A CAUSAL HIERARCHICAL MARKOV FRAMEWORK FOR THE CLASSIFICATION OF MULTIRESOLUTION AND MULTISENSOR REMOTE SENSING IMAGES

Abstract. In this paper, a multiscale Markov framework is proposed in order to address the problem of the classification of multiresolution and multisensor remotely sensed data. The proposed framework makes use of a quadtree to model the interactions across different spatial resolutions and a Markov model with respect to a generic total order relation to deal with contextual information at each scale in order to favor applicability to very high resolution imagery. The methodological properties of the proposed hierarchical framework are investigated. Firstly, we prove the causality of the overall proposed model, a particularly advantageous property in terms of computational cost of the inference. Secondly, we prove the expression of the marginal posterior mode criterion for inference on the proposed framework. Within this framework, a specific algorithm is formulated by defining, within each layer of the quadtree, a Markov chain model with respect to a pixel scan that combines both a zig-zag trajectory and a Hilbert space-filling curve. Data collected by distinct sensors at the same spatial resolution are fused through gradient boosted regression trees. The developed algorithm was experimentally validated with two very high resolution datasets including multispectral, panchromatic and radar satellite images. The experimental results confirm the effectiveness of the proposed algorithm as compared to previous techniques based on alternate approaches to multiresolution fusion

Towards Building Deep Networks with Bayesian Factor Graphs

We propose a Multi-Layer Network based on the Bayesian framework of the Factor Graphs in Reduced Normal Form (FGrn) applied to a two-dimensional lattice. The Latent Variable Model (LVM) is the basic building block of a quadtree hierarchy built on top of a bottom layer of random variables that represent pixels of an image, a feature map, or more generally a collection of spatially distributed discrete variables. The multi-layer architecture implements a hierarchical data representation that, via belief propagation, can be used for learning and inference. Typical uses are pattern completion, correction and classification. The FGrn paradigm provides great flexibility and modularity and appears as a promising candidate for building deep networks: the system can be easily extended by introducing new and different (in cardinality and in type) variables. Prior knowledge, or supervised information, can be introduced at different scales. The FGrn paradigm provides a handy way for building all kinds of architectures by interconnecting only three types of units: Single Input Single Output (SISO) blocks, Sources and Replicators. The network is designed like a circuit diagram and the belief messages flow bidirectionally in the whole system. The learning algorithms operate only locally within each block. The framework is demonstrated in this paper in a three-layer structure applied to images extracted from a standard data set.Comment: Submitted for journal publicatio

Probabilistic and Deep Learning Algorithms for the Analysis of Imagery Data

Accurate object classification is a challenging problem for various low to high resolution imagery data. This applies to both natural as well as synthetic image datasets. However, each object recognition dataset poses its own distinct set of domain-specific problems. In order to address these issues, we need to devise intelligent learning algorithms which require a deep understanding and careful analysis of the feature space. In this thesis, we introduce three new learning frameworks for the analysis of both airborne images (NAIP dataset) and handwritten digit datasets without and with noise (MNIST and n-MNIST respectively). First, we propose a probabilistic framework for the analysis of the NAIP dataset which includes (1) an unsupervised segmentation module based on the Statistical Region Merging algorithm, (2) a feature extraction module that extracts a set of standard hand-crafted texture features from the images, (3) a supervised classification algorithm based on Feedforward Backpropagation Neural Networks, and (4) a structured prediction framework using Conditional Random Fields that integrates the results of the segmentation and classification modules into a single composite model to generate the final class labels. Next, we introduce two new datasets SAT-4 and SAT-6 sampled from the NAIP imagery and use them to evaluate a multitude of Deep Learning algorithms including Deep Belief Networks (DBN), Convolutional Neural Networks (CNN) and Stacked Autoencoders (SAE) for generating class labels. Finally, we propose a learning framework by integrating hand-crafted texture features with a DBN. A DBN uses an unsupervised pre-training phase to perform initialization of the parameters of a Feedforward Backpropagation Neural Network to a global error basin which can then be improved using a round of supervised fine-tuning using Feedforward Backpropagation Neural Networks. These networks can subsequently be used for classification. In the following discussion, we show that the integration of hand-crafted features with DBN shows significant improvement in performance as compared to traditional DBN models which take raw image pixels as input. We also investigate why this integration proves to be particularly useful for aerial datasets using a statistical analysis based on Distribution Separability Criterion. Then we introduce a new dataset called noisy-MNIST (n-MNIST) by adding (1) additive white gaussian noise (AWGN), (2) motion blur and (3) Reduced contrast and AWGN to the MNIST dataset and present a learning algorithm by combining probabilistic quadtrees and Deep Belief Networks. This dynamic integration of the Deep Belief Network with the probabilistic quadtrees provide significant improvement over traditional DBN models on both the MNIST and the n-MNIST datasets. Finally, we extend our experiments on aerial imagery to the class of general texture images and present a theoretical analysis of Deep Neural Networks applied to texture classification. We derive the size of the feature space of textural features and also derive the Vapnik-Chervonenkis dimension of certain classes of Neural Networks. We also derive some useful results on intrinsic dimension and relative contrast of texture datasets and use these to highlight the differences between texture datasets and general object recognition datasets

Development of a SGM-based multi-view reconstruction framework for aerial imagery

Advances in the technology of digital airborne camera systems allow for the observation of surfaces with sampling rates in the range of a few centimeters. In combination with novel matching approaches, which estimate depth information for virtually every pixel, surface reconstructions of impressive density and precision can be generated. Therefore, image based surface generation meanwhile is a serious alternative to LiDAR based data collection for many applications. Surface models serve as primary base for geographic products as for example map creation, production of true-ortho photos or visualization purposes within the framework of virtual globes. The goal of the presented theses is the development of a framework for the fully automatic generation of 3D surface models based on aerial images - both standard nadir as well as oblique views. This comprises several challenges. On the one hand dimensions of aerial imagery is considerable and the extend of the areas to be reconstructed can encompass whole countries. Beside scalability of methods this also requires decent processing times and efficient handling of the given hardware resources. Moreover, beside high precision requirements, a high degree of automation has to be guaranteed to limit manual interaction as much as possible. Due to the advantages of scalability, a stereo method is utilized in the presented thesis. The approach for dense stereo is based on an adapted version of the semi global matching (SGM) algorithm. Following a hierarchical approach corresponding image regions and meaningful disparity search ranges are identified. It will be verified that, dependent on undulations of the scene, time and memory demands can be reduced significantly, by up to 90% within some of the conducted tests. This enables the processing of aerial datasets on standard desktop machines in reasonable times even for large fields of depth. Stereo approaches generate disparity or depth maps, in which redundant depth information is available. To exploit this redundancy, a method for the refinement of stereo correspondences is proposed. Thereby redundant observations across stereo models are identified, checked for geometric consistency and their reprojection error is minimized. This way outliers are removed and precision of depth estimates is improved. In order to generate consistent surfaces, two algorithms for depth map fusion were developed. The first fusion strategy aims for the generation of 2.5D height models, also known as digital surface models (DSM). The proposed method improves existing methods regarding quality in areas of depth discontinuities, for example at roof edges. Utilizing benchmarks designed for the evaluation of image based DSM generation we show that the developed approaches favorably compare to state-of-the-art algorithms and that height precisions of few GSDs can be achieved. Furthermore, methods for the derivation of meshes based on DSM data are discussed. The fusion of depth maps for 3D scenes, as e.g. frequently required during evaluation of high resolution oblique aerial images in complex urban environments, demands for a different approach since scenes can in general not be represented as height fields. Moreover, depths across depth maps possess varying precision and sampling rates due to variances in image scale, errors in orientation and other effects. Within this thesis a median-based fusion methodology is proposed. By using geometry-adaptive triangulation of depth maps depth-wise normals are extracted and, along the point coordinates are filtered and fused using tree structures. The output of this method are oriented points which then can be used to generate meshes. Precision and density of the method will be evaluated using established multi-view benchmarks. Beside the capability to process close range datasets, results for large oblique airborne data sets will be presented. The report closes with a summary, discussion of limitations and perspectives regarding improvements and enhancements. The implemented algorithms are core elements of the commercial software package SURE, which is freely available for scientific purposes

A robust patch-based synthesis framework for combining inconsistent images

Current methods for combining different images produce visible artifacts when the sources have very different textures and structures, come from far view points, or capture dynamic scenes with motions. In this thesis, we propose a patch-based synthesis algorithm to plausibly combine different images that have color, texture, structural, and geometric inconsistencies. For some applications such as cloning and stitching where a gradual blend is required, we present a new method for synthesizing a transition region between two source images, such that inconsistent properties change gradually from one source to the other. We call this process image melding. For gradual blending, we generalized patch-based optimization foundation with three key generalizations: First, we enrich the patch search space with additional geometric and photometric transformations. Second, we integrate image gradients into the patch representation and replace the usual color averaging with a screened Poisson equation solver. Third, we propose a new energy based on mixed L2/L0 norms for colors and gradients that produces a gradual transition between sources without sacrificing texture sharpness. Together, all three generalizations enable patch-based solutions to a broad class of image melding problems involving inconsistent sources: object cloning, stitching challenging panoramas, hole filling from multiple photos, and image harmonization. We also demonstrate another application which requires us to address inconsistencies across the images: high dynamic range (HDR) reconstruction using sequential exposures. In this application, the results will suffer from objectionable artifacts for dynamic scenes if the inconsistencies caused by significant scene motions are not handled properly. In this thesis, we propose a new approach to HDR reconstruction that uses information in all exposures while being more robust to motion than previous techniques. Our algorithm is based on a novel patch-based energy-minimization formulation that integrates alignment and reconstruction in a joint optimization through an equation we call the HDR image synthesis equation. This allows us to produce an HDR result that is aligned to one of the exposures yet contains information from all of them. These two applications (image melding and high dynamic range reconstruction) show that patch based methods like the one proposed in this dissertation can address inconsistent images and could open the door to many new image editing applications in the future

Development and Improvement of Tools and Algorithms for the Problem of Atom Type Perception and for the Assessment of Protein-Ligand-Complex Geometries

In context of the present work, a scoring function for protein-ligand complexes has been developed, not aimed at affinity prediction, but rather a good recognition rate of near native geometries. The developed program DSX makes use of the same formalism as the knowledge-based scoring function DrugScore, hence using the knowledge from crystallographic databases and atom-type specific distance-dependent distribution functions. It is based on newly defined atom-types. Additionally, the program is augmented by two novel potentials which evaluate the torsion angles and (de-)solvation effects. Validation of DSX is based on a literature-known, comprehensive data-set that allows for comparison with other popular scoring functions. DSX is intended for the recognition of near-native binding modes. In this important task, DSX outperforms the competitors, but is also among the best scoring functions regarding the ranking of different compounds. Another essential step in the development of DSX was the automatical assignment of the new atom types. A powerful programming framework was implemented to fulfill this task. Validation was done on a literature-known data-set and showed superior efficiency and quality compared to similar programs where this data was available. The front-end fconv was developed to share this functionality with the scientific community. Multiple features useful in computational drug-design workflows are also included and fconv was made freely available as Open Source Project. Based on the developed potentials for DSX, a number of further applications was created and impemented: The program HotspotsX calculates favorable interaction fields in protein binding pockets that can be used as a starting point for pharmacophoric models and that indicate possible directions for the optimization of lead structures. The program DSFP calculates scores based on fingerprints for given binding geometries. These fingerprints are compared with reference fingerprints that are derived from DSX interactions in known crystal structures of the particular target. Finally, the program DSX_wat was developed to predict stable water networks within a binding pocket. DSX interaction fields are used to calculate the putative water positions

Doctor of Philosophy

dissertationInteractive editing and manipulation of digital media is a fundamental component in digital content creation. One media in particular, digital imagery, has seen a recent increase in popularity of its large or even massive image formats. Unfortunately, current systems and techniques are rarely concerned with scalability or usability with these large images. Moreover, processing massive (or even large) imagery is assumed to be an off-line, automatic process, although many problems associated with these datasets require human intervention for high quality results. This dissertation details how to design interactive image techniques that scale. In particular, massive imagery is typically constructed as a seamless mosaic of many smaller images. The focus of this work is the creation of new technologies to enable user interaction in the formation of these large mosaics. While an interactive system for all stages of the mosaic creation pipeline is a long-term research goal, this dissertation concentrates on the last phase of the mosaic creation pipeline - the composition of registered images into a seamless composite. The work detailed in this dissertation provides the technologies to fully realize interactive editing in mosaic composition on image collections ranging from the very small to massive in scale

Automatic near real-time flood detection in high resolution X-band synthetic aperture radar satellite data using context-based classification on irregular graphs

This thesis is an outcome of the project “Flood and damage assessment using very high resolution SAR data” (SAR-HQ), which is embedded in the interdisciplinary oriented RIMAX (Risk Management of Extreme Flood Events) programme, funded by the Federal Ministry of Education and Research (BMBF). It comprises the results of three scientific papers on automatic near real-time flood detection in high resolution X-band synthetic aperture radar (SAR) satellite data for operational rapid mapping activities in terms of disaster and crisis-management support. Flood situations seem to become more frequent and destructive in many regions of the world. A rising awareness of the availability of satellite based cartographic information has led to an increase in requests to corresponding mapping services to support civil-protection and relief organizations with disaster-related mapping and analysis activities. Due to the rising number of satellite systems with high revisit frequencies, a strengthened pool of SAR data is available during operational flood mapping activities. This offers the possibility to observe the whole extent of even large-scale flood events and their spatio-temporal evolution, but also calls for computationally efficient and automatic flood detection methods, which should drastically reduce the user input required by an active image interpreter. This thesis provides solutions for the near real-time derivation of detailed flood parameters such as flood extent, flood-related backscatter changes as well as flood classification probabilities from the new generation of high resolution X-band SAR satellite imagery in a completely unsupervised way. These data are, in comparison to images from conventional medium-resolution SAR sensors, characterized by an increased intra-class and decreased inter-class variability due to the reduced mixed pixel phenomenon. This problem is addressed by utilizing multi-contextual models on irregular hierarchical graphs, which consider that semantic image information is less represented in single pixels but in homogeneous image objects and their mutual relation. A hybrid Markov random field (MRF) model is developed, which integrates scale-dependent as well as spatio-temporal contextual information into the classification process by combining hierarchical causal Markov image modeling on automatically generated irregular hierarchical graphs with noncausal Markov modeling related to planar MRFs. This model is initialized in an unsupervised manner by an automatic tile-based thresholding approach, which solves the flood detection problem in large-size SAR data with small a priori class probabilities by statistical parameterization of local bi-modal class-conditional density functions in a time efficient manner. Experiments performed on TerraSAR-X StripMap data of Southwest England and ScanSAR data of north-eastern Namibia during large-scale flooding show the effectiveness of the proposed methods in terms of classification accuracy, computational performance, and transferability. It is further demonstrated that hierarchical causal Markov models such as hierarchical maximum a posteriori (HMAP) and hierarchical marginal posterior mode (HMPM) estimation can be effectively used for modeling the inter-spatial context of X-band SAR data in terms of flood and change detection purposes. Although the HMPM estimator is computationally more demanding than the HMAP estimator, it is found to be more suitable in terms of classification accuracy. Further, it offers the possibility to compute marginal posterior entropy-based confidence maps, which are used for the generation of flood possibility maps that express that the uncertainty in labeling of each image element. The supplementary integration of intra-spatial and, optionally, temporal contextual information into the Markov model results in a reduction of classification errors. It is observed that the application of the hybrid multi-contextual Markov model on irregular graphs is able to enhance classification results in comparison to modeling on regular structures of quadtrees, which is the hierarchical representation of images usually used in MRF-based image analysis. X-band SAR systems are generally not suited for detecting flooding under dense vegetation canopies such as forests due to the low capability of the X-band signal to penetrate into media. Within this thesis a method is proposed for the automatic derivation of flood areas beneath shrubs and grasses from TerraSAR-X data. Furthermore, an approach is developed, which combines high resolution topographic information with multi-scale image segmentation to enhance the mapping accuracy in areas consisting of flooded vegetation and anthropogenic objects as well as to remove non-water look-alike areas

Methods for Real-time Visualization and Interaction with Landforms

This thesis presents methods to enrich data modeling and analysis in the geoscience domain with a particular focus on geomorphological applications. First, a short overview of the relevant characteristics of the used remote sensing data and basics of its processing and visualization are provided. Then, two new methods for the visualization of vector-based maps on digital elevation models (DEMs) are presented. The first method uses a texture-based approach that generates a texture from the input maps at runtime taking into account the current viewpoint. In contrast to that, the second method utilizes the stencil buffer to create a mask in image space that is then used to render the map on top of the DEM. A particular challenge in this context is posed by the view-dependent level-of-detail representation of the terrain geometry. After suitable visualization methods for vector-based maps have been investigated, two landform mapping tools for the interactive generation of such maps are presented. The user can carry out the mapping directly on the textured digital elevation model and thus benefit from the 3D visualization of the relief. Additionally, semi-automatic image segmentation techniques are applied in order to reduce the amount of user interaction required and thus make the mapping process more efficient and convenient. The challenge in the adaption of the methods lies in the transfer of the algorithms to the quadtree representation of the data and in the application of out-of-core and hierarchical methods to ensure interactive performance. Although high-resolution remote sensing data are often available today, their effective resolution at steep slopes is rather low due to the oblique acquisition angle. For this reason, remote sensing data are suitable to only a limited extent for visualization as well as landform mapping purposes. To provide an easy way to supply additional imagery, an algorithm for registering uncalibrated photos to a textured digital elevation model is presented. A particular challenge in registering the images is posed by large variations in the photos concerning resolution, lighting conditions, seasonal changes, etc. The registered photos can be used to increase the visual quality of the textured DEM, in particular at steep slopes. To this end, a method is presented that combines several georegistered photos to textures for the DEM. The difficulty in this compositing process is to create a consistent appearance and avoid visible seams between the photos. In addition to that, the photos also provide valuable means to improve landform mapping. To this end, an extension of the landform mapping methods is presented that allows the utilization of the registered photos during mapping. This way, a detailed and exact mapping becomes feasible even at steep slopes

Automatic Segmentation of Cells of Different Types in Fluorescence Microscopy Images

Recognition of different cell compartments, types of cells, and their interactions is a critical aspect of quantitative cell biology. This provides a valuable insight for understanding cellular and subcellular interactions and mechanisms of biological processes, such as cancer cell dissemination, organ development and wound healing. Quantitative analysis of cell images is also the mainstay of numerous clinical diagnostic and grading procedures, for example in cancer, immunological, infectious, heart and lung disease. Computer automation of cellular biological samples quantification requires segmenting different cellular and sub-cellular structures in microscopy images. However, automating this problem has proven to be non-trivial, and requires solving multi-class image segmentation tasks that are challenging owing to the high similarity of objects from different classes and irregularly shaped structures. This thesis focuses on the development and application of probabilistic graphical models to multi-class cell segmentation. Graphical models can improve the segmentation accuracy by their ability to exploit prior knowledge and model inter-class dependencies. Directed acyclic graphs, such as trees have been widely used to model top-down statistical dependencies as a prior for improved image segmentation. However, using trees, a few inter-class constraints can be captured. To overcome this limitation, polytree graphical models are proposed in this thesis that capture label proximity relations more naturally compared to tree-based approaches. Polytrees can effectively impose the prior knowledge on the inclusion of different classes by capturing both same-level and across-level dependencies. A novel recursive mechanism based on two-pass message passing is developed to efficiently calculate closed form posteriors of graph nodes on polytrees. Furthermore, since an accurate and sufficiently large ground truth is not always available for training segmentation algorithms, a weakly supervised framework is developed to employ polytrees for multi-class segmentation that reduces the need for training with the aid of modeling the prior knowledge during segmentation. Generating a hierarchical graph for the superpixels in the image, labels of nodes are inferred through a novel efficient message-passing algorithm and the model parameters are optimized with Expectation Maximization (EM). Results of evaluation on the segmentation of simulated data and multiple publicly available fluorescence microscopy datasets indicate the outperformance of the proposed method compared to state-of-the-art. The proposed method has also been assessed in predicting the possible segmentation error and has been shown to outperform trees. This can pave the way to calculate uncertainty measures on the resulting segmentation and guide subsequent segmentation refinement, which can be useful in the development of an interactive segmentation framework