Weakly Supervised Lymph Nodes Segmentation Based on Partial Instance Annotations with Pre-trained Dual-branch Network and Pseudo Label Learning

Assessing the presence of potentially malignant lymph nodes aids in estimating cancer progression, and identifying surrounding benign lymph nodes can assist in determining potential metastatic pathways for cancer. For quantitative analysis, automatic segmentation of lymph nodes is crucial. However, due to the labor-intensive and time-consuming manual annotation process required for a large number of lymph nodes, it is more practical to annotate only a subset of the lymph node instances to reduce annotation costs. In this study, we propose a pre-trained Dual-Branch network with Dynamically Mixed Pseudo label (DBDMP) to learn from partial instance annotations for lymph nodes segmentation. To obtain reliable pseudo labels for lymph nodes that are not annotated, we employ a dual-decoder network to generate different outputs that are then dynamically mixed. We integrate the original weak partial annotations with the mixed pseudo labels to supervise the network. To further leverage the extensive amount of unannotated voxels, we apply a self-supervised pre-training strategy to enhance the model's feature extraction capability. Experiments on the mediastinal Lymph Node Quantification (LNQ) dataset demonstrate that our method, compared to directly learning from partial instance annotations, significantly improves the Dice Similarity Coefficient (DSC) from 11.04% to 54.10% and reduces the Average Symmetric Surface Distance (ASSD) from 20.83 $mm$ to 8.72 $mm$. The code is available at https://github.com/WltyBY/LNQ2023_training_code.git

Rethinking Abdominal Organ Segmentation (RAOS) in the clinical scenario: A robustness evaluation benchmark with challenging cases

Deep learning has enabled great strides in abdominal multi-organ segmentation, even surpassing junior oncologists on common cases or organs. However, robustness on corner cases and complex organs remains a challenging open problem for clinical adoption. To investigate model robustness, we collected and annotated the RAOS dataset comprising 413 CT scans ($\sim$80k 2D images, $\sim$8k 3D organ annotations) from 413 patients each with 17 (female) or 19 (male) labelled organs, manually delineated by oncologists. We grouped scans based on clinical information into 1) diagnosis/radiotherapy (317 volumes), 2) partial excision without the whole organ missing (22 volumes), and 3) excision with the whole organ missing (74 volumes). RAOS provides a potential benchmark for evaluating model robustness including organ hallucination. It also includes some organs that can be very hard to access on public datasets like the rectum, colon, intestine, prostate and seminal vesicles. We benchmarked several state-of-the-art methods in these three clinical groups to evaluate performance and robustness. We also assessed cross-generalization between RAOS and three public datasets. This dataset and comprehensive analysis establish a potential baseline for future robustness research: \url{https://github.com/Luoxd1996/RAOS}.

Diversified and Personalized Multi-rater Medical Image Segmentation

Annotation ambiguity due to inherent data uncertainties such as blurred boundaries in medical scans and different observer expertise and preferences has become a major obstacle for training deep-learning based medical image segmentation models. To address it, the common practice is to gather multiple annotations from different experts, leading to the setting of multi-rater medical image segmentation. Existing works aim to either merge different annotations into the "groundtruth" that is often unattainable in numerous medical contexts, or generate diverse results, or produce personalized results corresponding to individual expert raters. Here, we bring up a more ambitious goal for multi-rater medical image segmentation, i.e., obtaining both diversified and personalized results. Specifically, we propose a two-stage framework named D-Persona (first Diversification and then Personalization). In Stage I, we exploit multiple given annotations to train a Probabilistic U-Net model, with a bound-constrained loss to improve the prediction diversity. In this way, a common latent space is constructed in Stage I, where different latent codes denote diversified expert opinions. Then, in Stage II, we design multiple attention-based projection heads to adaptively query the corresponding expert prompts from the shared latent space, and then perform the personalized medical image segmentation. We evaluated the proposed model on our in-house Nasopharyngeal Carcinoma dataset and the public lung nodule dataset (i.e., LIDC-IDRI). Extensive experiments demonstrated our D-Persona can provide diversified and personalized results at the same time, achieving new SOTA performance for multi-rater medical image segmentation. Our code will be released at https://github.com/ycwu1997/D-Persona.

SegRap2023: A Benchmark of Organs-at-Risk and Gross Tumor Volume Segmentation for Radiotherapy Planning of Nasopharyngeal Carcinoma

Radiation therapy is a primary and effective NasoPharyngeal Carcinoma (NPC) treatment strategy. The precise delineation of Gross Tumor Volumes (GTVs) and Organs-At-Risk (OARs) is crucial in radiation treatment, directly impacting patient prognosis. Previously, the delineation of GTVs and OARs was performed by experienced radiation oncologists. Recently, deep learning has achieved promising results in many medical image segmentation tasks. However, for NPC OARs and GTVs segmentation, few public datasets are available for model development and evaluation. To alleviate this problem, the SegRap2023 challenge was organized in conjunction with MICCAI2023 and presented a large-scale benchmark for OAR and GTV segmentation with 400 Computed Tomography (CT) scans from 200 NPC patients, each with a pair of pre-aligned non-contrast and contrast-enhanced CT scans. The challenge's goal was to segment 45 OARs and 2 GTVs from the paired CT scans. In this paper, we detail the challenge and analyze the solutions of all participants. The average Dice similarity coefficient scores for all submissions ranged from 76.68\% to 86.70\%, and 70.42\% to 73.44\% for OARs and GTVs, respectively. We conclude that the segmentation of large-size OARs is well-addressed, and more efforts are needed for GTVs and small-size or thin-structure OARs. The benchmark will remain publicly available here: https://segrap2023.grand-challenge.org

Dual-Reference Source-Free Active Domain Adaptation for Nasopharyngeal Carcinoma Tumor Segmentation across Multiple Hospitals

Nasopharyngeal carcinoma (NPC) is a prevalent and clinically significant malignancy that predominantly impacts the head and neck area. Precise delineation of the Gross Tumor Volume (GTV) plays a pivotal role in ensuring effective radiotherapy for NPC. Despite recent methods that have achieved promising results on GTV segmentation, they are still limited by lacking carefully-annotated data and hard-to-access data from multiple hospitals in clinical practice. Although some unsupervised domain adaptation (UDA) has been proposed to alleviate this problem, unconditionally mapping the distribution distorts the underlying structural information, leading to inferior performance. To address this challenge, we devise a novel Sourece-Free Active Domain Adaptation (SFADA) framework to facilitate domain adaptation for the GTV segmentation task. Specifically, we design a dual reference strategy to select domain-invariant and domain-specific representative samples from a specific target domain for annotation and model fine-tuning without relying on source-domain data. Our approach not only ensures data privacy but also reduces the workload for oncologists as it just requires annotating a few representative samples from the target domain and does not need to access the source data. We collect a large-scale clinical dataset comprising 1057 NPC patients from five hospitals to validate our approach. Experimental results show that our method outperforms the UDA methods and achieves comparable results to the fully supervised upper bound, even with few annotations, highlighting the significant medical utility of our approach. In addition, there is no public dataset about multi-center NPC segmentation, we will release code and dataset for future research.

Scribble-based 3D Multiple Abdominal Organ Segmentation via Triple-branch Multi-dilated Network with Pixel- and Class-wise Consistency

Multi-organ segmentation in abdominal Computed Tomography (CT) images is of great importance for diagnosis of abdominal lesions and subsequent treatment planning. Though deep learning based methods have attained high performance, they rely heavily on large-scale pixel-level annotations that are time-consuming and labor-intensive to obtain. Due to its low dependency on annotation, weakly supervised segmentation has attracted great attention. However, there is still a large performance gap between current weakly-supervised methods and fully supervised learning, leaving room for exploration. In this work, we propose a novel 3D framework with two consistency constraints for scribble-supervised multiple abdominal organ segmentation from CT. Specifically, we employ a Triple-branch multi-Dilated network (TDNet) with one encoder and three decoders using different dilation rates to capture features from different receptive fields that are complementary to each other to generate high-quality soft pseudo labels. For more stable unsupervised learning, we use voxel-wise uncertainty to rectify the soft pseudo labels and then supervise the outputs of each decoder. To further regularize the network, class relationship information is exploited by encouraging the generated class affinity matrices to be consistent across different decoders under multi-view projection. Experiments on the public WORD dataset show that our method outperforms five existing scribble-supervised methods.

CDDSA: Contrastive Domain Disentanglement and Style Augmentation for Generalizable Medical Image Segmentation

Generalization to previously unseen images with potential domain shifts and different styles is essential for clinically applicable medical image segmentation, and the ability to disentangle domain-specific and domain-invariant features is key for achieving Domain Generalization (DG). However, existing DG methods can hardly achieve effective disentanglement to get high generalizability. To deal with this problem, we propose an efficient Contrastive Domain Disentanglement and Style Augmentation (CDDSA) framework for generalizable medical image segmentation. First, a disentangle network is proposed to decompose an image into a domain-invariant anatomical representation and a domain-specific style code, where the former is sent to a segmentation model that is not affected by the domain shift, and the disentangle network is regularized by a decoder that combines the anatomical and style codes to reconstruct the input image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Thirdly, to further improve generalizability, we propose a style augmentation method based on the disentanglement representation to synthesize images in various unseen styles with shared anatomical structures. Our method was validated on a public multi-site fundus image dataset for optic cup and disc segmentation and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset for nasopharynx Gross Tumor Volume (GTVnx) segmentation. Experimental results showed that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in domain-generalizable segmentation.

Scribble-Supervised Medical Image Segmentation via Dual-Branch Network and Dynamically Mixed Pseudo Labels Supervision

Medical image segmentation plays an irreplaceable role in computer-assisted diagnosis, treatment planning, and following-up. Collecting and annotating a large-scale dataset is crucial to training a powerful segmentation model, but producing high-quality segmentation masks is an expensive and time-consuming procedure. Recently, weakly-supervised learning that uses sparse annotations (points, scribbles, bounding boxes) for network training has achieved encouraging performance and shown the potential for annotation cost reduction. However, due to the limited supervision signal of sparse annotations, it is still challenging to employ them for networks training directly. In this work, we propose a simple yet efficient scribble-supervised image segmentation method and apply it to cardiac MRI segmentation. Specifically, we employ a dual-branch network with one encoder and two slightly different decoders for image segmentation and dynamically mix the two decoders' predictions to generate pseudo labels for auxiliary supervision. By combining the scribble supervision and auxiliary pseudo labels supervision, the dual-branch network can efficiently learn from scribble annotations end-to-end. Experiments on the public ACDC dataset show that our method performs better than current scribble-supervised segmentation methods and also outperforms several semi-supervised segmentation methods.

WORD: Revisiting Organs Segmentation in the Whole Abdominal Region

Whole abdominal organs segmentation plays an important role in abdomen lesion diagnosis, radiotherapy planning, and follow-up. However, delineating all abdominal organs by oncologists manually is time-consuming and very expensive. Recently, deep learning-based medical image segmentation has shown the potential to reduce manual delineation efforts, but it still requires a large-scale fine annotated dataset for training. Although many efforts in this task, there are still few large image datasets covering the whole abdomen region with accurate and detailed annotations for the whole abdominal organ segmentation. In this work, we establish a large-scale \textit{W}hole abdominal \textit{OR}gans \textit{D}ataset (\textit{WORD}) for algorithms research and clinical applications development. This dataset contains 150 abdominal CT volumes (30495 slices) and each volume has 16 organs with fine pixel-level annotations and scribble-based sparse annotation, which may be the largest dataset with whole abdominal organs annotation. Several state-of-the-art segmentation methods are evaluated on this dataset. And, we also invited clinical oncologists to revise the model predictions to measure the gap between the deep learning method and real oncologists. We further introduce and evaluate a new scribble-based weakly supervised segmentation on this dataset. The work provided a new benchmark for the abdominal multi-organ segmentation task and these experiments can serve as the baseline for future research and clinical application development. The codebase and dataset will be released at: https://github.com/HiLab-git/WORD

Semi-supervised Segmentation via Uncertainty Rectified Pyramid Consistency and Its Application to Gross Target Volume of Nasopharyngeal Carcinoma

Gross Target Volume (GTV) segmentation plays an irreplaceable role in radiotherapy planning for Nasopharyngeal Carcinoma (NPC). Despite that convolutional neural networks (CNN) have achieved good performance for this task, they rely on a large set of labeled images for training, which is expensive and time-consuming to acquire. Recently, semi-supervised methods that learn from a small set of labeled images with a large set of unlabeled images have shown potential for dealing with this problem, but it is still challenging to train a high-performance model with the limited number of labeled data. In this paper, we propose a novel framework with Uncertainty Rectified Pyramid Consistency (URPC) regularization for semi-supervised NPC GTV segmentation. Concretely, we extend a backbone segmentation network to produce pyramid predictions at different scales, the pyramid predictions network (PPNet) was supervised by the ground truth of labeled images and a multi-scale consistency loss for unlabeled images, motivated by the fact that prediction at different scales for the same input should be similar and consistent. However, due to the different resolution of these predictions, encouraging them to be consistent at each pixel directly is not robust and may bring much noise and lead to a performance drop. To deal with this dilemma, we further design a novel uncertainty rectifying module to enable the framework to gradually learn from meaningful and reliable consensual regions at different scales. Extensive experiments on our collected NPC dataset with 258 volumes show that our method can largely improve performance by incorporating the unlabeled data, and this framework achieves a promising result compared with existing semi-supervised methods, which achieves 81.22% of mean DSC and 1.88 voxels of mean ASD on the test set, where the only 20% of the training set were annotated.