Multi-organ Segmentation Research Articles

Multi-phase CT synthesis-assisted segmentation of abdominal organs

To propose a method for abdominal multi-organ segmentation assisted by multi-phase CT synthesis. Multi-phase CT synthesis for synthesizing high-quality CT images was used to increase the information details for image segmentation. A transformer block was introduced to help to capture long-range semantic information in cooperation with perceptual loss to minimize the differences between the real image and synthesized image. The model was trained using multi-phase CT dataset of 526 total cases from Nanfang Hospital. The mean maximum absolute error (MAE) of the synthesized non-contrast CT, venous phase contrast- enhanced CT (CECT), and delay phase CECT images from arterial phase CECT was 19.192±3.381, 20.140±2.676 and 22.538±2.874, respectively, which were better than those of images synthesized using other methods. Validation of the multi-phase CT synthesis-assisted abdominal multi-organ segmentation method showed an average dice coefficient of 0.847 for the internal validation set and 0.823 for the external validation set. The propose method is capable of synthesizing high-quality multi-phase CT images to effectively reduce the errors in registration between different phase CT images and improve the performance for segmentation of 13 abdominal organs.

Whole-orbit radiomics: machine learning-based multi- and fused- region radiomics signatures for intravenous glucocorticoid response prediction in thyroid eye disease

BackgroundRadiomics analysis of orbital magnetic resonance imaging (MRI) shows preliminary potential for intravenous glucocorticoid (IVGC) response prediction of thyroid eye disease (TED). The current region of interest segmentation contains only a single organ as extraocular muscles (EOMs). It would be of great value to consider all orbital soft tissues and construct a better prediction model.MethodsIn this retrospective study, we enrolled 127 patients with TED that received 4·5 g IVGC therapy and had complete follow-up examinations. Pre-treatment orbital T2-weighted imaging (T2WI) was acquired for all subjects. Using multi-organ segmentation (MOS) strategy, we contoured the EOMs, lacrimal gland (LG), orbital fat (OF), and optic nerve (ON), respectively. By fused-organ segmentation (FOS), we contoured the aforementioned structures as a cohesive unit. Whole-orbit radiomics (WOR) models consisting of a multi-regional radiomics (MRR) model and a fused-regional radiomics (FRR) model were further constructed using six machine learning (ML) algorithms.ResultsThe support vector machine (SVM) classifier had the best performance on the MRR model (AUC = 0·961). The MRR model outperformed the single-regional radiomics (SRR) models (highest AUC = 0·766, XGBoost on EOMs, or LR on OF) and conventional semiquantitative imaging model (highest AUC = 0·760, NaiveBayes). The application of different ML algorithms for the comparison between the MRR model and the FRR model (highest AUC = 0·916, LR) led to different conclusions.ConclusionsThe WOR models achieved a satisfactory result in IVGC response prediction of TED. It would be beneficial to include more orbital structures and implement ML algorithms while constructing radiomics models. The selection of separate or overall segmentation of orbital soft tissues has not yet attained its final optimal result.

Impact of deep learning-based multiorgan segmentation methods on patient-specific internal dosimetry in PET/CT imaging: A comparative study.

Accurate and fast multiorgan segmentation is essential in image-based internal dosimetry in nuclear medicine. While conventional manual PET image segmentation is widely used, it suffers from both being time-consuming as well as subject to human error. This study exploited 2D and 3D deep learning (DL) models. Key organs in the trunk of the body were segmented and then used as a reference for networks. The pre-trained p2p-U-Net-GAN and HighRes3D architectures were fine-tuned with PET-only images as inputs. Additionally, the HighRes3D model was alternatively trained with PET/CT images. Evaluation metrics such as sensitivity (SEN), specificity (SPC), intersection over union (IoU), and Dice scores were considered to assess the performance of the networks. The impact of DL-assisted PET image segmentation methods was further assessed using the Monte Carlo (MC)-derived S-values to be used for internal dosimetry. A fair comparison with manual low-dose CT-aided segmentation of the PET images was also conducted. Although both 2D and 3D models performed well, the HighRes3D offers superior performance with Dice scores higher than 0.90. Key evaluation metrics such as SEN, SPC, and IoU vary between 0.89-0.93, 0.98-0.99, and 0.87-0.89 intervals, respectively, indicating the encouraging performance of the models. The percentage differences between the manual and DL segmentation methods in the calculated S-values varied between 0.1% and 6% with a maximum attributed to the stomach. The findings prove while the incorporation of anatomical information provided by the CT data offers superior performance in terms of Dice score, the performance of HighRes3D remains comparable without the extra CT channel. It is concluded that both proposed DL-based methods provide automated and fast segmentation of whole-body PET/CT images with promising evaluation metrics. Between them, the HighRes3D is more pronounced by providing better performance and can therefore be the method of choice for 18F-FDG-PET image segmentation.

CSSNet: Cascaded spatial shift network for multi-organ segmentation

Multi-organ segmentation is vital for clinical diagnosis and treatment. Although CNN and its extensions are popular in organ segmentation, they suffer from the local receptive field. In contrast, MultiLayer-Perceptron-based models (e.g., MLP-Mixer) have a global receptive field. However, these MLP-based models employ fully connected layers with many parameters and tend to overfit on sample-deficient medical image datasets. Therefore, we propose a Cascaded Spatial Shift Network, CSSNet, for multi-organ segmentation. Specifically, we design a novel cascaded spatial shift block to reduce the number of model parameters and aggregate feature segments in a cascaded way for efficient and effective feature extraction. Then, we propose a feature refinement network to aggregate multi-scale features with location information, and enhance the multi-scale features along the channel and spatial axis to obtain a high-quality feature map. Finally, we employ a self-attention-based fusion strategy to focus on the discriminative feature information for better multi-organ segmentation performance. Experimental results on the Synapse (multiply organs) and LiTS (liver & tumor) datasets demonstrate that our CSSNet achieves promising segmentation performance compared with CNN, MLP, and Transformer models. The source code will be available at https://github.com/zkyseu/CSSNet.

TSCA-Net: Transformer based spatial-channel attention segmentation network for medical images

Deep learning architectures based on convolutional neural network (CNN) and Transformer have achieved great success in medical image segmentation. Models based on the encoder–decoder framework like U-Net have been successfully employed in many realistic scenarios. However, due to the low contrast between object and background, various shapes and scales of objects, and complex background in medical images, it is difficult to locate targets and obtain better segmentation performance by extracting effective information from images. In this paper, an encoder–decoder architecture based on spatial and channel attention modules built by Transformer is proposed for medical image segmentation. Concretely, spatial and channel attention modules based on Transformer are utilized to extract spatial and channel global complementary information at different layers in U-shape network, which is beneficial to learn the detail features in different scales. To fuse better spatial and channel information from Transformer features, a spatial and channel feature fusion block is designed for the decoder. The proposed network inherits the advantages of both CNN and Transformer with the local feature representation and long-range dependency for medical images. Qualitative and quantitative experiments demonstrate that the proposed method outperforms against eight state-of-the-art segmentation methods on five publicly medical image datasets including different modalities, such as 80.23% and 93.56% Dice value, 67.13% and 88.94% Intersection over Union (IoU) value on the Multi-organ Nucleus Segmentation (MoNuSeg) and Combined Healthy Abdominal Organ Segmentation with Computed Tomography scans (CHAOS-CT) datasets.

Fully Automated Agatston Score Calculation From Electrocardiography-Gated Cardiac Computed Tomography Using Deep Learning and Multi-Organ Segmentation: A Validation Study.

To evaluate deep learning-based calcium segmentation and quantification on ECG-gated cardiac CT scans compared with manual evaluation. Automated calcium quantification was performed using a neural network based on mask regions with convolutional neural networks (R-CNNs) for multi-organ segmentation. Manual evaluation of calcium was carried out using proprietary software. This is a retrospective study of archived data. This study used 40 patients to train the segmentation model and 110 patients were used for the validation of the algorithm. The Pearson correlation coefficient between the reference actual and the computed predictive scores shows high level of correlation (0.84; P < .001) and high limits of agreement (±1.96 SD; -2000, 2000) in Bland-Altman plot analysis. The proposed method correctly classifies the risk group in 75.2% and classifies the subjects in the same group. In total, 81% of the predictive scores lie in the same categories and only seven patients out of 110 were more than one category off. For the presence/absence of coronary artery calcifications, the deep learning model achieved a sensitivity of 90% and a specificity of 94%. Fully automated model shows good correlation compared with reference standards. Automating process reduces evaluation time and optimizes clinical calcium scoring without additional resources.

Densely Convolutional BU-NET Framework for Breast Multi-Organ Cancer Nuclei Segmentation through Histopathological Slides and Classification Using Optimized Features

Densely Convolutional BU-NET Framework for Breast Multi-Organ Cancer Nuclei Segmentation through Histopathological Slides and Classification Using Optimized Features

Alleviating Class Imbalance in Semi-Supervised Multi-Organ Segmentation via Balanced Subclass Regularization

Alleviating Class Imbalance in Semi-Supervised Multi-Organ Segmentation via Balanced Subclass Regularization

Artificial Intelligence Generated Data Augmentation for Abdominal Multi-Organ Segmentation

Artificial Intelligence Generated Data Augmentation for Abdominal Multi-Organ Segmentation

Med-Query: Steerable Parsing of 9-DoF Medical Anatomies with Query Embedding.

Automatic parsing of human anatomies at the instance-level from 3D computed tomography (CT) is a prerequisite step for many clinical applications. The presence of pathologies, broken structures or limited field-of-view (FOV) can all make anatomy parsing algorithms vulnerable. In this work, we explore how to leverage and implement the successful detection-then-segmentation paradigm for 3D medical data, and propose a steerable, robust, and efficient computing framework for detection, identification, and segmentation of anatomies in CT scans. Considering the complicated shapes, sizes, and orientations of anatomies, without loss of generality, we present a nine degrees of freedom (9-DoF) pose estimation solution in full 3D space using a novel single-stage, non-hierarchical representation. Our whole framework is executed in a steerable manner where any anatomy of interest can be directly retrieved to further boost inference efficiency. We have validated our method on three medical imaging parsing tasks: ribs, spine, and abdominal organs. For rib parsing, CT scans have been annotated at the rib instance-level for quantitative evaluation, similarly for spine vertebrae and abdominal organs. Extensive experiments on 9-DoF box detection and rib instance segmentation demonstrate the high efficiency and effectiveness of our framework (with the identification rate of 97.0% and the segmentation Dice score of 90.9%), compared favorably against several strong baselines (e.g., CenterNet, FCOS, and nnU-Net). For spine parsing and abdominal multi-organ segmentation, our method achieves competitive results on par with stateof-the-art methods on the public CTSpine1K dataset and FLARE22 competition, respectively. Our annotations, code, and models are available at: Med-Query.

SEF-UNet: advancing abdominal multi-organ segmentation with SEFormer and depthwise cascaded upsampling.

The abdomen houses multiple vital organs, which are associated with various diseases posing significant risks to human health. Early detection of abdominal organ conditions allows for timely intervention and treatment, preventing deterioration of patients' health. Segmenting abdominal organs aids physicians in more accurately diagnosing organ lesions. However, the anatomical structures of abdominal organs are relatively complex, with organs overlapping each other, sharing similar features, thereby presenting challenges for segmentation tasks. In real medical scenarios, models must demonstrate real-time and low-latency features, necessitating an improvement in segmentation accuracy while minimizing the number of parameters. Researchers have developed various methods for abdominal organ segmentation, ranging from convolutional neural networks (CNNs) to Transformers. However, these methods often encounter difficulties in accurately identifying organ segmentation boundaries. MetaFormer abstracts the framework of Transformers, excluding the multi-head Self-Attention, offering a new perspective for solving computer vision problems and overcoming the limitations of Vision Transformers and CNN backbone networks. To further enhance segmentation effectiveness, we propose a U-shaped network, integrating SEFormer and depthwise cascaded upsampling (dCUP) as the encoder and decoder, respectively, into the UNet structure, named SEF-UNet. SEFormer combines Squeeze-and-Excitation modules with depthwise separable convolutions, instantiating the MetaFormer framework, enhancing the capture of local details and texture information, thereby improving edge segmentation accuracy. dCUP further integrates shallow and deep information layers during the upsampling process. Our model significantly improves segmentation accuracy while reducing the parameter count and exhibits superior performance in segmenting organ edges that overlap each other, thereby offering potential deployment in real medical scenarios.

D-SAT: dual semantic aggregation transformer with dual attention for medical image segmentation

Objective. Medical image segmentation is significantly essential to assist clinicians in facilitating a quick and accurate diagnoses. However, most of the existing methods are still challenged by the loss of semantic information, blurred boundaries and the huge semantic gap between the encoder and decoder. Approach. To tackle these issues, a dual semantic aggregation transformer with dual attention is proposed for medical image segmentation. Firstly, the dual-semantic feature aggregation module is designed to build a bridge between convolutional neural network (CNN) and Transformer, effectively aggregating CNN’s local feature detail ability and Transformer’s long-range modeling ability to mitigate semantic information loss. Thereafter, the strip spatial attention mechanism is put forward to alleviate the blurred boundaries during encoding by constructing pixel-level feature relations across CSWin Transformer blocks from different spatial dimensions. Finally, a feature distribution gated attention module is constructed in the skip connection between the encoder and decoder to decrease the large semantic gap by filtering out the noise in low-level semantic information when fusing low-level and high-level semantic features during decoding. Main results. Comprehensive experiments conducted on abdominal multi-organ segmentation, cardiac diagnosis, polyp segmentation and skin lesion segmentation serve to validate the generalization and effectiveness of the proposed dual semantic aggregation transformer with dual attention (D-SAT). The superiority of D-SAT over current state-of-the-art methods is substantiated by both subjective and objective evaluations, revealing its remarkable performance in terms of segmentation accuracy and quality. Significance. The proposed method subtly preserves the local feature details and global context information in medical image segmentation, providing valuable support to improve diagnostic efficiency for clinicians and early disease control for patients. Code is available at https://github.com/Dxkm/D-SAT.

Deep Learning Based on EfficientNet for Multiorgan Segmentation of Thoracic Structures on a 0.35 T MR-Linac Radiation Therapy System

The advent of the 0.35 T MR-Linac (MRIdian, ViewRay) system in radiation therapy allows precise tumor targeting for moving lesions. However, the lack of an automatic volume segmentation function in the MR-Linac’s treatment planning system poses a challenge. In this paper, we propose a deep-learning-based multiorgan segmentation approach for the thoracic region, using EfficientNet as the backbone for the network architecture. The objectives of this approach include accurate segmentation of critical organs, such as the left and right lungs, the heart, the spinal cord, and the esophagus, essential for minimizing radiation toxicity during external radiation therapy. Our proposed approach, when evaluated on an internal dataset comprising 81 patients, demonstrated superior performance compared to other state-of-the-art methods. Specifically, the results for our approach with a 2.5D strategy were as follows: a dice similarity coefficient (DSC) of 0.820 ± 0.041, an intersection over union (IoU) of 0.725 ± 0.052, and a 3D Hausdorff distance (HD) of 10.353 ± 4.974 mm. Notably, the 2.5D strategy surpassed the 2D strategy in all three metrics, exhibiting higher DSC and IoU values, as well as lower HD values. This improvement strongly suggests that our proposed approach with the 2.5D strategy may hold promise in achieving more precise and accurate segmentations when compared to the conventional 2D strategy. Our work has practical implications in the improvement of treatment planning precision, aligning with the evolution of medical imaging and innovative strategies for multiorgan segmentation tasks.

CPFTransformer: transformer fusion context pyramid medical image segmentation network.

The application of U-shaped convolutional neural network (CNN) methods in medical image segmentation tasks has yielded impressive results. However, this structure's single-level context information extraction capability can lead to problems such as boundary blurring, so it needs to be improved. Additionally, the convolution operation's inherent locality restricts its ability to capture global and long-distance semantic information interactions effectively. Conversely, the transformer model excels at capturing global information. Given these considerations, this paper presents a transformer fusion context pyramid medical image segmentation network (CPFTransformer). The CPFTransformer utilizes the Swin Transformer to integrate edge perception for segmentation edges. To effectively fuse global and multi-scale context information, we introduce an Edge-Aware module based on a context pyramid, which specifically emphasizes local features like edges and corners. Our approach employs a layered Swin Transformer with a shifted window mechanism as an encoder to extract contextual features. A decoder based on a symmetric Swin Transformer is employed for upsampling operations, thereby restoring the resolution of feature maps. The encoder and decoder are connected by an Edge-Aware module for the extraction of local features such as edges and corners. Experimental evaluations on the Synapse multi-organ segmentation task and the ACDC dataset demonstrate the effectiveness of our method, yielding a segmentation accuracy of 79.87% (DSC) and 20.83% (HD) in the Synapse multi-organ segmentation task. The method proposed in this paper, which combines the context pyramid mechanism and Transformer, enables fast and accurate automatic segmentation of medical images, thereby significantly enhancing the precision and reliability of medical diagnosis. Furthermore, the approach presented in this study can potentially be extended to image segmentation of other organs in the future.

3D Multi-Organ and Tumor Segmentation Based on Re-Parameterize Diverse Experts

Automated segmentation of abdominal organs and tumors in medical images is a challenging yet essential task in medical image analysis. Deep learning has shown excellent performance in many medical image segmentation tasks, but most prior efforts were fragmented, addressing individual organ and tumor segmentation tasks with specialized networks. To tackle the challenges of abdominal organ and tumor segmentation using partially labeled datasets, we introduce Re-parameterizing Mixture-of-Diverse-Experts (RepMode) to abdominal organ and tumor segmentation. Within the RepMode framework, the Mixture-of-Diverse-Experts (MoDE) block forms the foundation, learning generalized parameters applicable across all tasks. We seamlessly integrate the MoDE block into a U-shaped network with dynamic heads, addressing multi-scale challenges by dynamically combining experts with varying receptive fields for each organ and tumor. Our framework incorporates task encoding in both the encoder–decoder section and the segmentation head, enabling the network to adapt throughout the entire system based on task-related information. We evaluate our approach on the multi-organ and tumor segmentation (MOTS) dataset. Experiments show that DoDRepNet outperforms previous methods, including multi-head networks and single-network approaches, giving a highly competitive performance compared with the original single network with dynamic heads. DoDRepNet offers a promising approach to address the complexities of abdominal organ and tumor segmentation using partially labeled datasets, enhancing segmentation accuracy and robustness.

Learning from partially labeled data for multi-organ and tumor segmentation.

Medical image benchmarks for the segmentation of organs and tumors suffer from the partially labeling issue due to its intensive cost of labor and expertise. Current mainstream approaches follow the practice of one network solving one task. With this pipeline, not only the performance is limited by the typically small dataset of a single task, but also the computation cost linearly increases with the number of tasks. To address this, we propose a Transformer based dynamic on-demand network (TransDoDNet) that learns to segment organs and tumors on multiple partially labeled datasets. Specifically, TransDoDNet has a hybrid backbone that is composed of the convolutional neural network and Transformer. A dynamic head enables the network to accomplish multiple segmentation tasks flexibly. Unlike existing approaches that fix kernels after training, the kernels in the dynamic head are generated adaptively by the Transformer, which employs the self-attention mechanism to model long-range organ-wise dependencies and decodes the organ embedding that can represent each organ. We create a large-scale partially labeled Multi-Organ and Tumor Segmentation benchmark, termed MOTS, and demonstrate the superior performance of our TransDoDNet over other competitors on seven organ and tumor segmentation tasks. This study also provides a general 3D medical image segmentation model, which has been pre-trained on the large-scale MOTS benchmark and has demonstrated advanced performance over current predominant self-supervised learning methods. Code and data are available at https://github.com/jianpengz/DoDNet.

Adaptive t-vMF dice loss: An effective expansion of dice loss for medical image segmentation

Dice loss is widely used for medical image segmentation, and many improved loss functions have been proposed. However, further Dice loss improvements are still possible. In this study, we reconsidered the use of Dice loss and discovered that Dice loss can be rewritten in the loss function using the cosine similarity through a simple equation transformation. Using this knowledge, we present a novel t-vMF Dice loss based on the t-vMF similarity instead of the cosine similarity. Based on the t-vMF similarity, our proposed Dice loss is formulated in a more compact similarity loss function than the original Dice loss. Furthermore, we present an effective algorithm that automatically determines the parameter κ for the t-vMF similarity using a validation accuracy, called Adaptive t-vMF Dice loss. Using this algorithm, it is possible to apply more compact similarities for easy classes and wider similarities for difficult classes, and we are able to achieve adaptive training based on the accuracy of each class. We evaluated binary segmentation datasets of CVC-ClinicDB and Kvasir-SEG, and multi-class segmentation datasets of Automated Cardiac Diagnosis Challenge and Synapse multi-organ segmentation. Through experiments conducted on four datasets using a five-fold cross-validation, we confirmed that the Dice score coefficient (DSC) was further improved in comparison with the original Dice loss and other loss functions.

Reducing annotation burden in MR: A novel MR-contrast guided contrastive learning approach for image segmentation.

Contrastive learning, a successful form of representational learning, has shown promising results in pretraining deep learning (DL) models for downstream tasks. When working with limited annotation data, as in medical image segmentation tasks, learning domain-specific local representations can further improve the performance of DL models. In this work, we extend the contrastive learning framework to utilize domain-specific contrast information from unlabeled Magnetic Resonance (MR) images to improve the performance of downstream MR image segmentation tasks in the presence of limited labeled data. The contrast in MR images is controlled by underlying tissue properties (e.g., T1 or T2) and image acquisition parameters. We hypothesize that learning to discriminate local representations based on underlying tissue properties should improve subsequent segmentation tasks on MR images. We propose a novel constrained contrastive learning (CCL) strategy that uses tissue-specific information via a constraint map to define positive and negative local neighborhoods for contrastive learning, embedding this information in the representational space during pretraining. For a given MR contrast image, the proposed strategy uses local signal characteristics (constraint map) across a set of related multi-contrast MR images as a surrogate for underlying tissue information. We demonstrate the utility of the approach for downstream: (1) multi-organ segmentation tasks in T2-weighted images where a DL model learns T2 information with constraint maps from a set of 2D multi-echo T2-weighted images (n=101) and (2) tumor segmentation tasks in multi-parametric images from the public brain tumor segmentation (BraTS) (n=80) dataset where DL models learn T1 and T2 information from multi-parametric BraTS images. Performance is evaluated on downstream multi-label segmentation tasks with limited data in (1) T2-weighted images of the abdomen from an in-house Radial-T2 (Train/Test=30/20), (2) public Cartesian-T2 (Train/Test=6/12) dataset, and (3) multi-parametric MR images from the public brain tumor segmentation dataset (BraTS) (Train/Test=40/50). The performance of the proposed CCL strategy is compared to state-of-the-art self-supervised contrastive learning techniques. In each task, a model is also trained using all available labeled data for supervised baseline performance. The proposed CCL strategy consistently yielded improved Dice scores, Precision, and Recall metrics, and reduced HD95 values across all segmentation tasks. We also observed performance comparable to the baseline with reduced annotation effort. The t-SNE visualization of features for T2-weighted images demonstrates its ability to embed T2 information in the representational space. On the BraTS dataset, we also observed that using an appropriate multi-contrast space to learn T1+T2, T1, or T2 information during pretraining further improved the performance of tumor segmentation tasks. Learning to embed tissue-specific information that controls MR image contrast with the proposed constrained contrastive learning improved the performance of DL models on subsequent segmentation tasks compared to conventional self-supervised contrastive learning techniques. The use of such domain-specific local representations could help understand, improve performance, and mitigate the scarcity of labeled data in MR image segmentation tasks.

SUnet: A multi-organ segmentation network based on multiple attention

Organ segmentation in abdominal or thoracic computed tomography (CT) images plays a crucial role in medical diagnosis as it enables doctors to locate and evaluate organ abnormalities quickly, thereby guiding surgical planning, and aiding treatment decision-making. This paper proposes a novel and efficient medical image segmentation method called SUnet for multi-organ segmentation in the abdomen and thorax. SUnet is a fully attention-based neural network. Firstly, an efficient spatial reduction attention (ESRA) module is introduced not only to extract image features better, but also to reduce overall model parameters, and to alleviate overfitting. Secondly, SUnet's multiple attention-based feature fusion module enables effective cross-scale feature integration. Additionally, an enhanced attention gate (EAG) module is considered by using grouped convolution and residual connections, providing richer semantic features. We evaluate the performance of the proposed model on synapse multiple organ segmentation dataset and automated cardiac diagnostic challenge dataset. SUnet achieves an average Dice of 84.29% and 92.25% on these two datasets, respectively, outperforming other models of similar complexity and size, and achieving state-of-the-art results.

Multi-organ segmentation of CT via convolutional neural network: impact of training setting and scanner manufacturer

Objective. Automated organ segmentation on CT images can enable the clinical use of advanced quantitative software devices, but model performance sensitivities must be understood before widespread adoption can occur. The goal of this study was to investigate performance differences between Convolutional Neural Networks (CNNs) trained to segment one (single-class) versus multiple (multi-class) organs, and between CNNs trained on scans from a single manufacturer versus multiple manufacturers. Methods. The multi-class CNN was trained on CT images obtained from 455 whole-body PET/CT scans (413 for training, 42 for testing) taken with Siemens, GE, and Phillips PET/CT scanners where 16 organs were segmented. The multi-class CNN was compared to 16 smaller single-class CNNs trained using the same data, but with segmentations of only one organ per model. In addition, CNNs trained on Siemens-only (N = 186) and GE-only (N = 219) scans (manufacturer-specific) were compared with CNNs trained on data from both Siemens and GE scanners (manufacturer-mixed). Segmentation performance was quantified using five performance metrics, including the Dice Similarity Coefficient (DSC). Results. The multi-class CNN performed well compared to previous studies, even in organs usually considered difficult auto-segmentation targets (e.g., pancreas, bowel). Segmentations from the multi-class CNN were significantly superior to those from smaller single-class CNNs in most organs, and the 16 single-class models took, on average, six times longer to segment all 16 organs compared to the single multi-class model. The manufacturer-mixed approach achieved minimally higher performance over the manufacturer-specific approach. Significance. A CNN trained on contours of multiple organs and CT data from multiple manufacturers yielded high-quality segmentations. Such a model is an essential enabler of image processing in a software device that quantifies and analyzes such data to determine a patient’s treatment response. To date, this activity of whole organ segmentation has not been adopted due to the intense manual workload and time required.