Intensity-based image registration approaches rely on similarity measures to guide the search for geometric correspondences with high affinity between images. The properties of the used measure are vital for the robustness and accuracy of the registration. In this study a symmetric, intensity interpolation-free, affine registration framework based on a combination of intensity and spatial information is proposed. The excellent performance of the framework is demonstrated on a combination of synthetic tests, recovering known transformations in the presence of noise, and real applications in biomedical and medical image registration, for both 2D and 3D images. The method exhibits greater robustness and higher accuracy than similarity measures in common use, when inserted into a standard gradient-based registration framework available as part of the open source Insight Segmentation and Registration Toolkit (ITK). The method is also empirically shown to have a low computational cost, making it practical for real applications. Source code is available.
Breast lesion localization using tactile imaging is a new and developing direction in medical science. To achieve the goal, proper image reconstruction and image registration can be a valuable asset. In this paper, a new approach of the segmentation-based image surface reconstruction algorithm is used to reconstruct the surface of a breast phantom. In breast tissue, the sub-dermal vein network is used as a distinguishable pattern for reconstruction. The proposed image capturing device contacts the surface of the phantom, and surface deformation will occur due to applied force at the time of scanning. A novel force based surface rectification system is used to reconstruct a deformed surface image to its original structure. For the construction of the full surface from rectified images, advanced affine scale-invariant feature transform (A-SIFT) is proposed to reduce the affine effect in time when data capturing. Camera position based image stitching approach is applied to construct the final original non-rigid surface. The proposed model is validated in theoretical models and real scenarios, to demonstrate its advantages with respect to competing methods. The result of the proposed method, applied to path reconstruction, ends with a positioning accuracy of 99.7%
3D medical image registration is of great clinical importance. However, supervised learning methods require a large amount of accurately annotated corresponding control points (or morphing). The ground truth for 3D medical images is very difficult to obtain. Unsupervised learning methods ease the burden of manual annotation by exploiting unlabeled data without supervision. In this paper, we propose a new unsupervised learning method using convolutional neural networks under an end-to-end framework, Volume Tweening Network (VTN), to register 3D medical images. Three technical components ameliorate our unsupervised learning system for 3D end-to-end medical image registration: (1) We cascade the registration subnetworks; (2) We integrate affine registration into our network; and (3) We incorporate an additional invertibility loss into the training process. Experimental results demonstrate that our algorithm is 880x faster (or 3.3x faster without GPU acceleration) than traditional optimization-based methods and achieves state-of-the-art performance in medical image registration.
Spectral methods such as the improved Fourier Mellin Invariant (iFMI) transform have proved faster, more robust and accurate than feature based methods on image registration. However, iFMI is restricted to work only when the camera moves in 2D space and has not been applied on omni-cameras images so far. In this work, we extend the iFMI method and apply a motion model to estimate an omni-camera's pose when it moves in 3D space. This is particularly useful in field robotics applications to get a rapid and comprehensive view of unstructured environments, and to estimate robustly the robot pose. In the experiment section, we compared the extended iFMI method against ORB and AKAZE feature based approaches on three datasets showing different type of environments: office, lawn and urban scenery (MPI-omni dataset). The results show that our method boosts the accuracy of the robot pose estimation two to four times with respect to the feature registration techniques, while offering lower processing times. Furthermore, the iFMI approach presents the best performance against motion blur typically present in mobile robotics.
Objective: Deformable brain MR image registration is challenging due to large inter-subject anatomical variation. For example, the highly complex cortical folding pattern makes it hard to accurately align corresponding cortical structures of individual images. In this paper, we propose a novel deep learning way to simplify the difficult registration problem of brain MR images. Methods: We train a morphological simplification network (MS-Net), which can generate a "simple" image with less anatomical details based on the "complex" input. With MS-Net, the complexity of the fixed image or the moving image under registration can be reduced gradually, thus building an individual (simplification) trajectory represented by MS-Net outputs. Since the generated images at the ends of the two trajectories (of the fixed and moving images) are so simple and very similar in appearance, they are easy to register. Thus, the two trajectories can act as a bridge to link the fixed and the moving images, and guide their registration. Results: Our experiments show that the proposed method can achieve highly accurate registration performance on different datasets (i.e., NIREP, LPBA, IBSR, CUMC, and MGH). Moreover, the method can be also easily transferred across diverse image datasets and obtain superior accuracy on surface alignment. Conclusion and Significance: We propose MS-Net as a powerful and flexible tool to simplify brain MR images and their registration. To our knowledge, this is the first work to simplify brain MR image registration by deep learning, instead of estimating deformation field directly.
Arctic sea ice plays an important role in the global climate. Sea ice models governed by physical equations have been used to simulate the state of the ice including characteristics such as ice thickness, concentration, and motion. More recent models also attempt to capture features such as fractures or leads in the ice. These simulated features can be partially misaligned or misshapen when compared to observational data, whether due to numerical approximation or incomplete physics. In order to make realistic forecasts and improve understanding of the underlying processes, it is necessary to calibrate the numerical model to field data. Traditional calibration methods based on generalized least-square metrics are flawed for linear features such as sea ice cracks. We develop a statistical emulation and calibration framework that accounts for feature misalignment and misshapenness, which involves optimally aligning model output with observed features using cutting edge image registration techniques. This work can also have application to other physical models which produce coherent structures.
Consecutive thin sections of tissue samples make it possible to study local variation in e.g. protein expression and tumor heterogeneity by staining for a new protein in each section. In order to compare and correlate patterns of different proteins, the images have to be registered with high accuracy. The problem we want to solve is registration of gigapixel whole slide images (WSI). This presents 3 challenges: (i) Images are very large; (ii) Thin sections result in artifacts that make global affine registration prone to very large local errors; (iii) Local affine registration is required to preserve correct tissue morphology (local size, shape and texture). In our approach we compare WSI registration based on automatic and manual feature selection on either the full image or natural sub-regions (as opposed to square tiles). Working with natural sub-regions, in an interactive tool makes it possible to exclude regions containing scientifically irrelevant information. We also present a new way to visualize local registration quality by a Registration Confidence Map (RCM). With this method, intra-tumor heterogeneity and charateristics of the tumor microenvironment can be observed and quantified.
A recent line of research termed unlabeled sensing and shuffled linear regression has been exploring under great generality the recovery of signals from subsampled and permuted measurements; a challenging problem in diverse fields of data science and machine learning. In this paper we introduce an abstraction of this problem which we call homomorphic sensing. Given a linear subspace and a finite set of linear transformations we develop an algebraic theory which establishes conditions guaranteeing that points in the subspace are uniquely determined from their homomorphic image under some transformation in the set. As a special case, we recover known conditions for unlabeled sensing, as well as new results and extensions. On the algorithmic level we exhibit two dynamic programming based algorithms, which to the best of our knowledge are the first working solutions for the unlabeled sensing problem for small dimensions. One of them, additionally based on branch-and-bound, when applied to image registration under affine transformations, performs on par with or outperforms state-of-the-art methods on benchmark datasets.
We propose a novel image sampling method for differentiable image transformation in deep neural networks. The sampling schemes currently used in deep learning, such as Spatial Transformer Networks, rely on bilinear interpolation, which performs poorly under severe scale changes, and more importantly, results in poor gradient propagation. This is due to their strict reliance on direct neighbors. Instead, we propose to generate random auxiliary samples in the vicinity of each pixel in the sampled image, and create a linear approximation using their intensity values. We then use this approximation as a differentiable formula for the transformed image. However, we observe that these auxiliary samples may collapse to a single pixel under severe image transformations, and propose to address it by adding constraints to the distance between the center pixel and the auxiliary samples. We demonstrate that our approach produces more representative gradients with a wider basin of convergence for image alignment, which leads to considerable performance improvements when training networks for image registration and classification tasks, particularly under large downsampling.
We present a detailed description and reference implementation of preprocessing steps necessary to prepare the public Retrospective Image Registration Evaluation (RIRE) dataset for the task of magnetic resonance imaging (MRI) to X-ray computed tomography (CT) translation. Furthermore we describe and implement three state of the art convolutional neural network (CNN) and generative adversarial network (GAN) models where we report statistics and visual results of two of them.
In spite of the high accuracy of the existing optical mark reading (OMR) systems and devices, a few restrictions remain existent. In this work, we aim to reduce the restrictions of multiple choice questions (MCQ) within tests. We use an image registration technique to extract the answer boxes from answer sheets. Unlike other systems that rely on simple image processing steps to recognize the extracted answer boxes, we address the problem from another perspective by training a machine learning classifier to recognize the class of each answer box (i.e., confirmed, crossed out, or blank answer). This gives us the ability to deal with a variety of shading and mark patterns, and distinguish between chosen (i.e., confirmed) and canceled answers (i.e., crossed out). All existing machine learning techniques require a large number of examples in order to train a model for classification, therefore we present a dataset including six real MCQ assessments with different answer sheet templates. We evaluate two strategies of classification: a straight-forward approach and a two-stage classifier approach. We test two handcrafted feature methods and a convolutional neural network. In the end, we present an easy-to-use graphical user interface of the proposed system. Compared with existing OMR systems, the proposed system has the least constraints and achieves a high accuracy. We believe that the presented work will further direct the development of OMR systems towards reducing the restrictions of the MCQ tests.