腹部器官分割是一项艰巨且耗时的任务。为了减轻临床专家的负担，非常需要完全自动化的方法。当前的方法由卷积神经网络（CNN）主导，但是计算要求和对大数据集的需求限制了其在实践中的应用。通过实施小而高效的自定义3D CNN，编译训练的模型并优化计算图：我们的方法可产生高精度分割（骰子相似性系数（％）：肝脏：97.3 $ \ pm 1.3，肾脏：94.8 $ \ pm $ 3.6，$ 3.6，，$ 3.6，，$ 3.6，，，$ 3.6，，，$ 3.6，，，$ 3.6，，$ \ pm $ 3.6，，肝气脾脏：96.4 $ \ pm $ 3.0，pancreas：80.9 $ \ pm $ 10.1），每张图像1.6秒。至关重要的是，我们能够仅在CPU上执行细分推断（无需GPU），从而在没有专家硬件的情况下便利地促进模型的简单和广泛部署。

尽管存在能够在许多医疗数据集上表现出很好的语义分割方法，但是通常，它们不设计用于直接用于临床实践。两个主要问题是通过不同的视觉外观的解开数据的概括，例如，使用不同的扫描仪获取的图像，以及计算时间和所需图形处理单元（GPU）存储器的效率。在这项工作中，我们使用基于SpatialConfiguration-Net（SCN）的多器官分段模型，该模型集成了标记器官中的空间配置的先验知识，以解决网络输出中的虚假响应。此外，我们修改了分割模型的体系结构，尽可能地减少其存储器占用空间，而不会急剧影响预测的质量。最后，我们实现了最小的推理脚本，我们优化了两者，执行时间和所需的GPU内存。

Segmentation of lung tissue in computed tomography (CT) images is a precursor to most pulmonary image analysis applications. Semantic segmentation methods using deep learning have exhibited top-tier performance in recent years. This paper presents a fully automatic method for identifying the lungs in three-dimensional (3D) pulmonary CT images, which we call it Lung-Net. We conjectured that a significant deeper network with inceptionV3 units can achieve a better feature representation of lung CT images without increasing the model complexity in terms of the number of trainable parameters. The method has three main advantages. First, a U-Net architecture with InceptionV3 blocks is developed to resolve the problem of performance degradation and parameter overload. Then, using information from consecutive slices, a new data structure is created to increase generalization potential, allowing more discriminating features to be extracted by making data representation as efficient as possible. Finally, the robustness of the proposed segmentation framework was quantitatively assessed using one public database to train and test the model (LUNA16) and two public databases (ISBI VESSEL12 challenge and CRPF dataset) only for testing the model; each database consists of 700, 23, and 40 CT images, respectively, that were acquired with a different scanner and protocol. Based on the experimental results, the proposed method achieved competitive results over the existing techniques with Dice coefficient of 99.7, 99.1, and 98.8 for LUNA16, VESSEL12, and CRPF datasets, respectively. For segmenting lung tissue in CT images, the proposed model is efficient in terms of time and parameters and outperforms other state-of-the-art methods. Additionally, this model is publicly accessible via a graphical user interface.

最近关于Covid-19的研究表明，CT成像提供了评估疾病进展和协助诊断的有用信息，以及帮助理解疾病。有越来越多的研究，建议使用深度学习来使用胸部CT扫描提供快速准确地定量Covid-19。兴趣的主要任务是胸部CT扫描的肺和肺病变的自动分割，确认或疑似Covid-19患者。在这项研究中，我们使用多中心数据集比较12个深度学习算法，包括开源和内部开发的算法。结果表明，合并不同的方法可以提高肺部分割，二元病变分割和多种子病变分割的总体测试集性能，从而分别为0.982,0.724和0.469的平均骰子分别。将得到的二元病变分段为91.3ml的平均绝对体积误差。通常，区分不同病变类型的任务更加困难，分别具有152mL的平均绝对体积差，分别为整合和磨碎玻璃不透明度为0.369和0.523的平均骰子分数。所有方法都以平均体积误差进行二元病变分割，该分段优于人类评估者的视觉评估，表明这些方法足以用于临床实践中使用的大规模评估。

大脑磁共振成像（MRI）扫描的自动分割和体积对于诊断帕金森氏病（PD）和帕金森氏症综合症（P-Plus）至关重要。为了提高诊断性能，我们在大脑分割中采用了深度学习（DL）模型，并将其性能与金标准的非DL方法进行了比较。我们收集了健康对照组（n = 105）和PD患者（n = 105），多个全身性萎缩（n = 132）和渐进性超核麻痹（n = 69）的大脑MRI扫描。 2020.使用金标准的非DL模型FreeSurfer（FS），我们对六个脑结构进行了分割：中脑，PON，CAUDATE，CAUDATE，PUTATATE，pALLIDUM和THIRD CNTRICLE，并将其视为DL模型的注释数据，代表性V -net和unet。计算了分化正常，PD和P-Plus病例的曲线下的骰子分数和面积。每位患者六个大脑结构的V-NET和UNETR的分割时间分别为3.48 +-0.17和48.14 +-0.97 s，比FS（15,735 +-1.07 s）快至少300倍。两种DL模型的骰子得分都足够高（> 0.85），它们的疾病分类AUC优于FS。为了分类正常与P-Plus和PD与多个全身性萎缩（小脑型）的分类，DL模型和FS显示出高于0.8的AUC。 DL显着减少了分析时间，而不会损害大脑分割和差异诊断的性能。我们的发现可能有助于在临床环境中采用DL脑MRI分割并提高大脑研究。

作为新一代神经体系结构的变形金刚在自然语言处理和计算机视觉方面表现出色。但是，现有的视觉变形金刚努力使用有限的医学数据学习，并且无法概括各种医学图像任务。为了应对这些挑战，我们将Medformer作为数据量表变压器呈现为可推广的医学图像分割。关键设计结合了理想的电感偏差，线性复杂性的层次建模以及以空间和语义全局方式以线性复杂性的关注以及多尺度特征融合。 Medformer可以在不预训练的情况下学习微小至大规模的数据。广泛的实验表明，Medformer作为一般分割主链的潜力，在三个具有多种模式（例如CT和MRI）和多样化的医学靶标（例如，健康器官，疾病，疾病组织和肿瘤）的三个公共数据集上优于CNN和视觉变压器。我们将模型和评估管道公开可用，为促进广泛的下游临床应用提供固体基线和无偏比较。

An increasing number of public datasets have shown a marked clinical impact on assessing anatomical structures. However, each of the datasets is small, partially labeled, and rarely investigates severe tumor subjects. Moreover, current models are limited to segmenting specific organs/tumors, which can not be extended to novel domains and classes. To tackle these limitations, we introduce embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models, dubbed the CLIP-Driven Universal Model. The Universal Model can better segment 25 organs and 6 types of tumors by exploiting the semantic relationship between abdominal structures. The model is developed from an assembly of 14 datasets with 3,410 CT scans and evaluated on 6,162 external CT scans from 3 datasets. We rank first on the public leaderboard of the Medical Segmentation Decathlon (MSD) and achieve the state-of-the-art results on Beyond The Cranial Vault (BTCV). Compared with dataset-specific models, the Universal Model is computationally more efficient (6x faster), generalizes better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks. The design of CLIP embedding enables the Universal Model to be easily extended to new classes without catastrophically forgetting the previously learned classes.

Quantitative cancer image analysis relies on the accurate delineation of tumours, a very specialised and time-consuming task. For this reason, methods for automated segmentation of tumours in medical imaging have been extensively developed in recent years, being Computed Tomography one of the most popular imaging modalities explored. However, the large amount of 3D voxels in a typical scan is prohibitive for the entire volume to be analysed at once in conventional hardware. To overcome this issue, the processes of downsampling and/or resampling are generally implemented when using traditional convolutional neural networks in medical imaging. In this paper, we propose a new methodology that introduces a process of sparsification of the input images and submanifold sparse convolutional networks as an alternative to downsampling. As a proof of concept, we applied this new methodology to Computed Tomography images of renal cancer patients, obtaining performances of segmentations of kidneys and tumours competitive with previous methods (~84.6% Dice similarity coefficient), while achieving a significant improvement in computation time (2-3 min per training epoch).

目的：要开发和验证计算机工具，用于在计算机断层扫描（CT）扫描上描绘的上述组织的自动和同时分割的计算机工具：内脏脂肪（VAT），皮下脂肪（SAT），骨骼脂肪（IMAT），骨骼肌（SM）和骨头。方法：使用了从癌症成像档案（TCIA）获得的100 CT扫描的队列 - 50个全身正电子发射断层扫描（PET）-CTS，25胸和25腹部。手动注释五种不同的身体组合物（VAT，SAT，IMAT，SM和骨骼）。培训次训练策略用于效率。使用已经注释的案例训练了UNET模型。然后，该模型用于为剩余情况启用半自动注释。使用10倍的交叉验证方法来开发和验证几种卷积神经网络（CNNS）的性能，包括UNET，复发性残留的UNET（R2UNET）和UNET ++。在培训CNN模型时使用3-D贴片采样操作。测试了单独培训的CNN模型，看看它们是否可以达到更好的性能而不是共同分割它们。配对样品T检验用于测试统计显着性。结果：在三种CNN模型中，UNET在共同分割五个身体组合物中表现出最佳的整体性能，骰子系数为0.840 +/- 0.091,0.908 +/- 0.067,0.603 +/- 0.084,0.889 +/- 0.027，和0.884 +/- 0.031，Jaccard指数为0.734 +/- 0.119，0.837 +/- 0.096,0.437 +/- 0.082,0.800 +/- 0.042,0.793 +/- 0.049，分别用于增值税，SAT，IMAT， SM和骨头。结论：分段体组合物中的CNN模型中没有显着差异，但共同分段体组合物比分别分割更好的性能。

Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we optimise during training, based on Dice coefficient. In this way we can deal with situations where there is a strong imbalance between the number of foreground and background voxels. To cope with the limited number of annotated volumes available for training, we augment the data applying random non-linear transformations and histogram matching. We show in our experimental evaluation that our approach achieves good performances on challenging test data while requiring only a fraction of the processing time needed by other previous methods.

临床实践中使用的医学图像是异质的，与学术研究中研究的扫描质量不同。在解剖学，伪影或成像参数不寻常或方案不同的极端情况下，预处理会分解。最需要对这些变化的方法可靠。提出了一种新颖的深度学习方法，以将人脑快速分割为132个区域。提出的模型使用有效的U-NET型网络，并从不同视图和分层关系的交点上受益，以在端到端训练期间融合正交2D平面和脑标签。部署了弱监督的学习，以利用部分标记的数据来进行整个大脑分割和颅内体积（ICV）的估计。此外，数据增强用于通过生成具有较高的脑扫描的磁共振成像（MRI）数据来扩展模型训练，同时保持数据隐私。提出的方法可以应用于脑MRI数据，包括头骨或任何其他工件，而无需预处理图像或性能下降。与最新的一些实验相比，使用了不同的Atlases的几项实验，以评估受过训练模型的分割性能，并且与不同内部和不同内部和不同内部方法的现有方法相比，结果显示了较高的分割精度和鲁棒性。间域数据集。

异常气道扩张，称为牵引支气管扩张，是特发性肺纤维化（IPF）的典型特征。体积计算断层扫描（CT）成像捕获IPF中逐渐变细的丢失。我们假设气道异常的自动化量化可以提供IPF疾病程度和严重程度的估算。我们提出了一种自动化计算管道，系统地将气道树木从基于深度学习的气道分割中划分到其裂片和世代分支，从而从胸部CT获得气道结构措施。重要的是，透气阻止通过厚波传播的杂散气道分支的发生，并通过图表搜索去除气道树中的环，克服现有气道骨架算法的限制。在14名健康参与者和14名IPF患者之间比较了透气段（跨空间）和透气曲线曲线之间的逐渐变化。 IPF患者中，Airway interberering显着降低，与健康对照相比，Airway曲线曲调显着增加。差异在下叶中最大标记，符合IPF相关损伤的典型分布。透气是一种开源管道，避免了现有的气道定量算法的限制，并具有临床解释性。自动化气道测量可能具有作为IPF严重程度和疾病程度的新型成像生物标志物。

机器学习和计算机视觉技术近年来由于其自动化，适合性和产生惊人结果的能力而迅速发展。因此，在本文中，我们调查了2014年至2022年之间发表的关键研究，展示了不同的机器学习算法研究人员用来分割肝脏，肝肿瘤和肝脉管结构的研究。我们根据感兴趣的组织（肝果，肝肿瘤或肝毒剂）对被调查的研究进行了划分，强调了同时解决多个任务的研究。此外，机器学习算法被归类为受监督或无监督的，如果属于某个方案的工作量很大，则将进一步分区。此外，对文献和包含上述组织面具的网站发现的不同数据集和挑战进行了彻底讨论，强调了组织者的原始贡献和其他研究人员的贡献。同样，在我们的评论中提到了文献中过度使用的指标，这强调了它们与手头的任务的相关性。最后，强调创新研究人员应对需要解决的差距的关键挑战和未来的方向，例如许多关于船舶分割挑战的研究的稀缺性以及为什么需要早日处理他们的缺席。

胰腺癌是与癌症相关死亡的全球主要原因之一。尽管深度学习在计算机辅助诊断和检测方法（CAD）方法中取得了成功，但很少关注胰腺癌的检测。我们提出了一种检测胰腺肿瘤的方法，该方法在周围的解剖结构中利用临床上的特征，从而更好地旨在利用放射科医生的知识，而不是其他常规的深度学习方法。为此，我们收集了一个新的数据集，该数据集由99例胰腺导管腺癌（PDAC）和97例没有胰腺肿瘤的对照病例组成。由于胰腺癌的生长模式，肿瘤可能总是可见为低音病变，因此，专家指的是二次外部特征的可见性，这些特征可能表明肿瘤的存在。我们提出了一种基于U-NET样深的CNN的方法，该方法利用以下外部次要特征：胰管，常见的胆管和胰腺以及处理后的CT扫描。使用这些功能，该模型如果存在胰腺肿瘤。这种用于分类和本地化方法的细分实现了99％的敏感性（一个案例）和99％的特异性，这比以前的最新方法的灵敏度增加了5％。与以前的PDAC检测方法相比，该模型还以合理的精度和较短的推理时间提供位置信息。这些结果提供了显着的性能改善，并强调了在开发新型CAD方法时纳入临床专家知识的重要性。

发现采用时间分离技术（TST）的基于模型的重建可以使用C臂锥束计算机断层扫描（CBCT）改善肝脏的动态灌注成像。要使用从CT灌注数据中提取的先验知识应用TST，应从CT扫描中准确分割肝脏。需要对主要和基于模型的CBCT数据进行重建，以正确可视化和解释灌注图。这项研究提出了Turbolift Learning，该学习按照培训CT，CBCT，CBCT，CBCT TST的顺序训练多尺度关注的多尺度注意力，UNET串行序列上的不同肝脏细分任务 - 使先前的培训作为前培训作为预训练阶段的阶段随后的问题 - 解决培训数据集数量有限的问题。对于CBCT TST的肝脏分割的最终任务，提议的方法的总骰子得分为0.874 $ \ pm $ 0.031和0.905 $ \ pm $ \ $ \ $ 0.007，分别为6倍和4倍的交叉验证实验 - 获得统计上显着的改进 - 在模型上，该模型仅接受该任务。实验表明，涡轮增压不仅提高了模型的整体性能，而且还使其与源自栓塞材料和截断物品的人工制品具有稳健性。此外，深入分析确认了分割任务的顺序。本文显示了从CT，CBCT和CBCT TST分割肝脏的潜力，从可用的有限培训数据中学习，将来可能会用于可视化和评估灌注图的肝病评估。 。

Owing to the success of transformer models, recent works study their applicability in 3D medical segmentation tasks. Within the transformer models, the self-attention mechanism is one of the main building blocks that strives to capture long-range dependencies, compared to the local convolutional-based design. However, the self-attention operation has quadratic complexity which proves to be a computational bottleneck, especially in volumetric medical imaging, where the inputs are 3D with numerous slices. In this paper, we propose a 3D medical image segmentation approach, named UNETR++, that offers both high-quality segmentation masks as well as efficiency in terms of parameters and compute cost. The core of our design is the introduction of a novel efficient paired attention (EPA) block that efficiently learns spatial and channel-wise discriminative features using a pair of inter-dependent branches based on spatial and channel attention. Our spatial attention formulation is efficient having linear complexity with respect to the input sequence length. To enable communication between spatial and channel-focused branches, we share the weights of query and key mapping functions that provide a complimentary benefit (paired attention), while also reducing the overall network parameters. Our extensive evaluations on three benchmarks, Synapse, BTCV and ACDC, reveal the effectiveness of the proposed contributions in terms of both efficiency and accuracy. On Synapse dataset, our UNETR++ sets a new state-of-the-art with a Dice Similarity Score of 87.2%, while being significantly efficient with a reduction of over 71% in terms of both parameters and FLOPs, compared to the best existing method in the literature. Code: https://github.com/Amshaker/unetr_plus_plus.

医学成像深度学习模型通常是大而复杂的，需要专门的硬件来训练和评估这些模型。为了解决此类问题，我们提出了PocketNet范式，以减少深度学习模型的规模，通过促进卷积神经网络中的渠道数量的增长。我们证明，对于一系列的分割和分类任务，PocketNet架构产生的结果与常规神经网络相当，同时将参数数量减少多个数量级，最多使用90％的GPU记忆，并加快训练时间的加快。高达40％，从而允许在资源约束设置中培训和部署此类模型。

In medical image analysis, automated segmentation of multi-component anatomical structures, which often have a spectrum of potential anomalies and pathologies, is a challenging task. In this work, we develop a multi-step approach using U-Net-based neural networks to initially detect anomalies (bone marrow lesions, bone cysts) in the distal femur, proximal tibia and patella from 3D magnetic resonance (MR) images of the knee in individuals with varying grades of osteoarthritis. Subsequently, the extracted data are used for downstream tasks involving semantic segmentation of individual bone and cartilage volumes as well as bone anomalies. For anomaly detection, the U-Net-based models were developed to reconstruct the bone profiles of the femur and tibia in images via inpainting so anomalous bone regions could be replaced with close to normal appearances. The reconstruction error was used to detect bone anomalies. A second anomaly-aware network, which was compared to anomaly-na\"ive segmentation networks, was used to provide a final automated segmentation of the femoral, tibial and patellar bones and cartilages from the knee MR images containing a spectrum of bone anomalies. The anomaly-aware segmentation approach provided up to 58% reduction in Hausdorff distances for bone segmentations compared to the results from the anomaly-na\"ive segmentation networks. In addition, the anomaly-aware networks were able to detect bone lesions in the MR images with greater sensitivity and specificity (area under the receiver operating characteristic curve [AUC] up to 0.896) compared to the anomaly-na\"ive segmentation networks (AUC up to 0.874).

We present VoxelMorph, a fast learning-based framework for deformable, pairwise medical image registration. Traditional registration methods optimize an objective function for each pair of images, which can be time-consuming for large datasets or rich deformation models. In contrast to this approach, and building on recent learning-based methods, we formulate registration as a function that maps an input image pair to a deformation field that aligns these images. We parameterize the function via a convolutional neural network (CNN), and optimize the parameters of the neural network on a set of images. Given a new pair of scans, VoxelMorph rapidly computes a deformation field by directly evaluating the function. In this work, we explore two different training strategies. In the first (unsupervised) setting, we train the model to maximize standard image matching objective functions that are based on the image intensities. In the second setting, we leverage auxiliary segmentations available in the training data. We demonstrate that the unsupervised model's accuracy is comparable to state-of-the-art methods, while operating orders of magnitude faster. We also show that VoxelMorph trained with auxiliary data improves registration accuracy at test time, and evaluate the effect of training set size on registration. Our method promises to speed up medical image analysis and processing pipelines, while facilitating novel directions in learning-based registration and its applications. Our code is freely available at http://voxelmorph.csail.mit.edu.

人类生理学中的各种结构遵循特异性形态，通常在非常细的尺度上表达复杂性。这种结构的例子是胸前气道，视网膜血管和肝血管。可以观察到可以观察到可以观察到可以观察到可以观察到空间排列的磁共振成像（MRI），计算机断层扫描（CT），光学相干断层扫描（OCT）等医学成像模式（MRI），计算机断层扫描（CT），可以观察到空间排列的大量2D和3D图像的集合。这些结构在医学成像中的分割非常重要，因为对结构的分析提供了对疾病诊断，治疗计划和预后的见解。放射科医生手动标记广泛的数据通常是耗时且容易出错的。结果，在过去的二十年中，自动化或半自动化的计算模型已成为医学成像的流行研究领域，迄今为止，许多计算模型已经开发出来。在这项调查中，我们旨在对当前公开可用的数据集，细分算法和评估指标进行全面审查。此外，讨论了当前的挑战和未来的研究方向。