-phasic MRIs., (Copyright © 2021. Published by Elsevier Inc.)

The recent outbreak of Coronavirus Disease 2019 (COVID-19) has led to urgent needs for reliable diagnosis and management of SARS-CoV-2 infection. The current guideline is using RT-PCR for testing. As a complimentary tool with diagnostic imaging, chest Computed Tomography (CT) has been shown to be able to reveal visual patterns characteristic for COVID-19, which has definite value at several stages during the disease course. To facilitate CT analysis, recent efforts have focused on computer-aided characterization and diagnosis with chest CT scan, which has shown promising results. However, domain shift of data across clinical data centers poses a serious challenge when deploying learning-based models. A common way to alleviate this issue is to fine-tune the model locally with the target domains local data and annotations. Unfortunately, the availability and quality of local annotations usually varies due to heterogeneity in equipment and distribution of medical resources across the globe. This impact may be pronounced in the detection of COVID-19, since the relevant patterns vary in size, shape, and texture. In this work, we attempt to find a solution for this challenge via federated and semi-supervised learning. A multi-national database consisting of 1704 scans from three countries is adopted to study the performance gap, when training a model with one dataset and applying it to another. Expert radiologists manually delineated 945 scans for COVID-19 findings. In handling the variability in both the data and annotations, a novel federated semi-supervised learning technique is proposed to fully utilize all available data (with or without annotations). Federated learning avoids the need for sensitive data-sharing, which makes it favorable for institutions and nations with strict regulatory policy on data privacy. Moreover, semi-supervision potentially reduces the annotation burden under a distributed setting. The proposed framework is shown to be effective compared to fully supervised scenarios with conventional data sharing instead of model weight sharing., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Although having achieved great success in medical image segmentation, deep learning-based approaches usually require large amounts of well-annotated data, which can be extremely expensive in the field of medical image analysis. Unlabeled data, on the other hand, is much easier to acquire. Semi-supervised learning and unsupervised domain adaptation both take the advantage of unlabeled data, and they are closely related to each other. In this paper, we propose uncertainty-aware multi-view co-training (UMCT), a unified framework that addresses these two tasks for volumetric medical image segmentation. Our framework is capable of efficiently utilizing unlabeled data for better performance. We firstly rotate and permute the 3D volumes into multiple views and train a 3D deep network on each view. We then apply co-training by enforcing multi-view consistency on unlabeled data, where an uncertainty estimation of each view is utilized to achieve accurate labeling. Experiments on the NIH pancreas segmentation dataset and a multi-organ segmentation dataset show state-of-the-art performance of the proposed framework on semi-supervised medical image segmentation. Under unsupervised domain adaptation settings, we validate the effectiveness of this work by adapting our multi-organ segmentation model to two pathological organs from the Medical Segmentation Decathlon Datasets. Additionally, we show that our UMCT-DA model can even effectively handle the challenging situation where labeled source data is inaccessible, demonstrating strong potentials for real-world applications., Competing Interests: Declaration of Competing Interest Patents relating to the content of this article are filed and but currently not in the public domain., (Copyright © 2020. Published by Elsevier B.V.)