Miaomiao Zhang

Jian Wang, Miaomiao Zhang

Deformable shapes provide important and complex geometric features of objects presented in images. However, such information is oftentimes missing or underutilized as implicit knowledge in many image analysis tasks. This paper presents Geo-SIC, the first deep learning model to learn deformable shapes in a deformation space for an improved performance of image classification. We introduce a newly designed framework that (i) simultaneously derives features from both image and latent shape spaces with large intra-class variations; and (ii) gains increased model interpretability by allowing direct access to the underlying geometric features of image data. In particular, we develop a boosted classification network, equipped with an unsupervised learning of geometric shape representations characterized by diffeomorphic transformations within each class. In contrast to previous approaches using pre-extracted shapes, our model provides a more fundamental approach by naturally learning the most relevant shape features jointly with an image classifier. We demonstrate the effectiveness of our method on both simulated 2D images and real 3D brain magnetic resonance (MR) images. Experimental results show that our model substantially improves the image classification accuracy with an additional benefit of increased model interpretability. Our code is publicly available at https://github.com/jw4hv/Geo-SIC

Jian Wang, Jiarui Xing, Jason Druzgal et al.

This paper presents a novel predictive model, MetaMorph, for metamorphic registration of images with appearance changes (i.e., caused by brain tumors). In contrast to previous learning-based registration methods that have little or no control over appearance-changes, our model introduces a new regularization that can effectively suppress the negative effects of appearance changing areas. In particular, we develop a piecewise regularization on the tangent space of diffeomorphic transformations (also known as initial velocity fields) via learned segmentation maps of abnormal regions. The geometric transformation and appearance changes are treated as joint tasks that are mutually beneficial. Our model MetaMorph is more robust and accurate when searching for an optimal registration solution under the guidance of segmentation, which in turn improves the segmentation performance by providing appropriately augmented training labels. We validate MetaMorph on real 3D human brain tumor magnetic resonance imaging (MRI) scans. Experimental results show that our model outperforms the state-of-the-art learning-based registration models. The proposed MetaMorph has great potential in various image-guided clinical interventions, e.g., real-time image-guided navigation systems for tumor removal surgery.

Nian Wu, Jiarui Xing, Miaomiao Zhang

This paper presents a novel approach, termed {\em Temporal Latent Residual Network (TLRN)}, to predict a sequence of deformation fields in time-series image registration. The challenge of registering time-series images often lies in the occurrence of large motions, especially when images differ significantly from a reference (e.g., the start of a cardiac cycle compared to the peak stretching phase). To achieve accurate and robust registration results, we leverage the nature of motion continuity and exploit the temporal smoothness in consecutive image frames. Our proposed TLRN highlights a temporal residual network with residual blocks carefully designed in latent deformation spaces, which are parameterized by time-sequential initial velocity fields. We treat a sequence of residual blocks over time as a dynamic training system, where each block is designed to learn the residual function between desired deformation features and current input accumulated from previous time frames. We validate the effectivenss of TLRN on both synthetic data and real-world cine cardiac magnetic resonance (CMR) image videos. Our experimental results shows that TLRN is able to achieve substantially improved registration accuracy compared to the state-of-the-art. Our code is publicly available at https://github.com/nellie689/TLRN.

Farhana Hossain Swarnali, Miaomiao Zhang, Tonmoy Hossain

Modeling group actions on latent representations enables controllable transformations of high-dimensional image data. Prior works applying group-theoretic priors or modeling transformations typically operate in the high-dimensional data space, where group actions apply uniformly across the entire input, making it difficult to disentangle the subspace that varies under transformations. While latent-space methods offer greater flexibility, they still require manual partitioning of latent variables into equivariant and invariant subspaces, limiting the ability to robustly learn and operate group actions within the representation space. To address this, we introduce a novel end-to-end framework that for the first time learns group actions on latent image manifolds, automatically discovering transformation-relevant structures without manual intervention. Our method uses learnable binary masks with straight-through estimation to dynamically partition latent representations into transformation-sensitive and invariant components. We formulate this within a unified optimization framework that jointly learns latent disentanglement and group transformation mappings. The framework can be seamlessly integrated with any standard encoder-decoder architecture. We validate our approach on five 2D/3D image datasets, demonstrating its ability to automatically learn disentangled latent factors for group actions in diverse data, while downstream classification tasks confirm the effectiveness of the learned representations. Our code is publicly available at https://github.com/farhanaswarnali/Learning-Group-Actions-In-Disentangled-Latent-Image-Representations .

Nivetha Jayakumar, Tonmoy Hossain, Miaomiao Zhang

3D image reconstruction from a limited number of 2D images has been a long-standing challenge in computer vision and image analysis. While deep learning-based approaches have achieved impressive performance in this area, existing deep networks often fail to effectively utilize the shape structures of objects presented in images. As a result, the topology of reconstructed objects may not be well preserved, leading to the presence of artifacts such as discontinuities, holes, or mismatched connections between different parts. In this paper, we propose a shape-aware network based on diffusion models for 3D image reconstruction, named SADIR, to address these issues. In contrast to previous methods that primarily rely on spatial correlations of image intensities for 3D reconstruction, our model leverages shape priors learned from the training data to guide the reconstruction process. To achieve this, we develop a joint learning network that simultaneously learns a mean shape under deformation models. Each reconstructed image is then considered as a deformed variant of the mean shape. We validate our model, SADIR, on both brain and cardiac magnetic resonance images (MRIs). Experimental results show that our method outperforms the baselines with lower reconstruction error and better preservation of the shape structure of objects within the images.

Jian Wang, Miaomiao Zhang

This paper presents a novel hierarchical Bayesian model for unbiased atlas building with subject-specific regularizations of image registration. We develop an atlas construction process that automatically selects parameters to control the smoothness of diffeomorphic transformation according to individual image data. To achieve this, we introduce a hierarchical prior distribution on regularization parameters that allows multiple penalties on images with various degrees of geometric transformations. We then treat the regularization parameters as latent variables and integrate them out from the model by using the Monte Carlo Expectation Maximization (MCEM) algorithm. Another advantage of our algorithm is that it eliminates the need for manual parameter tuning, which can be tedious and infeasible. We demonstrate the effectiveness of our model on 3D brain MR images. Experimental results show that our model provides a sharper atlas compared to the current atlas building algorithms with single-penalty regularizations. Our code is publicly available at https://github.com/jw4hv/HierarchicalBayesianAtlasBuild.

Jian Wang, Miaomiao Zhang

This paper presents DeepFLASH, a novel network with efficient training and inference for learning-based medical image registration. In contrast to existing approaches that learn spatial transformations from training data in the high dimensional imaging space, we develop a new registration network entirely in a low dimensional bandlimited space. This dramatically reduces the computational cost and memory footprint of an expensive training and inference. To achieve this goal, we first introduce complex-valued operations and representations of neural architectures that provide key components for learning-based registration models. We then construct an explicit loss function of transformation fields fully characterized in a bandlimited space with much fewer parameterizations. Experimental results show that our method is significantly faster than the state-of-the-art deep learning based image registration methods, while producing equally accurate alignment. We demonstrate our algorithm in two different applications of image registration: 2D synthetic data and 3D real brain magnetic resonance (MR) images. Our code is available at https://github.com/jw4hv/deepflash.

Nian Wu, Jian Wang, Miaomiao Zhang et al.

Registration-based atlas building often poses computational challenges in high-dimensional image spaces. In this paper, we introduce a novel hybrid atlas building algorithm that fast estimates atlas from large-scale image datasets with much reduced computational cost. In contrast to previous approaches that iteratively perform registration tasks between an estimated atlas and individual images, we propose to use learned priors of registration from pre-trained neural networks. This newly developed hybrid framework features several advantages of (i) providing an efficient way of atlas building without losing the quality of results, and (ii) offering flexibility in utilizing a wide variety of deep learning based registration methods. We demonstrate the effectiveness of this proposed model on 3D brain magnetic resonance imaging (MRI) scans.

Jian Wang, Miaomiao Zhang

This paper presents a predictive model for estimating regularization parameters of diffeomorphic image registration. We introduce a novel framework that automatically determines the parameters controlling the smoothness of diffeomorphic transformations. Our method significantly reduces the effort of parameter tuning, which is time and labor-consuming. To achieve the goal, we develop a predictive model based on deep convolutional neural networks (CNN) that learns the mapping between pairwise images and the regularization parameter of image registration. In contrast to previous methods that estimate such parameters in a high-dimensional image space, our model is built in an efficient bandlimited space with much lower dimensions. We demonstrate the effectiveness of our model on both 2D synthetic data and 3D real brain images. Experimental results show that our model not only predicts appropriate regularization parameters for image registration, but also improving the network training in terms of time and memory efficiency.

Jie Luo, Matt Toews, Ines Machado et al.

A reliable Ultrasound (US)-to-US registration method to compensate for brain shift would substantially improve Image-Guided Neurological Surgery. Developing such a registration method is very challenging, due to factors such as missing correspondence in images, the complexity of brain pathology and the demand for fast computation. We propose a novel feature-driven active framework. Here, landmarks and their displacement are first estimated from a pair of US images using corresponding local image features. Subsequently, a Gaussian Process (GP) model is used to interpolate a dense deformation field from the sparse landmarks. Kernels of the GP are estimated by using variograms and a discrete grid search method. If necessary, the user can actively add new landmarks based on the image context and visualization of the uncertainty measure provided by the GP to further improve the result. We retrospectively demonstrate our registration framework as a robust and accurate brain shift compensation solution on clinical data acquired during neurosurgery.

Jie Luo, Alireza Sedghi, Karteek Popuri et al.

Estimating the uncertainty in (probabilistic) image registration enables, e.g., surgeons to assess the operative risk based on the trustworthiness of the registered image data. If surgeons receive inaccurately calculated registration uncertainty and misplace unwarranted confidence in the alignment solutions, severe consequences may result. For probabilistic image registration (PIR), the predominant way to quantify the registration uncertainty is using summary statistics of the distribution of transformation parameters. The majority of existing research focuses on trying out different summary statistics as well as a means to exploit them. Distinctively, in this paper, we study two rarely examined topics: (1) whether those summary statistics of the transformation distribution most informatively represent the registration uncertainty; (2) Does utilizing the registration uncertainty always be beneficial. We show that there are two types of uncertainties: the transformation uncertainty, Ut, and label uncertainty Ul. The conventional way of using Ut to quantify Ul is inappropriate and can be misleading. By a real data experiment, we also share a potentially critical finding that making use of the registration uncertainty may not always be an improvement.