Deformation equivariant cross-modality image synthesis with paired non-aligned training data

Cross-modality image synthesis is an active research topic with multiple medical clinically relevant applications. Recently, methods allowing training with paired but misaligned data have started to emerge. However, no robust and well-performing methods applicable to a wide range of real world data sets exist. In this work, we propose a generic solution to the problem of cross-modality image synthesis with paired but non-aligned data by introducing new deformation equivariance encouraging loss functions. The method consists of joint training of an image synthesis network together with separate registration networks and allows adversarial training conditioned on the input even with misaligned data. The work lowers the bar for new clinical applications by allowing effortless training of cross-modality image synthesis networks for more difficult data sets

A Vision-Based Automatic Safe landing-Site Detection System

An automatic safe landing-site detection system is proposed for aircraft emergency landing, based on visible information acquired by aircraft-mounted cameras. Emergency landing is an unplanned event in response to emergency situations. If, as is unfortunately usually the case, there is no airstrip or airfield that can be reached by the un-powered aircraft, a crash landing or ditching has to be carried out. Identifying a safe landing-site is critical to the survival of passengers and crew. Conventionally, the pilot chooses the landing-site visually by looking at the terrain through the cockpit. The success of this vital decision greatly depends on the external environmental factors that can impair human vision, and on the pilot\u27s flight experience that can vary significantly among pilots. Therefore, we propose a robust, reliable and efficient detection system that is expected to alleviate the negative impact of these factors. In this study, we focus on the detection mechanism of the proposed system and assume that the image enhancement for increased visibility and image stitching for a larger field-of-view have already been performed on terrain images acquired by aircraft-mounted cameras. Specifically, we first propose a hierarchical elastic horizon detection algorithm to identify ground in rile image. Then the terrain image is divided into non-overlapping blocks which are clustered according to a roughness measure. Adjacent smooth blocks are merged to form potential landing-sites whose dimensions are measured with principal component analysis and geometric transformations. If the dimensions of a candidate region exceed the minimum requirement for safe landing, the potential landing-site is considered a safe candidate and highlighted on the human machine interface. At the end, the pilot makes the final decision by confirming one of the candidates, also considering other factors such as wind speed and wind direction, etc

Toward Global Localization of Unmanned Aircraft Systems using Overhead Image Registration with Deep Learning Convolutional Neural Networks

Global localization, in which an unmanned aircraft system (UAS) estimates its unknown current location without access to its take-off location or other locational data from its flight path, is a challenging problem. This research brings together aspects from the remote sensing, geoinformatics, and machine learning disciplines by framing the global localization problem as a geospatial image registration problem in which overhead aerial and satellite imagery serve as a proxy for UAS imagery. A literature review is conducted covering the use of deep learning convolutional neural networks (DLCNN) with global localization and other related geospatial imagery applications. Differences between geospatial imagery taken from the overhead perspective and terrestrial imagery are discussed, as well as difficulties in using geospatial overhead imagery for image registration due to a lack of suitable machine learning datasets. Geospatial analysis is conducted to identify suitable areas for future UAS imagery collection. One of these areas, Jerusalem northeast (JNE) is selected as the area of interest (AOI) for this research. Multi-modal, multi-temporal, and multi-resolution geospatial overhead imagery is aggregated from a variety of publicly available sources and processed to create a controlled image dataset called Jerusalem northeast rural controlled imagery (JNE RCI). JNE RCI is tested with handcrafted feature-based methods SURF and SIFT and a non-handcrafted feature-based pre-trained fine-tuned VGG-16 DLCNN on coarse-grained image registration. Both handcrafted and non-handcrafted feature based methods had difficulty with the coarse-grained registration process. The format of JNE RCI is determined to be unsuitable for the coarse-grained registration process with DLCNNs and the process to create a new supervised machine learning dataset, Jerusalem northeast machine learning (JNE ML) is covered in detail. A multi-resolution grid based approach is used, where each grid cell ID is treated as the supervised training label for that respective resolution. Pre-trained fine-tuned VGG-16 DLCNNs, two custom architecture two-channel DLCNNs, and a custom chain DLCNN are trained on JNE ML for each spatial resolution of subimages in the dataset. All DLCNNs used could more accurately coarsely register the JNE ML subimages compared to the pre-trained fine-tuned VGG-16 DLCNN on JNE RCI. This shows the process for creating JNE ML is valid and is suitable for using machine learning with the coarse-grained registration problem. All custom architecture two-channel DLCNNs and the custom chain DLCNN were able to more accurately coarsely register the JNE ML subimages compared to the fine-tuned pre-trained VGG-16 approach. Both the two-channel custom DLCNNs and the chain DLCNN were able to generalize well to new imagery that these networks had not previously trained on. Through the contributions of this research, a foundation is laid for future work to be conducted on the UAS global localization problem within the rural forested JNE AOI

Large-Scale Light Field Capture and Reconstruction

This thesis discusses approaches and techniques to convert Sparsely-Sampled Light Fields (SSLFs) into Densely-Sampled Light Fields (DSLFs), which can be used for visualization on 3DTV and Virtual Reality (VR) devices. Exemplarily, a movable 1D large-scale light field acquisition system for capturing SSLFs in real-world environments is evaluated. This system consists of 24 sparsely placed RGB cameras and two Kinect V2 sensors. The real-world SSLF data captured with this setup can be leveraged to reconstruct real-world DSLFs. To this end, three challenging problems require to be solved for this system: (i) how to estimate the rigid transformation from the coordinate system of a Kinect V2 to the coordinate system of an RGB camera; (ii) how to register the two Kinect V2 sensors with a large displacement; (iii) how to reconstruct a DSLF from a SSLF with moderate and large disparity ranges. To overcome these three challenges, we propose: (i) a novel self-calibration method, which takes advantage of the geometric constraints from the scene and the cameras, for estimating the rigid transformations from the camera coordinate frame of one Kinect V2 to the camera coordinate frames of 12-nearest RGB cameras; (ii) a novel coarse-to-fine approach for recovering the rigid transformation from the coordinate system of one Kinect to the coordinate system of the other by means of local color and geometry information; (iii) several novel algorithms that can be categorized into two groups for reconstructing a DSLF from an input SSLF, including novel view synthesis methods, which are inspired by the state-of-the-art video frame interpolation algorithms, and Epipolar-Plane Image (EPI) inpainting methods, which are inspired by the Shearlet Transform (ST)-based DSLF reconstruction approaches

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)

In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences. Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low-and high-grade glioma patients-manually annotated by up to four raters-and to 65 comparable scans generated using tumor image simulation software. Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%-85%), illustrating the difficulty of this task. We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously. Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements. The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource

Characterizing Unstructured Motor Behaviors in the Epilepsy Monitoring Unit

Key advancements in recording hardware, data computation, clinical care, and cognitive science continue to drive new possibilities in how humans and machines can interact directly through thought. Neural data analyses with these advancements has progressed neuroscience research in functional brain mapping and brain-computer interfaces (BCIs). Much of our knowledge about BCIs is informed by data collected through carefully controlled experiments. Constraining BCI experiments with structured paradigms allows researchers to collect a high number of consistent data in a short amount of time, while also controlling for external confounds. Very little is currently known about how well these task-based relationships extend to daily life, in part because collecting data outside of the lab is challenging. To further understand natural brain activity, we must study more complex behaviors in more environmentally relevant settings. The results of this dissertation address three general challenges to studying neural correlates to unstructured behaviors. First, we continuously monitored unstructured human movements in the epilepsy monitoring unit using a video sensor synchronized to clinical intracortical electrodes. Second, we annotated unstructured behaviors from these video using both manual and computer vision methods. Finally, analyzed neural features with respect to unstructured human movements, and evaluated the performance of features identified in previous task-based studies. The preliminary nature of this work means that a majority of our demonstrations are whether the continuous paradigm can be leveraged, how one might go about leveraging it, and evaluations that tie our results back to earlier task-based studies. Our advances here motivate future works that focus more intently on what types of behaviors and neural signal features to explore

Structural analysis of fMRI data revisited: improving the sensitivity and reliability of fMRI group studies.

International audienceGroup studies of functional magnetic resonance imaging datasets are usually based on the computation of the mean signal across subjects at each voxel (random effects analyses), assuming that all subjects have been set in the same anatomical space (normalization). Although this approach allows for a correct specificity (rate of false detections), it is not very efficient for three reasons: i) its underlying hypotheses, perfect coregistration of the individual datasets and normality of the measured signal at the group level are frequently violated; ii) the group size is small in general, so that asymptotic approximations on the parameters distributions do not hold; iii) the large size of the images requires some conservative strategies to control the false detection rate, at the risk of increasing the number of false negatives. Given that it is still very challenging to build generative or parametric models of intersubject variability, we rely on a rule based, bottom-up approach: we present a set of procedures that detect structures of interest from each subject's data, then search for correspondences across subjects and outline the most reproducible activation regions in the group studied. This framework enables a strict control on the number of false detections. It is shown here that this analysis demonstrates increased validity and improves both the sensitivity and reliability of group analyses compared with standard methods. Moreover, it directly provides information on the spatial position correspondence or variability of the activated regions across subjects, which is difficult to obtain in standard voxel-based analyses