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

Intergrated Segmentation and Detection Models for Dentex Challenge 2023

Dental panoramic x-rays are commonly used in dental diagnosing. With the development of deep learning, auto detection of diseases from dental panoramic x-rays can help dentists to diagnose diseases more efficiently.The Dentex Challenge 2023 is a competition for automatic detection of abnormal teeth along with their enumeration ids from dental panoramic x-rays. In this paper, we propose a method integrating segmentation and detection models to detect abnormal teeth as well as obtain their enumeration ids.Our codes are available at https://github.com/xyzlancehe/DentexSegAndDet.

Inferior Alveolar Nerve Segmentation in CBCT images using Connectivity-Based Selective Re-training

Inferior Alveolar Nerve (IAN) canal detection in CBCT is an important step in many dental and maxillofacial surgery applications to prevent irreversible damage to the nerve during the procedure.The ToothFairy2023 Challenge aims to establish a 3D maxillofacial dataset consisting of all sparse labels and partial dense labels, and improve the ability of automatic IAN segmentation. In this work, in order to avoid the negative impact brought by sparse labeling, we transform the mixed supervised problem into a semi-supervised problem. Inspired by self-training via pseudo labeling, we propose a selective re-training framework based on IAN connectivity. Our method is quantitatively evaluated on the ToothFairy verification cases, achieving the dice similarity coefficient (DSC) of 0.7956, and 95\% hausdorff distance (HD95) of 4.4905, and wining the champion in the competition. Code is available at https://github.com/GaryNico517/SSL-IAN-Retraining.

The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT

This paper presents the challenge report for the 2021 Kidney and Kidney Tumor Segmentation Challenge (KiTS21) held in conjunction with the 2021 international conference on Medical Image Computing and Computer Assisted Interventions (MICCAI). KiTS21 is a sequel to its first edition in 2019, and it features a variety of innovations in how the challenge was designed, in addition to a larger dataset. A novel annotation method was used to collect three separate annotations for each region of interest, and these annotations were performed in a fully transparent setting using a web-based annotation tool. Further, the KiTS21 test set was collected from an outside institution, challenging participants to develop methods that generalize well to new populations. Nonetheless, the top-performing teams achieved a significant improvement over the state of the art set in 2019, and this performance is shown to inch ever closer to human-level performance. An in-depth meta-analysis is presented describing which methods were used and how they faired on the leaderboard, as well as the characteristics of which cases generally saw good performance, and which did not. Overall KiTS21 facilitated a significant advancement in the state of the art in kidney tumor segmentation, and provides useful insights that are applicable to the field of semantic segmentation as a whole.

Exploring Visual Prompts for Whole Slide Image Classification with Multiple Instance Learning

Multiple instance learning (MIL) has emerged as a popular method for classifying histopathology whole slide images (WSIs). However, existing approaches typically rely on pre-trained models from large natural image datasets, such as ImageNet, to generate instance features, which can be sub-optimal due to the significant differences between natural images and histopathology images that lead to a domain shift. In this paper, we present a novel, simple yet effective method for learning domain-specific knowledge transformation from pre-trained models to histopathology images. Our approach entails using a prompt component to assist the pre-trained model in discerning differences between the pre-trained dataset and the target histopathology dataset, resulting in improved performance of MIL models. We validate our method on two publicly available datasets, Camelyon16 and TCGA-NSCLC. Extensive experimental results demonstrate the significant performance improvement of our method for different MIL models and backbones. Upon publication of this paper, we will release the source code for our method.

Koos Classification of Vestibular Schwannoma via Image Translation-Based Unsupervised Cross-Modality Domain Adaptation

The Koos grading scale is a classification system for vestibular schwannoma (VS) used to characterize the tumor and its effects on adjacent brain structures. The Koos classification captures many of the characteristics of treatment deci-sions and is often used to determine treatment plans. Although both contrast-enhanced T1 (ceT1) scanning and high-resolution T2 (hrT2) scanning can be used for Koos Classification, hrT2 scanning is gaining interest because of its higher safety and cost-effectiveness. However, in the absence of annotations for hrT2 scans, deep learning methods often inevitably suffer from performance deg-radation due to unsupervised learning. If ceT1 scans and their annotations can be used for unsupervised learning of hrT2 scans, the performance of Koos classifi-cation using unlabeled hrT2 scans will be greatly improved. In this regard, we propose an unsupervised cross-modality domain adaptation method based on im-age translation by transforming annotated ceT1 scans into hrT2 modality and us-ing their annotations to achieve supervised learning of hrT2 modality. Then, the VS and 7 adjacent brain structures related to Koos classification in hrT2 scans were segmented. Finally, handcrafted features are extracted from the segmenta-tion results, and Koos grade is classified using a random forest classifier. The proposed method received rank 1 on the Koos classification task of the Cross-Modality Domain Adaptation (crossMoDA 2022) challenge, with Macro-Averaged Mean Absolute Error (MA-MAE) of 0.2148 for the validation set and 0.26 for the test set.

3D Vessel Segmentation with Limited Guidance of 2D Structure-agnostic Vessel Annotations

Delineating 3D blood vessels is essential for clinical diagnosis and treatment, however, is challenging due to complex structure variations and varied imaging conditions. Supervised deep learning has demonstrated its superior capacity in automatic 3D vessel segmentation. However, the reliance on expensive 3D manual annotations and limited capacity for annotation reuse hinder the clinical applications of supervised models. To avoid the repetitive and laborious annotating and make full use of existing vascular annotations, this paper proposes a novel 3D shape-guided local discrimination model for 3D vascular segmentation under limited guidance from public 2D vessel annotations. The primary hypothesis is that 3D vessels are composed of semantically similar voxels and exhibit tree-shaped morphology. Accordingly, the 3D region discrimination loss is firstly proposed to learn the discriminative representation measuring voxel-wise similarities and cluster semantically consistent voxels to form the candidate 3D vascular segmentation in unlabeled images; secondly, based on the similarity of the tree-shaped morphology between 2D and 3D vessels, the Crop-and-Overlap strategy is presented to generate reference masks from 2D structure-agnostic vessel annotations, which are fit for varied vascular structures, and the adversarial loss is introduced to guide the tree-shaped morphology of 3D vessels; thirdly, the temporal consistency loss is proposed to foster the training stability and keep the model updated smoothly. To further enhance the model's robustness and reliability, the orientation-invariant CNN module and Reliability-Refinement algorithm are presented. Experimental results from the public 3D cerebrovascular and 3D arterial tree datasets demonstrate that our model achieves comparable effectiveness against nine supervised models.

A Multi-Stage Framework for the 2022 Multi-Structure Segmentation for Renal Cancer Treatment

Three-dimensional (3D) kidney parsing on computed tomography angiography (CTA) images is of great clinical significance. Automatic segmentation of kidney, renal tumor, renal vein and renal artery benefits a lot on surgery-based renal cancer treatment. In this paper, we propose a new nnhra-unet network, and use a multi-stage framework which is based on it to segment the multi-structure of kidney and participate in the KiPA2022 challenge.

Fetal Brain Tissue Annotation and Segmentation Challenge Results

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

Unsupervised Local Discrimination for Medical Images

Contrastive representation learning is an effective unsupervised method to alleviate the demand for expensive annotated data in medical image processing. Recent work mainly based on instance-wise discrimination to learn global features, while neglect local details, which limit their application in processing tiny anatomical structures, tissues and lesions. Therefore, we aim to propose a universal local discrmination framework to learn local discriminative features to effectively initialize medical models, meanwhile, we systematacially investigate its practical medical applications. Specifically, based on the common property of intra-modality structure similarity, i.e. similar structures are shared among the same modality images, a systematic local feature learning framework is proposed. Instead of making instance-wise comparisons based on global embedding, our method makes pixel-wise embedding and focuses on measuring similarity among patches and regions. The finer contrastive rule makes the learnt representation more generalized for segmentation tasks and outperform extensive state-of-the-art methods by wining 11 out of all 12 downstream tasks in color fundus and chest X-ray. Furthermore, based on the property of inter-modality shape similarity, i.e. structures may share similar shape although in different medical modalities, we joint across-modality shape prior into region discrimination to realize unsupervised segmentation. It shows the feaibility of segmenting target only based on shape description from other modalities and inner pattern similarity provided by region discrimination. Finally, we enhance the center-sensitive ability of patch discrimination by introducing center-sensitive averaging to realize one-shot landmark localization, this is an effective application for patch discrimination.