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We present Hybrid-CSR, a geometric deep-learning model that combines explicit and implicit shape representations for cortical surface reconstruction. Specifically, Hybrid-CSR begins with explicit deformations of template meshes to obtain coarsely reconstructed cortical surfaces, based on which the oriented point clouds are estimated for the subsequent differentiable poisson surface reconstruction. By doing so, our method unifies explicit (oriented point clouds) and implicit (indicator function) cortical surface reconstruction. Compared to explicit representation-based methods, our hybrid approach is more friendly to capture detailed structures, and when compared with implicit representation-based methods, our method can be topology aware because of end-to-end training with a mesh-based deformation module. In order to address topology defects, we propose a new topology correction pipeline that relies on optimization-based diffeomorphic surface registration. Experimental results on three brain datasets show that our approach surpasses existing implicit and explicit cortical surface reconstruction methods in numeric metrics in terms of accuracy, regularity, and consistency.

Acquiring and annotating sufficient labeled data is crucial in developing accurate and robust learning-based models, but obtaining such data can be challenging in many medical image segmentation tasks. One promising solution is to synthesize realistic data with ground-truth mask annotations. However, no prior studies have explored generating complete 3D volumetric images with masks. In this paper, we present MedGen3D, a deep generative framework that can generate paired 3D medical images and masks. First, we represent the 3D medical data as 2D sequences and propose the Multi-Condition Diffusion Probabilistic Model (MC-DPM) to generate multi-label mask sequences adhering to anatomical geometry. Then, we use an image sequence generator and semantic diffusion refiner conditioned on the generated mask sequences to produce realistic 3D medical images that align with the generated masks. Our proposed framework guarantees accurate alignment between synthetic images and segmentation maps. Experiments on 3D thoracic CT and brain MRI datasets show that our synthetic data is both diverse and faithful to the original data, and demonstrate the benefits for downstream segmentation tasks. We anticipate that MedGen3D's ability to synthesize paired 3D medical images and masks will prove valuable in training deep learning models for medical imaging tasks., Accepted by MICCAI 2023. Project Page: https://krishan999.github.io/MedGen3D/

Recent advancements in self-supervised learning have demonstrated that effective visual representations can be learned from unlabeled images. This has led to increased interest in applying self-supervised learning to the medical domain, where unlabeled images are abundant and labeled images are difficult to obtain. However, most self-supervised learning approaches are modeled as image level discriminative or generative proxy tasks, which may not capture the finer level representations necessary for dense prediction tasks like multi-organ segmentation. In this paper, we propose a novel contrastive learning framework that integrates Localized Region Contrast (LRC) to enhance existing self-supervised pre-training methods for medical image segmentation. Our approach involves identifying Super-pixels by Felzenszwalb's algorithm and performing local contrastive learning using a novel contrastive sampling loss. Through extensive experiments on three multi-organ segmentation datasets, we demonstrate that integrating LRC to an existing self-supervised method in a limited annotation setting significantly improves segmentation performance. Moreover, we show that LRC can also be applied to fully-supervised pre-training methods to further boost performance.

Image registration is an essential step in many medical image analysis tasks. Traditional methods for image registration are primarily optimization-driven, finding the optimal deformations that maximize the similarity between two images. Recent learning-based methods, trained to directly predict transformations between two images, run much faster, but suffer from performance deficiencies due to model generalization and the inefficiency in handling individual image specific deformations. Here we present a new neural net based image registration framework, called NIR (Neural Image Registration), which is based on optimization but utilizes deep neural nets to model deformations between image pairs. NIR represents the transformation between two images with a continuous function implemented via neural fields, receiving a 3D coordinate as input and outputting the corresponding deformation vector. NIR provides two ways of generating deformation field: directly output a displacement vector field for general deformable registration, or output a velocity vector field and integrate the velocity field to derive the deformation field for diffeomorphic image registration. The optimal registration is discovered by updating the parameters of the neural field via stochastic gradient descent. We describe several design choices that facilitate model optimization, including coordinate encoding, sinusoidal activation, coordinate sampling, and intensity sampling. Experiments on two 3D MR brain scan datasets demonstrate that NIR yields state-of-the-art performance in terms of both registration accuracy and regularity, while running significantly faster than traditional optimization-based methods.

Deep Implicit Functions (DIFs) represent 3D geometry with continuous signed distance functions learned through deep neural nets. Recently DIFs-based methods have been proposed to handle shape reconstruction and dense point correspondences simultaneously, capturing semantic relationships across shapes of the same class by learning a DIFs-modeled shape template. These methods provide great flexibility and accuracy in reconstructing 3D shapes and inferring correspondences. However, the point correspondences built from these methods do not intrinsically preserve the topology of the shapes, unlike mesh-based template matching methods. This limits their applications on 3D geometries where underlying topological structures exist and matter, such as anatomical structures in medical images. In this paper, we propose a new model called Neural Diffeomorphic Flow (NDF) to learn deep implicit shape templates, representing shapes as conditional diffeomorphic deformations of templates, intrinsically preserving shape topologies. The diffeomorphic deformation is realized by an auto-decoder consisting of Neural Ordinary Differential Equation (NODE) blocks that progressively map shapes to implicit templates. We conduct extensive experiments on several medical image organ segmentation datasets to evaluate the effectiveness of NDF on reconstructing and aligning shapes. NDF achieves consistently state-of-the-art organ shape reconstruction and registration results in both accuracy and quality. The source code is publicly available at https://github.com/Siwensun/Neural_Diffeomorphic_Flow--NDF.

Recently, the vision transformer and its variants have played an increasingly important role in both monocular and multi-view human pose estimation. Considering image patches as tokens, transformers can model the global dependencies within the entire image or across images from other views. However, global attention is computationally expensive. As a consequence, it is difficult to scale up these transformer-based methods to high-resolution features and many views. In this paper, we propose the token-Pruned Pose Transformer (PPT) for 2D human pose estimation, which can locate a rough human mask and performs self-attention only within selected tokens. Furthermore, we extend our PPT to multi-view human pose estimation. Built upon PPT, we propose a new cross-view fusion strategy, called human area fusion, which considers all human foreground pixels as corresponding candidates. Experimental results on COCO and MPII demonstrate that our PPT can match the accuracy of previous pose transformer methods while reducing the computation. Moreover, experiments on Human 3.6M and Ski-Pose demonstrate that our Multi-view PPT can efficiently fuse cues from multiple views and achieve new state-of-the-art results., Comment: ECCV 2022. Code is available at https://github.com/HowieMa/PPT

Reconstructing 3D hand meshes from monocular RGB images has attracted increasing amount of attention due to its enormous potential applications in the field of AR/VR. Most state-of-the-art methods attempt to tackle this task in an anonymous manner. Specifically, the identity of the subject is ignored even though it is practically available in real applications where the user is unchanged in a continuous recording session. In this paper, we propose an identity-aware hand mesh estimation model, which can incorporate the identity information represented by the intrinsic shape parameters of the subject. We demonstrate the importance of the identity information by comparing the proposed identity-aware model to a baseline which treats subject anonymously. Furthermore, to handle the use case where the test subject is unseen, we propose a novel personalization pipeline to calibrate the intrinsic shape parameters using only a few unlabeled RGB images of the subject. Experiments on two large scale public datasets validate the state-of-the-art performance of our proposed method., Comment: ECCV 2022. Github https://github.com/deyingk/PersonalizedHandMeshEstimation

Estimating the 2D human poses in each view is typically the first step in calibrated multi-view 3D pose estimation. But the performance of 2D pose detectors suffers from challenging situations such as occlusions and oblique viewing angles. To address these challenges, previous works derive point-to-point correspondences between different views from epipolar geometry and utilize the correspondences to merge prediction heatmaps or feature representations. Instead of post-prediction merge/calibration, here we introduce a transformer framework for multi-view 3D pose estimation, aiming at directly improving individual 2D predictors by integrating information from different views. Inspired by previous multi-modal transformers, we design a unified transformer architecture, named TransFusion, to fuse cues from both current views and neighboring views. Moreover, we propose the concept of epipolar field to encode 3D positional information into the transformer model. The 3D position encoding guided by the epipolar field provides an efficient way of encoding correspondences between pixels of different views. Experiments on Human 3.6M and Ski-Pose show that our method is more efficient and has consistent improvements compared to other fusion methods. Specifically, we achieve 25.8 mm MPJPE on Human 3.6M with only 5M parameters on 256 x 256 resolution., BMVC 2021. Code is available at: https://github.com/HowieMa/TransFusion-Pose