Deep Learning-Based Automatic Delineation of Liver Domes in kV Triggered Images for Online Breath-hold Reproducibility Verification of Liver Stereotactic Body Radiation Therapy

Stereotactic Body Radiation Therapy (SBRT) can be a precise, minimally invasive treatment method for liver cancer and liver metastases. However, the effectiveness of SBRT relies on the accurate delivery of the dose to the tumor while sparing healthy tissue. Challenges persist in ensuring breath-hold reproducibility, with current methods often requiring manual verification of liver dome positions from kV-triggered images. To address this, we propose a proof-of-principle study of a deep learning-based pipeline to automatically delineate the liver dome from kV-planar images. From 24 patients who received SBRT for liver cancer or metastasis inside liver, 711 KV-triggered images acquired for online breath-hold verification were included in the current study. We developed a pipeline comprising a trained U-Net for automatic liver dome region segmentation from the triggered images followed by extraction of the liver dome via thresholding, edge detection, and morphological operations. The performance and generalizability of the pipeline was evaluated using 2-fold cross validation. The training of the U-Net model for liver region segmentation took under 30 minutes and the automatic delineation of a liver dome for any triggered image took less than one second. The RMSE and rate of detection for Fold1 with 366 images was (6.4 +/- 1.6) mm and 91.7%, respectively. For Fold2 with 345 images, the RMSE and rate of detection was (7.7 +/- 2.3) mm and 76.3% respectively.

MFA-Net: Multi-Scale feature fusion attention network for liver tumor segmentation

Segmentation of organs of interest in medical CT images is beneficial for diagnosis of diseases. Though recent methods based on Fully Convolutional Neural Networks (F-CNNs) have shown success in many segmentation tasks, fusing features from images with different scales is still a challenge: (1) Due to the lack of spatial awareness, F-CNNs share the same weights at different spatial locations. (2) F-CNNs can only obtain surrounding information through local receptive fields. To address the above challenge, we propose a new segmentation framework based on attention mechanisms, named MFA-Net (Multi-Scale Feature Fusion Attention Network). The proposed framework can learn more meaningful feature maps among multiple scales and result in more accurate automatic segmentation. We compare our proposed MFA-Net with SOTA methods on two 2D liver CT datasets. The experimental results show that our MFA-Net produces more precise segmentation on images with different scales.

CAFCT: Contextual and Attentional Feature Fusions of Convolutional Neural Networks and Transformer for Liver Tumor Segmentation

Medical image semantic segmentation techniques can help identify tumors automatically from computed tomography (CT) scans. In this paper, we propose a Contextual and Attentional feature Fusions enhanced Convolutional Neural Network (CNN) and Transformer hybrid network (CAFCT) model for liver tumor segmentation. In the proposed model, three other modules are introduced in the network architecture: Attentional Feature Fusion (AFF), Atrous Spatial Pyramid Pooling (ASPP) of DeepLabv3, and Attention Gates (AGs) to improve contextual information related to tumor boundaries for accurate segmentation. Experimental results show that the proposed CAFCT achieves a mean Intersection over Union (IoU) of 90.38% and Dice score of 86.78%, respectively, on the Liver Tumor Segmentation Benchmark (LiTS) dataset, outperforming pure CNN or Transformer methods, e.g., Attention U-Net, and PVTFormer.

Anisotropic Hybrid Networks for liver tumor segmentation with uncertainty quantification

The burden of liver tumors is important, ranking as the fourth leading cause of cancer mortality. In case of hepatocellular carcinoma (HCC), the delineation of liver and tumor on contrast-enhanced magnetic resonance imaging (CE-MRI) is performed to guide the treatment strategy. As this task is time-consuming, needs high expertise and could be subject to inter-observer variability there is a strong need for automatic tools. However, challenges arise from the lack of available training data, as well as the high variability in terms of image resolution and MRI sequence. In this work we propose to compare two different pipelines based on anisotropic models to obtain the segmentation of the liver and tumors. The first pipeline corresponds to a baseline multi-class model that performs the simultaneous segmentation of the liver and tumor classes. In the second approach, we train two distinct binary models, one segmenting the liver only and the other the tumors. Our results show that both pipelines exhibit different strengths and weaknesses. Moreover we propose an uncertainty quantification strategy allowing the identification of potential false positive tumor lesions. Both solutions were submitted to the MICCAI 2023 Atlas challenge regarding liver and tumor segmentation.

3D Medical Image Segmentation based on multi-scale MPU-Net

The high cure rate of cancer is inextricably linked to physicians' accuracy in diagnosis and treatment, therefore a model that can accomplish high-precision tumor segmentation has become a necessity in many applications of the medical industry. It can effectively lower the rate of misdiagnosis while considerably lessening the burden on clinicians. However, fully automated target organ segmentation is problematic due to the irregular stereo structure of 3D volume organs. As a basic model for this class of real applications, U-Net excels. It can learn certain global and local features, but still lacks the capacity to grasp spatial long-range relationships and contextual information at multiple scales. This paper proposes a tumor segmentation model MPU-Net for patient volume CT images, which is inspired by Transformer with a global attention mechanism. By combining image serialization with the Position Attention Module, the model attempts to comprehend deeper contextual dependencies and accomplish precise positioning. Each layer of the decoder is also equipped with a multi-scale module and a cross-attention mechanism. The capability of feature extraction and integration at different levels has been enhanced, and the hybrid loss function developed in this study can better exploit high-resolution characteristic information. Moreover, the suggested architecture is tested and evaluated on the Liver Tumor Segmentation Challenge 2017 (LiTS 2017) dataset. Compared with the benchmark model U-Net, MPU-Net shows excellent segmentation results. The dice, accuracy, precision, specificity, IOU, and MCC metrics for the best model segmentation results are 92.17%, 99.08%, 91.91%, 99.52%, 85.91%, and 91.74%, respectively. Outstanding indicators in various aspects illustrate the exceptional performance of this framework in automatic medical image segmentation.

Encoding feature supervised UNet++: Redesigning Supervision for liver and tumor segmentation

Liver tumor segmentation in CT images is a critical step in the diagnosis, surgical planning and postoperative evaluation of liver disease. An automatic liver and tumor segmentation method can greatly relieve physicians of the heavy workload of examining CT images and better improve the accuracy of diagnosis. In the last few decades, many modifications based on U-Net model have been proposed in the literature. However, there are relatively few improvements for the advanced UNet++ model. In our paper, we propose an encoding feature supervised UNet++(ES-UNet++) and apply it to the liver and tumor segmentation. ES-UNet++ consists of an encoding UNet++ and a segmentation UNet++. The well-trained encoding UNet++ can extract the encoding features of label map which are used to additionally supervise the segmentation UNet++. By adding supervision to the each encoder of segmentation UNet++, U-Nets of different depths that constitute UNet++ outperform the original version by average 5.7% in dice score and the overall dice score is thus improved by 2.1%. ES-UNet++ is evaluated with dataset LiTS, achieving 95.6% for liver segmentation and 67.4% for tumor segmentation in dice score. In this paper, we also concluded some valuable properties of ES-UNet++ by conducting comparative anaylsis between ES-UNet++ and UNet++:(1) encoding feature supervision can accelerate the convergence of the model.(2) encoding feature supervision enhances the effect of model pruning by achieving huge speedup while providing pruned models with fairly good performance.

Label-Free Liver Tumor Segmentation

We demonstrate that AI models can accurately segment liver tumors without the need for manual annotation by using synthetic tumors in CT scans. Our synthetic tumors have two intriguing advantages: (I) realistic in shape and texture, which even medical professionals can confuse with real tumors; (II) effective for training AI models, which can perform liver tumor segmentation similarly to the model trained on real tumors -- this result is exciting because no existing work, using synthetic tumors only, has thus far reached a similar or even close performance to real tumors. This result also implies that manual efforts for annotating tumors voxel by voxel (which took years to create) can be significantly reduced in the future. Moreover, our synthetic tumors can automatically generate many examples of small (or even tiny) synthetic tumors and have the potential to improve the success rate of detecting small liver tumors, which is critical for detecting the early stages of cancer. In addition to enriching the training data, our synthesizing strategy also enables us to rigorously assess the AI robustness.

A Cascaded Approach for ultraly High Performance Lesion Detection and False Positive Removal in Liver CT Scans

Liver cancer has high morbidity and mortality rates in the world. Multi-phase CT is a main medical imaging modality for detecting/identifying and diagnosing liver tumors. Automatically detecting and classifying liver lesions in CT images have the potential to improve the clinical workflow. This task remains challenging due to liver lesions' large variations in size, appearance, image contrast, and the complexities of tumor types or subtypes. In this work, we customize a multi-object labeling tool for multi-phase CT images, which is used to curate a large-scale dataset containing 1,631 patients with four-phase CT images, multi-organ masks, and multi-lesion (six major types of liver lesions confirmed by pathology) masks. We develop a two-stage liver lesion detection pipeline, where the high-sensitivity detecting algorithms in the first stage discover as many lesion proposals as possible, and the lesion-reclassification algorithms in the second stage remove as many false alarms as possible. The multi-sensitivity lesion detection algorithm maximizes the information utilization of the individual probability maps of segmentation, and the lesion-shuffle augmentation effectively explores the texture contrast between lesions and the liver. Independently tested on 331 patient cases, the proposed model achieves high sensitivity and specificity for malignancy classification in the multi-phase contrast-enhanced CT (99.2%, 97.1%, diagnosis setting) and in the noncontrast CT (97.3%, 95.7%, screening setting).

Free-form Lesion Synthesis Using a Partial Convolution Generative Adversarial Network for Enhanced Deep Learning Liver Tumor Segmentation

Automatic deep learning segmentation models has been shown to improve both the segmentation efficiency and the accuracy. However, training a robust segmentation model requires considerably large labeled training samples, which may be impractical. This study aimed to develop a deep learning framework for generating synthetic lesions that can be used to enhance network training. The lesion synthesis network is a modified generative adversarial network (GAN). Specifically, we innovated a partial convolution strategy to construct an Unet-like generator. The discriminator is designed using Wasserstein GAN with gradient penalty and spectral normalization. A mask generation method based on principal component analysis was developed to model various lesion shapes. The generated masks are then converted into liver lesions through a lesion synthesis network. The lesion synthesis framework was evaluated for lesion textures, and the synthetic lesions were used to train a lesion segmentation network to further validate the effectiveness of this framework. All the networks are trained and tested on the public dataset from LITS. The synthetic lesions generated by the proposed approach have very similar histogram distributions compared to the real lesions for the two employed texture parameters, GLCM-energy and GLCM-correlation. The Kullback-Leibler divergence of GLCM-energy and GLCM-correlation were 0.01 and 0.10, respectively. Including the synthetic lesions in the tumor segmentation network improved the segmentation dice performance of U-Net significantly from 67.3% to 71.4% (p<0.05). Meanwhile, the volume precision and sensitivity improve from 74.6% to 76.0% (p=0.23) and 66.1% to 70.9% (p<0.01), respectively. The synthetic data significantly improves the segmentation performance.

Efficient liver segmentation with 3D CNN using computed tomography scans

The liver is one of the most critical metabolic organs in vertebrates due to its vital functions in the human body, such as detoxification of the blood from waste products and medications. Liver diseases due to liver tumors are one of the most common mortality reasons around the globe. Hence, detecting liver tumors in the early stages of tumor development is highly required as a critical part of medical treatment. Many imaging modalities can be used as aiding tools to detect liver tumors. Computed tomography (CT) is the most used imaging modality for soft tissue organs such as the liver. This is because it is an invasive modality that can be captured relatively quickly. This paper proposed an efficient automatic liver segmentation framework to detect and segment the liver out of CT abdomen scans using the 3D CNN DeepMedic network model. Segmenting the liver region accurately and then using the segmented liver region as input to tumors segmentation method is adopted by many studies as it reduces the false rates resulted from segmenting abdomen organs as tumors. The proposed 3D CNN DeepMedic model has two pathways of input rather than one pathway, as in the original 3D CNN model. In this paper, the network was supplied with multiple abdomen CT versions, which helped improve the segmentation quality. The proposed model achieved 94.36%, 94.57%, 91.86%, and 93.14% for accuracy, sensitivity, specificity, and Dice similarity score, respectively. The experimental results indicate the applicability of the proposed method.