Deep learning models have demonstrated remarkable success in multi-organ segmentation but typically require large-scale datasets with all organs of interest annotated. However, medical image datasets are often low in sample size and only partially labeled, i.e., only a subset of organs are annotated. Therefore, it is crucial to investigate how to learn a unified model on the available partially labeled datasets to leverage their synergistic potential. In this paper, we systematically investigate the partial-label segmentation problem with theoretical and empirical analyses on the prior techniques. We revisit the problem from a perspective of partial label supervision signals and identify two signals derived from ground truth and one from pseudo labels. We propose a novel two-stage framework termed COSST, which effectively and efficiently integrates comprehensive supervision signals with self-training. Concretely, we first train an initial unified model using two ground truth-based signals and then iteratively incorporate the pseudo label signal to the initial model using self-training. To mitigate performance degradation caused by unreliable pseudo labels, we assess the reliability of pseudo labels via outlier detection in latent space and exclude the most unreliable pseudo labels from each self-training iteration. Extensive experiments are conducted on one public and three private partial-label segmentation tasks over 12 CT datasets. Experimental results show that our proposed COSST achieves significant improvement over the baseline method, i.e., individual networks trained on each partially labeled dataset. Compared to the state-of-the-art partial-label segmentation methods, COSST demonstrates consistent superior performance on various segmentation tasks and with different training data sizes.

Deep learning has been utilized in knowledge-based radiotherapy planning in which a system trained with a set of clinically approved plans is employed to infer a three-dimensional dose map for a given new patient. However, previous deep methods are primarily limited to simple scenarios, e.g., a fixed planning type or a consistent beam angle configuration. This in fact limits the usability of such approaches and makes them not generalizable over a larger set of clinical scenarios. Herein, we propose a novel conditional generative model, Flexible-Cm GAN, utilizing additional information regarding planning types and various beam geometries. A miss-consistency loss is proposed to deal with the challenge of having a limited set of conditions on the input data, e.g., incomplete training samples. To address the challenges of including clinical preferences, we derive a differentiable shift-dose-volume loss to incorporate the well-known dose-volume histogram constraints. During inference, users can flexibly choose a specific planning type and a set of beam angles to meet the clinical requirements. We conduct experiments on an illustrative face dataset to show the motivation of Flexible-Cm GAN and further validate our model's potential clinical values with two radiotherapy datasets. The results demonstrate the superior performance of the proposed method in a practical heterogeneous radiotherapy planning application compared to existing deep learning-based approaches.

The findings of splenomegaly, abnormal enlargement of the spleen, is a non-invasive clinical biomarker for liver and spleen diseases. Automated segmentation methods are essential to efficiently quantify splenomegaly from clinically acquired abdominal magnetic resonance imaging (MRI) scans. However, the task is challenging due to: 1) large anatomical and spatial variations of splenomegaly; 2) large inter- and intra-scan intensity variations on multi-modal MRI; and 3) limited numbers of labeled splenomegaly scans. In this paper, we propose the Splenomegaly Segmentation Network (SS-Net) to introduce the deep convolutional neural network (DCNN) approaches in multi-modal MRI splenomegaly segmentation. Large convolutional kernel layers were used to address the spatial and anatomical variations, while the conditional generative adversarial networks were employed to leverage the segmentation performance of SS-Net in an end-to-end manner. A clinically acquired cohort containing both T1-weighted (T1w) and T2-weighted (T2w) MRI splenomegaly scans was used to train and evaluate the performance of multi-atlas segmentation (MAS), 2D DCNN networks, and a 3-D DCNN network. From the experimental results, the DCNN methods achieved superior performance to the state-of-the-art MAS method. The proposed SS-Net method has achieved the highest median and mean Dice scores among the investigated baseline DCNN methods.

A key limitation of deep convolutional neural networks (DCNN) based image segmentation methods is the lack of generalizability. Manually traced training images are typically required when segmenting organs in a new imaging modality or from distinct disease cohort. The manual efforts can be alleviated if the manually traced images in one imaging modality (e.g., MRI) are able to train a segmentation network for another imaging modality (e.g., CT). In this paper, we propose an end-to-end synthetic segmentation network (SynSeg-Net) to train a segmentation network for a target imaging modality without having manual labels. SynSeg-Net is trained by using (1) unpaired intensity images from source and target modalities, and (2) manual labels only from source modality. SynSeg-Net is enabled by the recent advances of cycle generative adversarial networks (CycleGAN) and DCNN. We evaluate the performance of the SynSeg-Net on two experiments: (1) MRI to CT splenomegaly synthetic segmentation for abdominal images, and (2) CT to MRI total intracranial volume synthetic segmentation (TICV) for brain images. The proposed end-to-end approach achieved superior performance to two stage methods. Moreover, the SynSeg-Net achieved comparable performance to the traditional segmentation network using target modality labels in certain scenarios. The source code of SynSeg-Net is publicly available 2.