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Register a new userRAP-Net: Coarse-to-Fine Multi-Organ Segmentation with Single Random Anatomical Prior
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Performing coarse-to-fine abdominal multi-organ segmentation facilitates to extract high-resolution segmentation minimizing the lost of spatial contextual information. However, current coarse-to-refine approaches require a significant number of models to perform single organ refine segmentation corresponding to the extracted organ region of interest (ROI). We propose a coarse-to-fine pipeline, which starts from the extraction of the global prior context of multiple organs from 3D volumes using a low-resolution coarse network, followed by a fine phase that uses a single refined model to segment all abdominal organs instead of multiple organ corresponding models. We combine the anatomical prior with corresponding extracted patches to preserve the anatomical locations and boundary information for performing high-resolution segmentation across all organs in a single model. To train and evaluate our method, a clinical research cohort consisting of 100 patient volumes with 13 organs well-annotated is used. We tested our algorithms with 4-fold cross-validation and computed the Dice score for evaluating the segmentation performance of the 13 organs. Our proposed method using single auto-context outperforms the state-of-the-art on 13 models with an average Dice score 84.58% versus 81.69% (p<0.0001).
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Segmentation of multiple anatomical structures is of great importance in medical image analysis. In this study, we proposed a $mathcal{W}$-net to simultaneously segment both the optic disc (OD) and the exudates in retinal images based on the multi-task learning (MTL) scheme. We introduced a class-balanced loss and a multi-task weighted loss to alleviate the imbalanced problem and to improve the robustness and generalization property of the $mathcal{W}$-net. We demonstrated the effectiveness of our approach by applying five-fold cross-validation experiments on two public datasets e_ophtha_EX and DiaRetDb1. We achieved F1-score of 94.76% and 95.73% for OD segmentation, and 92.80% and 94.14% for exudates segmentation. To further prove the generalization property of the proposed method, we applied the trained model on the DRIONS-DB dataset for OD segmentation and on the MESSIDOR dataset for exudate segmentation. Our results demonstrated that by choosing the optimal weights of each task, the MTL based $mathcal{W}$-net outperformed separate models trained individually on each task. Code and pre-trained models will be available at: url{https://github.com/FundusResearch/MTL_for_OD_and_exudates.git}.
Automatic airway segmentation from chest computed tomography (CT) scans plays an important role in pulmonary disease diagnosis and computer-assisted therapy. However, low contrast at peripheral branches and complex tree-like structures remain as two mainly challenges for airway segmentation. Recent research has illustrated that deep learning methods perform well in segmentation tasks. Motivated by these works, a coarse-to-fine segmentation framework is proposed to obtain a complete airway tree. Our framework segments the overall airway and small branches via the multi-information fusion convolution neural network (Mif-CNN) and the CNN-based region growing, respectively. In Mif-CNN, atrous spatial pyramid pooling (ASPP) is integrated into a u-shaped network, and it can expend the receptive field and capture multi-scale information. Meanwhile, boundary and location information are incorporated into semantic information. These information are fused to help Mif-CNN utilize additional context knowledge and useful features. To improve the performance of the segmentation result, the CNN-based region growing method is designed to focus on obtaining small branches. A voxel classification network (VCN), which can entirely capture the rich information around each voxel, is applied to classify the voxels into airway and non-airway. In addition, a shape reconstruction method is used to refine the airway tree.
Human in-the-loop quality assurance (QA) is typically performed after medical image segmentation to ensure that the systems are performing as intended, as well as identifying and excluding outliers. By performing QA on large-scale, previously unlabeled testing data, categorical QA scores can be generatedIn this paper, we propose a semi-supervised multi-organ segmentation deep neural network consisting of a traditional segmentation model generator and a QA involved discriminator. A large-scale dataset of 2027 volumes are used to train the generator, whose 2-D montage images and segmentation mask with QA scores are used to train the discriminator. To generate the QA scores, the 2-D montage images were reviewed manually and coded 0 (success), 1 (errors consistent with published performance), and 2 (gross failure). Then, the ResNet-18 network was trained with 1623 montage images in equal distribution of all three code labels and achieved an accuracy 94% for classification predictions with 404 montage images withheld for the test cohort. To assess the performance of using the QA supervision, the discriminator was used as a loss function in a multi-organ segmentation pipeline. The inclusion of QA-loss function boosted performance on the unlabeled test dataset from 714 patients to 951 patients over the baseline model. Additionally, the number of failures decreased from 606 (29.90%) to 402 (19.83%). The contributions of the proposed method are threefold: We show that (1) the QA scores can be used as a loss function to perform semi-supervised learning for unlabeled data, (2) the well trained discriminator is learnt by QA score rather than traditional true/false, and (3) the performance of multi-organ segmentation on unlabeled datasets can be fine-tuned with more robust and higher accuracy than the original baseline method.
Fine-tuning a network which has been trained on a large dataset is an alternative to full training in order to overcome the problem of scarce and expensive data in medical applications. While the shallow layers of the network are usually kept unchanged, deeper layers are modified according to the new dataset. This approach may not work for ultrasound images due to their drastically different appearance. In this study, we investigated the effect of fine-tuning different layers of a U-Net which was trained on segmentation of natural images in breast ultrasound image segmentation. Tuning the contracting part and fixing the expanding part resulted in substantially better results compared to fixing the contracting part and tuning the expanding part. Furthermore, we showed that starting to fine-tune the U-Net from the shallow layers and gradually including more layers will lead to a better performance compared to fine-tuning the network from the deep layers moving back to shallow layers. We did not observe the same results on segmentation of X-ray images, which have different salient features compared to ultrasound, it may therefore be more appropriate to fine-tune the shallow layers rather than deep layers. Shallow layers learn lower level features (including speckle pattern, and probably the noise and artifact properties) which are critical in automatic segmentation in this modality.
Segmentation of multiple organs-at-risk (OARs) is essential for radiation therapy treatment planning and other clinical applications. We developed an Automated deep Learning-based Abdominal Multi-Organ segmentation (ALAMO) framework based on 2D U-net and a densely connected network structure with tailored design in data augmentation and training procedures such as deep connection, auxiliary supervision, and multi-view. The model takes in multi-slice MR images and generates the output of segmentation results. Three-Tesla T1 VIBE (Volumetric Interpolated Breath-hold Examination) images of 102 subjects were collected and used in our study. Ten OARs were studied, including the liver, spleen, pancreas, left/right kidneys, stomach, duodenum, small intestine, spinal cord, and vertebral bodies. Two radiologists manually labeled and obtained the consensus contours as the ground-truth. In the complete cohort of 102, 20 samples were held out for independent testing, and the rest were used for training and validation. The performance was measured using volume overlapping and surface distance. The ALAMO framework generated segmentation labels in good agreement with the manual results. Specifically, among the 10 OARs, 9 achieved high Dice Similarity Coefficients (DSCs) in the range of 0.87-0.96, except for the duodenum with a DSC of 0.80. The inference completes within one minute for a 3D volume of 320x288x180. Overall, the ALAMO model matches the state-of-the-art performance. The proposed ALAMO framework allows for fully automated abdominal MR segmentation with high accuracy and low memory and computation time demands.
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