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Register a new userDeep Implicit Statistical Shape Models for 3D Medical Image Delineation
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Added by
Ashwin Raju
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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3D delineation of anatomical structures is a cardinal goal in medical imaging analysis. Prior to deep learning, statistical shape models that imposed anatomical constraints and produced high quality surfaces were a core technology. Prior to deep learning, statistical shape models that imposed anatomical constraints and produced high quality surfaces were a core technology. Today fully-convolutional networks (FCNs), while dominant, do not offer these capabilities. We present deep implicit statistical shape models (DISSMs), a new approach to delineation that marries the representation power of convolutional neural networks (CNNs) with the robustness of SSMs. DISSMs use a deep implicit surface representation to produce a compact and descriptive shape latent space that permits statistical models of anatomical variance. To reliably fit anatomically plausible shapes to an image, we introduce a novel rigid and non-rigid pose estimation pipeline that is modelled as a Markov decision process(MDP). We outline a training regime that includes inverted episodic training and a deep realization of marginal space learning (MSL). Intra-dataset experiments on the task of pathological liver segmentation demonstrate that DISSMs can perform more robustly than three leading FCN models, including nnU-Net: reducing the mean Hausdorff distance (HD) by 7.7-14.3mm and improving the worst case Dice-Sorensen coefficient (DSC) by 1.2-2.3%. More critically, cross-dataset experiments on a dataset directly reflecting clinical deployment scenarios demonstrate that DISSMs improve the mean DSC and HD by 3.5-5.9% and 12.3-24.5mm, respectively, and the worst-case DSC by 5.4-7.3%. These improvements are over and above any benefits from representing delineations with high-quality surface.
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The goal of this project is to learn a 3D shape representation that enables accurate surface reconstruction, compact storage, efficient computation, consistency for similar shapes, generalization across diverse shape categories, and inference from depth camera observations. Towards this end, we introduce Local Deep Implicit Functions (LDIF), a 3D shape representation that decomposes space into a structured set of learned implicit functions. We provide networks that infer the space decomposition and local deep implicit functions from a 3D mesh or posed depth image. During experiments, we find that it provides 10.3 points higher surface reconstruction accuracy (F-Score) than the state-of-the-art (OccNet), while requiring fewer than 1 percent of the network parameters. Experiments on posed depth image completion and generalization to unseen classes show 15.8 and 17.8 point improvements over the state-of-the-art, while producing a structured 3D representation for each input with consistency across diverse shape collections.
Deep implicit functions (DIFs), as a kind of 3D shape representation, are becoming more and more popular in the 3D vision community due to their compactness and strong representation power. However, unlike polygon mesh-based templates, it remains a challenge to reason dense correspondences or other semantic relationships across shapes represented by DIFs, which limits its applications in texture transfer, shape analysis and so on. To overcome this limitation and also make DIFs more interpretable, we propose Deep Implicit Templates, a new 3D shape representation that supports explicit correspondence reasoning in deep implicit representations. Our key idea is to formulate DIFs as conditional deformations of a template implicit function. To this end, we propose Spatial Warping LSTM, which decomposes the conditional spatial transformation into multiple affine transformations and guarantees generalization capability. Moreover, the training loss is carefully designed in order to achieve high reconstruction accuracy while learning a plausible template with accurate correspondences in an unsupervised manner. Experiments show that our method can not only learn a common implicit template for a collection of shapes, but also establish dense correspondences across all the shapes simultaneously without any supervision.
We introduce Multiresolution Deep Implicit Functions (MDIF), a hierarchical representation that can recover fine geometry detail, while being able to perform global operations such as shape completion. Our model represents a complex 3D shape with a hierarchy of latent grids, which can be decoded into different levels of detail and also achieve better accuracy. For shape completion, we propose latent grid dropout to simulate partial data in the latent space and therefore defer the completing functionality to the decoder side. This along with our multires design significantly improves the shape completion quality under decoder-only latent optimization. To the best of our knowledge, MDIF is the first deep implicit function model that can at the same time (1) represent different levels of detail and allow progressive decoding; (2) support both encoder-decoder inference and decoder-only latent optimization, and fulfill multiple applications; (3) perform detailed decoder-only shape completion. Experiments demonstrate its superior performance against prior art in various 3D reconstruction tasks.
Implicit surface representations, such as signed-distance functions, combined with deep learning have led to impressive models which can represent detailed shapes of objects with arbitrary topology. Since a continuous function is learned, the reconstructions can also be extracted at any arbitrary resolution. However, large datasets such as ShapeNet are required to train such models. In this paper, we present a new mid-level patch-based surface representation. At the level of patches, objects across different categories share similarities, which leads to more generalizable models. We then introduce a novel method to learn this patch-based representation in a canonical space, such that it is as object-agnostic as possible. We show that our representation trained on one category of objects from ShapeNet can also well represent detailed shapes from any other category. In addition, it can be trained using much fewer shapes, compared to existing approaches. We show several applications of our new representation, including shape interpolation and partial point cloud completion. Due to explicit control over positions, orientations and scales of patches, our representation is also more controllable compared to object-level representations, which enables us to deform encoded shapes non-rigidly.
We present imGHUM, the first holistic generative model of 3D human shape and articulated pose, represented as a signed distance function. In contrast to prior work, we model the full human body implicitly as a function zero-level-set and without the use of an explicit template mesh. We propose a novel network architecture and a learning paradigm, which make it possible to learn a detailed implicit generative model of human pose, shape, and semantics, on par with state-of-the-art mesh-based models. Our model features desired detail for human models, such as articulated pose including hand motion and facial expressions, a broad spectrum of shape variations, and can be queried at arbitrary resolutions and spatial locations. Additionally, our model has attached spatial semantics making it straightforward to establish correspondences between different shape instances, thus enabling applications that are difficult to tackle using classical implicit representations. In extensive experiments, we demonstrate the model accuracy and its applicability to current research problems.
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