Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data

Image matching techniques are proven to be necessary in various fields of science and engineering, with many new methods and applications introduced over the years. In this PhD thesis, several computational image matching methods are introduced and investigated for improving the analysis of various biomedical image data. These improvements include the use of matching techniques for enhancing visualization of cross-sectional imaging modalities such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), denoising of retinal Optical Coherence Tomography (OCT), and high quality 3D reconstruction of surfaces from Scanning Electron Microscope (SEM) images. This work greatly improves the process of data interpretation of image data with far reaching consequences for basic sciences research. The thesis starts with a general notion of the problem of image matching followed by an overview of the topics covered in the thesis. This is followed by introduction and investigation of several applications of image matching/registration in biomdecial image processing: a) registration-based slice interpolation, b) fast mesh-based deformable image registration and c) use of simultaneous rigid registration and Robust Principal Component Analysis (RPCA) for speckle noise reduction of retinal OCT images. Moving towards a different notion of image matching/correspondence, the problem of view synthesis and 3D reconstruction, with a focus on 3D reconstruction of microscopic samples from 2D images captured by SEM, is considered next. Starting from sparse feature-based matching techniques, an extensive analysis is provided for using several well-known feature detector/descriptor techniques, namely ORB, BRIEF, SURF and SIFT, for the problem of multi-view 3D reconstruction. This chapter contains qualitative and quantitative comparisons in order to reveal the shortcomings of the sparse feature-based techniques. This is followed by introduction of a novel framework using sparse-dense matching/correspondence for high quality 3D reconstruction of SEM images. As will be shown, the proposed framework results in better reconstructions when compared with state-of-the-art sparse-feature based techniques. Even though the proposed framework produces satisfactory results, there is room for improvements. These improvements become more necessary when dealing with higher complexity microscopic samples imaged by SEM as well as in cases with large displacements between corresponding points in micrographs. Therefore, based on the proposed framework, a new approach is proposed for high quality 3D reconstruction of microscopic samples. While in case of having simpler microscopic samples the performance of the two proposed techniques are comparable, the new technique results in more truthful reconstruction of highly complex samples. The thesis is concluded with an overview of the thesis and also pointers regarding future directions of the research using both multi-view and photometric techniques for 3D reconstruction of SEM images

Incremental Dense Reconstruction from Monocular Video with Guided Sparse Feature Volume Fusion

Incrementally recovering 3D dense structures from monocular videos is of paramount importance since it enables various robotics and AR applications. Feature volumes have recently been shown to enable efficient and accurate incremental dense reconstruction without the need to first estimate depth, but they are not able to achieve as high of a resolution as depth-based methods due to the large memory consumption of high-resolution feature volumes. This letter proposes a real-time feature volume-based dense reconstruction method that predicts TSDF (Truncated Signed Distance Function) values from a novel sparsified deep feature volume, which is able to achieve higher resolutions than previous feature volume-based methods, and is favorable in large-scale outdoor scenarios where the majority of voxels are empty. An uncertainty-aware multi-view stereo (MVS) network is leveraged to infer initial voxel locations of the physical surface in a sparse feature volume. Then for refining the recovered 3D geometry, deep features are attentively aggregated from multiview images at potential surface locations, and temporally fused. Besides achieving higher resolutions than before, our method is shown to produce more complete reconstructions with finer detail in many cases. Extensive evaluations on both public and self-collected datasets demonstrate a very competitive real-time reconstruction result for our method compared to state-of-the-art reconstruction methods in both indoor and outdoor settings.Comment: 8 pages, 5 figures, RA-L 202

3D Human Pose and Shape Estimation Based on Parametric Model and Deep Learning

3D human body reconstruction from monocular images has wide applications in our life, such as movie, animation, Virtual/Augmented Reality, medical research and so on. Due to the high freedom of human body in real scene and the ambiguity of inferring 3D objects from 2D images, it is a challenging task to accurately recover 3D human body models from images. In this thesis, we explore the methods for estimating 3D human body models from images based on parametric model and deep learning.In the first part, the coarse 3D human body models are estimated automatically from multi-view images based on a parametric human body model called SMPL model. Two routes are exploited for estimating the pose and shape parameters of the SMPL model to obtain the 3D models: (1) Optimization based methods; and (2) Deep learning based methods. For the optimization based methods, we propose the novel energy functions based on some prior information including the 2D joint points and silhouettes. Through minimizing the energy functions, the SMPL model is fitted to the prior information, and then, the coarse 3D human body is obtained. In addition to the traditional optimization based methods, a deep learning based method is also proposed in the following work to regress the pose and shape parameters of the SMPL model. A novel architecture is proposed to put the optimization into a training loop of convolutional neural network (CNN) to form a self-supervision structure based on the multi-view images. The proposed methods are evaluated on both synthetic and real datasets to demonstrate that they can obtain better estimation of the pose and shape of 3D human body than previous approaches.In the second part, the problem is shifted to the detailed 3D human body reconstruction from multi-view images. Instead of using the SMPL model, implicit function is utilized to represent 3D models because implicit representation can generate continuous surface and has better flexibility for arbitrary topology. Firstly, a multi-scale features based method is proposed to learn the implicit representation for 3D models through multi-stage hourglass networks from multi-view images. Furthermore, a coarse-to-fine method is proposed to refine the 3D models from multi-view images through learning the voxel super-resolution. In this method, the coarse 3D models are estimated firstly by the learned implicit function based on multi-scale features from multi-view images. Afterwards, by voxelizing the coarse 3D models to low resolution voxel grids, voxel super-resolution is learned through a multi-stage 3D CNN for feature extraction from low resolution voxel grids and fully connected neural network for predicting the implicit function. Voxel super-resolution is able to remove the false reconstruction and preserve the surface details. The proposed methods are evaluated on both real and synthetic datasets in which our method can estimate 3D model with higher accuracy and better surface quality than some previous methods

On the use of INS to improve Feature Matching

The continuous technological improvement of mobile devices opens the frontiers of Mobile Mapping systems to very compact systems, i.e. a smartphone or a tablet. This motivates the development of efficient 3D reconstruction techniques based on the sensors typically embedded in such devices, i.e. imaging sensors, GPS and Inertial Navigation System (INS). Such methods usually exploits photogrammetry techniques (structure from motion) to provide an estimation of the geometry of the scene. Actually, 3D reconstruction techniques (e.g. structure from motion) rely on use of features properly matched in different images to compute the 3D positions of objects by means of triangulation. Hence, correct feature matching is of fundamental importance to ensure good quality 3D reconstructions. Matching methods are based on the appearance of features, that can change as a consequence of variations of camera position and orientation, and environment illumination. For this reason, several methods have been developed in recent years in order to provide feature descriptors robust (ideally invariant) to such variations, e.g. Scale-Invariant Feature Transform (SIFT), Affine SIFT, Hessian affine and Harris affine detectors, Maximally Stable Extremal Regions (MSER). This work deals with the integration of information provided by the INS in the feature matching procedure: a previously developed navigation algorithm is used to constantly estimate the device position and orientation. Then, such information is exploited to estimate the transformation of feature regions between two camera views. This allows to compare regions from different images but associated to the same feature as seen by the same point of view, hence significantly easing the comparison of feature characteristics and, consequently, improving matching. SIFT-like descriptors are used in order to ensure good matching results in presence of illumination variations and to compensate the approximations related to the estimation process

Quality control of laser welds based on the weld surface and the weld profile

2D or 3D sensor technology can be used for data acquisition to monitor the weld quality during laser welding. Compared to a 2D camera image, the 3D height data contains additional relevant information for quality inspection. However, the disadvantages are system complexity, higher costs, and longer acquisition times. Therefore, we compare two image-based methods with the quality assessment based on height data. The first method uses feature vectors of coaxial acquired grayscale images. The significant advantage is that a camera is often integrated into the laser system, so no additional hardware is required. In the second approach, we use an AI-based single-view 3D reconstruction method. The height profile is calculated from a camera image and used for further quality assessment. Thus, we combine the advantages of 2D data acquisition with higher accuracy in evaluating 3D data. In this paper, we analyze a dataset of welded hairpins with different defect types and compare the quality assessment using the height data acquired with OCT, the feature vectors from the camera images, and the reconstructed height data

Global-correlated 3D-decoupling Transformer for Clothed Avatar Reconstruction

Reconstructing 3D clothed human avatars from single images is a challenging task, especially when encountering complex poses and loose clothing. Current methods exhibit limitations in performance, largely attributable to their dependence on insufficient 2D image features and inconsistent query methods. Owing to this, we present the Global-correlated 3D-decoupling Transformer for clothed Avatar reconstruction (GTA), a novel transformer-based architecture that reconstructs clothed human avatars from monocular images. Our approach leverages transformer architectures by utilizing a Vision Transformer model as an encoder for capturing global-correlated image features. Subsequently, our innovative 3D-decoupling decoder employs cross-attention to decouple tri-plane features, using learnable embeddings as queries for cross-plane generation. To effectively enhance feature fusion with the tri-plane 3D feature and human body prior, we propose a hybrid prior fusion strategy combining spatial and prior-enhanced queries, leveraging the benefits of spatial localization and human body prior knowledge. Comprehensive experiments on CAPE and THuman2.0 datasets illustrate that our method outperforms state-of-the-art approaches in both geometry and texture reconstruction, exhibiting high robustness to challenging poses and loose clothing, and producing higher-resolution textures. Codes will be available at https://github.com/River-Zhang/GTA.Comment: Accepted by NeurIPS 2023. Project page: https://river-zhang.github.io/GTA-projectpage

Learning-based depth and pose prediction for 3D scene reconstruction in endoscopy

Colorectal cancer is the third most common cancer worldwide. Early detection and treatment of pre-cancerous tissue during colonoscopy is critical to improving prognosis. However, navigating within the colon and inspecting the endoluminal tissue comprehensively are challenging, and success in both varies based on the endoscopist's skill and experience. Computer-assisted interventions in colonoscopy show much promise in improving navigation and inspection. For instance, 3D reconstruction of the colon during colonoscopy could promote more thorough examinations and increase adenoma detection rates which are associated with improved survival rates. Given the stakes, this thesis seeks to advance the state of research from feature-based traditional methods closer to a data-driven 3D reconstruction pipeline for colonoscopy. More specifically, this thesis explores different methods that improve subtasks of learning-based 3D reconstruction. The main tasks are depth prediction and camera pose estimation. As training data is unavailable, the author, together with her co-authors, proposes and publishes several synthetic datasets and promotes domain adaptation models to improve applicability to real data. We show, through extensive experiments, that our depth prediction methods produce more robust results than previous work. Our pose estimation network trained on our new synthetic data outperforms self-supervised methods on real sequences. Our box embeddings allow us to interpret the geometric relationship and scale difference between two images of the same surface without the need for feature matches that are often unobtainable in surgical scenes. Together, the methods introduced in this thesis help work towards a complete, data-driven 3D reconstruction pipeline for endoscopy

ImmFusion: Robust mmWave-RGB Fusion for 3D Human Body Reconstruction in All Weather Conditions

3D human reconstruction from RGB images achieves decent results in good weather conditions but degrades dramatically in rough weather. Complementary, mmWave radars have been employed to reconstruct 3D human joints and meshes in rough weather. However, combining RGB and mmWave signals for robust all-weather 3D human reconstruction is still an open challenge, given the sparse nature of mmWave and the vulnerability of RGB images. In this paper, we present ImmFusion, the first mmWave-RGB fusion solution to reconstruct 3D human bodies in all weather conditions robustly. Specifically, our ImmFusion consists of image and point backbones for token feature extraction and a Transformer module for token fusion. The image and point backbones refine global and local features from original data, and the Fusion Transformer Module aims for effective information fusion of two modalities by dynamically selecting informative tokens. Extensive experiments on a large-scale dataset, mmBody, captured in various environments demonstrate that ImmFusion can efficiently utilize the information of two modalities to achieve a robust 3D human body reconstruction in all weather conditions. In addition, our method's accuracy is significantly superior to that of state-of-the-art Transformer-based LiDAR-camera fusion methods