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Rib fractures are a common and potentially severe injury that can be challenging and labor-intensive to detect in CT scans. While there have been efforts to address this field, the lack of large-scale annotated datasets and evaluation benchmarks has hindered the development and validation of deep learning algorithms. To address this issue, the RibFrac Challenge was introduced, providing a benchmark dataset of over 5,000 rib fractures from 660 CT scans, with voxel-level instance mask annotations and diagnosis labels for four clinical categories (buckle, nondisplaced, displaced, or segmental). The challenge includes two tracks: a detection (instance segmentation) track evaluated by an FROC-style metric and a classification track evaluated by an F1-style metric. During the MICCAI 2020 challenge period, 243 results were evaluated, and seven teams were invited to participate in the challenge summary. The analysis revealed that several top rib fracture detection solutions achieved performance comparable or even better than human experts. Nevertheless, the current rib fracture classification solutions are hardly clinically applicable, which can be an interesting area in the future. As an active benchmark and research resource, the data and online evaluation of the RibFrac Challenge are available at the challenge website. As an independent contribution, we have also extended our previous internal baseline by incorporating recent advancements in large-scale pretrained networks and point-based rib segmentation techniques. The resulting FracNet+ demonstrates competitive performance in rib fracture detection, which lays a foundation for further research and development in AI-assisted rib fracture detection and diagnosis., Comment: Challenge paper for MICCAI RibFrac Challenge (https://ribfrac.grand-challenge.org/)

Automatic rib labeling and anatomical centerline extraction are common prerequisites for various clinical applications. Prior studies either use in-house datasets that are inaccessible to communities, or focus on rib segmentation that neglects the clinical significance of rib labeling. To address these issues, we extend our prior dataset (RibSeg) on the binary rib segmentation task to a comprehensive benchmark, named RibSeg v2, with 660 CT scans (15,466 individual ribs in total) and annotations manually inspected by experts for rib labeling and anatomical centerline extraction. Based on the RibSeg v2, we develop a pipeline including deep learning-based methods for rib labeling, and a skeletonization-based method for centerline extraction. To improve computational efficiency, we propose a sparse point cloud representation of CT scans and compare it with standard dense voxel grids. Moreover, we design and analyze evaluation metrics to address the key challenges of each task. Our dataset, code, and model are available online to facilitate open research at https://github.com/M3DV/RibSeg, Comment: 10 pages, 6 figures, journal

The human annotations are imperfect, especially when produced by junior practitioners. Multi-expert consensus is usually regarded as golden standard, while this annotation protocol is too expensive to implement in many real-world projects. In this study, we propose a method to refine human annotation, named Neural Annotation Refinement (NeAR). It is based on a learnable implicit function, which decodes a latent vector into represented shape. By integrating the appearance as an input of implicit functions, the appearance-aware NeAR fixes the annotation artefacts. Our method is demonstrated on the application of adrenal gland analysis. We first show that the NeAR can repair distorted golden standards on a public adrenal gland segmentation dataset. Besides, we develop a new Adrenal gLand ANalysis (ALAN) dataset with the proposed NeAR, where each case consists of a 3D shape of adrenal gland and its diagnosis label (normal vs. abnormal) assigned by experts. We show that models trained on the shapes repaired by the NeAR can diagnose adrenal glands better than the original ones. The ALAN dataset will be open-source, with 1,584 shapes for adrenal gland diagnosis, which serves as a new benchmark for medical shape analysis. Code and dataset are available at https://github.com/M3DV/NeAR., Comment: MICCAI 2022

Projection map (PM) from optical coherence tomography (OCT) B-scan is an important tool to diagnose retinal diseases, which typically requires retinal layer segmentation. In this study, we present a novel end-to-end framework to predict PMs from B-scans. Instead of segmenting retinal layers explicitly, we represent them implicitly as predicted coordinates. By pixel interpolation on uniformly sampled coordinates between retinal layers, the corresponding PMs could be easily obtained with pooling. Notably, all the operators are differentiable; therefore, this Differentiable Projection Module (DPM) enables end-to-end training with the ground truth of PMs rather than retinal layer segmentation. Our framework produces high-quality PMs, significantly outperforming baselines, including a vanilla CNN without DPM and an optimization-based DPM without a deep prior. Furthermore, the proposed DPM, as a novel neural representation of areas/volumes between curves/surfaces, could be of independent interest for geometric deep learning., Comment: ISBI2022

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/., Comment: The data and code are publicly available at https://medmnist.com/. arXiv admin note: text overlap with arXiv:2010.14925

The style-based GAN (StyleGAN) architecture achieved state-of-the-art results for generating high-quality images, but it lacks explicit and precise control over camera poses. The recently proposed NeRF-based GANs made great progress towards 3D-aware generators, but they are unable to generate high-quality images yet. This paper presents CIPS-3D, a style-based, 3D-aware generator that is composed of a shallow NeRF network and a deep implicit neural representation (INR) network. The generator synthesizes each pixel value independently without any spatial convolution or upsampling operation. In addition, we diagnose the problem of mirror symmetry that implies a suboptimal solution and solve it by introducing an auxiliary discriminator. Trained on raw, single-view images, CIPS-3D sets new records for 3D-aware image synthesis with an impressive FID of 6.97 for images at the $256\times256$ resolution on FFHQ. We also demonstrate several interesting directions for CIPS-3D such as transfer learning and 3D-aware face stylization. The synthesis results are best viewed as videos, so we recommend the readers to check our github project at https://github.com/PeterouZh/CIPS-3D, Comment: 3D-aware GANs based on NeRF, https://github.com/PeterouZh/CIPS-3D

Modeling 3D context is essential for high-performance 3D medical image analysis. Although 2D networks benefit from large-scale 2D supervised pretraining, it is weak in capturing 3D context. 3D networks are strong in 3D context yet lack supervised pretraining. As an emerging technique, \emph{3D context fusion operator}, which enables conversion from 2D pretrained networks, leverages the advantages of both and has achieved great success. Existing 3D context fusion operators are designed to be spatially symmetric, i.e., performing identical operations on each 2D slice like convolutions. However, these operators are not truly equivariant to translation, especially when only a few 3D slices are used as inputs. In this paper, we propose a novel asymmetric 3D context fusion operator (A3D), which uses different weights to fuse 3D context from different 2D slices. Notably, A3D is NOT translation-equivariant while it significantly outperforms existing symmetric context fusion operators without introducing large computational overhead. We validate the effectiveness of the proposed method by extensive experiments on DeepLesion benchmark, a large-scale public dataset for universal lesion detection from computed tomography (CT). The proposed A3D consistently outperforms symmetric context fusion operators by considerable margins, and establishes a new \emph{state of the art} on DeepLesion. To facilitate open research, our code and model in PyTorch are available at https://github.com/M3DV/AlignShift., Comment: MICCAI 2021. The code and model are available at https://github.com/M3DV/AlignShift

Manual rib inspections in computed tomography (CT) scans are clinically critical but labor-intensive, as 24 ribs are typically elongated and oblique in 3D volumes. Automatic rib segmentation methods can speed up the process through rib measurement and visualization. However, prior arts mostly use in-house labeled datasets that are publicly unavailable and work on dense 3D volumes that are computationally inefficient. To address these issues, we develop a labeled rib segmentation benchmark, named \emph{RibSeg}, including 490 CT scans (11,719 individual ribs) from a public dataset. For ground truth generation, we used existing morphology-based algorithms and manually refined its results. Then, considering the sparsity of ribs in 3D volumes, we thresholded and sampled sparse voxels from the input and designed a point cloud-based baseline method for rib segmentation. The proposed method achieves state-of-the-art segmentation performance (Dice~$\approx95\%$) with significant efficiency ($10\sim40\times$ faster than prior arts). The RibSeg dataset, code, and model in PyTorch are available at https://github.com/M3DV/RibSeg., Comment: MICCAI 2021. The dataset, code, and model are available at https://github.com/M3DV/RibSeg

Diagnosis of pulmonary lesions from computed tomography (CT) is important but challenging for clinical decision making in lung cancer related diseases. Deep learning has achieved great success in computer aided diagnosis (CADx) area for lung cancer, whereas it suffers from label ambiguity due to the difficulty in the radiological diagnosis. Considering that invasive pathological analysis serves as the clinical golden standard of lung cancer diagnosis, in this study, we solve the label ambiguity issue via a large-scale radio-pathomics dataset containing 5,134 radiological CT images with pathologically confirmed labels, including cancers (e.g., invasive/non-invasive adenocarcinoma, squamous carcinoma) and non-cancer diseases (e.g., tuberculosis, hamartoma). This retrospective dataset, named Pulmonary-RadPath, enables development and validation of accurate deep learning systems to predict invasive pathological labels with a non-invasive procedure, i.e., radiological CT scans. A three-level hierarchical classification system for pulmonary lesions is developed, which covers most diseases in cancer-related diagnosis. We explore several techniques for hierarchical classification on this dataset, and propose a Leaky Dense Hierarchy approach with proven effectiveness in experiments. Our study significantly outperforms prior arts in terms of data scales (6x larger), disease comprehensiveness and hierarchies. The promising results suggest the potentials to facilitate precision medicine., Comment: MICCAI 2020 (Early Accepted)

Diagnosis and treatment of multiple pulmonary nodules are clinically important but challenging. Prior studies on nodule characterization use solitary-nodule approaches on multiple nodular patients, which ignores the relations between nodules. In this study, we propose a multiple instance learning (MIL) approach and empirically prove the benefit to learn the relations between multiple nodules. By treating the multiple nodules from a same patient as a whole, critical relational information between solitary-nodule voxels is extracted. To our knowledge, it is the first study to learn the relations between multiple pulmonary nodules. Inspired by recent advances in natural language processing (NLP) domain, we introduce a self-attention transformer equipped with 3D CNN, named {NoduleSAT}, to replace typical pooling-based aggregation in multiple instance learning. Extensive experiments on lung nodule false positive reduction on LUNA16 database, and malignancy classification on LIDC-IDRI database, validate the effectiveness of the proposed method., Comment: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI 2020)

There have been considerable debates over 2D and 3D representation learning on 3D medical images. 2D approaches could benefit from large-scale 2D pretraining, whereas they are generally weak in capturing large 3D contexts. 3D approaches are natively strong in 3D contexts, however few publicly available 3D medical dataset is large and diverse enough for universal 3D pretraining. Even for hybrid (2D + 3D) approaches, the intrinsic disadvantages within the 2D / 3D parts still exist. In this study, we bridge the gap between 2D and 3D convolutions by reinventing the 2D convolutions. We propose ACS (axial-coronal-sagittal) convolutions to perform natively 3D representation learning, while utilizing the pretrained weights on 2D datasets. In ACS convolutions, 2D convolution kernels are split by channel into three parts, and convoluted separately on the three views (axial, coronal and sagittal) of 3D representations. Theoretically, ANY 2D CNN (ResNet, DenseNet, or DeepLab) is able to be converted into a 3D ACS CNN, with pretrained weight of a same parameter size. Extensive experiments on several medical benchmarks (including classification, segmentation and detection tasks) validate the consistent superiority of the pretrained ACS CNNs, over the 2D / 3D CNN counterparts with / without pretraining. Even without pretraining, the ACS convolution can be used as a plug-and-play replacement of standard 3D convolution, with smaller model size and less computation., Comment: IEEE Journal of Biomedical and Health Informatics (IEEE JBHI). Code is available at https://github.com/m3dv/ACSConv

In this work, we use facial landmarks to make the deformation for facial images more authentic. The deformation includes the expansion of eyes and the shrinking of noses, mouths, and cheeks. An advanced 106-point facial landmark detector is utilized to provide control points for deformation. Bilinear interpolation is used in the expansion and Moving Least Squares methods (MLS) including Affine Deformation, Similarity Deformation and Rigid Deformation are used in the shrinking. We compare the running time as well as the quality of deformed images using different MLS methods. The experimental results show that the Rigid Deformation which can keep other parts of the images unchanged performs better even if it takes the longest time.

Radiomics analysis has achieved great success in recent years. However, conventional Radiomics analysis suffers from insufficiently expressive hand-crafted features. Recently, emerging deep learning techniques, e.g., convolutional neural networks (CNNs), dominate recent research in Computer-Aided Diagnosis (CADx). Unfortunately, as black-box predictors, we argue that CNNs are "diagnosing" voxels (or pixels), rather than lesions; in other words, visual saliency from a trained CNN is not necessarily concentrated on the lesions. On the other hand, classification in clinical applications suffers from inherent ambiguities: radiologists may produce diverse diagnosis on challenging cases. To this end, we propose a controllable and explainable {\em Probabilistic Radiomics} framework, by combining the Radiomics analysis and probabilistic deep learning. In our framework, 3D CNN feature is extracted upon lesion region only, then encoded into lesion representation, by a controllable Non-local Shape Analysis Module (NSAM) based on self-attention. Inspired from variational auto-encoders (VAEs), an Ambiguity PriorNet is used to approximate the ambiguity distribution over human experts. The final diagnosis is obtained by combining the ambiguity prior sample and lesion representation, and the whole network named $DenseSharp^{+}$ is end-to-end trainable. We apply the proposed method on lung nodule diagnosis on LIDC-IDRI database to validate its effectiveness., Comment: MICCAI 2019 (early accept), with supplementary materials