Learning to Segment Breast Biopsy Whole Slide Images

We trained and applied an encoder-decoder model to semantically segment breast biopsy images into biologically meaningful tissue labels. Since conventional encoder-decoder networks cannot be applied directly on large biopsy images and the different sized structures in biopsies present novel challenges, we propose four modifications: (1) an input-aware encoding block to compensate for information loss, (2) a new dense connection pattern between encoder and decoder, (3) dense and sparse decoders to combine multi-level features, (4) a multi-resolution network that fuses the results of encoder-decoders run on different resolutions. Our model outperforms a feature-based approach and conventional encoder-decoders from the literature. We use semantic segmentations produced with our model in an automated diagnosis task and obtain higher accuracies than a baseline approach that employs an SVM for feature-based segmentation, both using the same segmentation-based diagnostic features.Comment: Added more WSI images in appendi

Page layout analysis and classification in complex scanned documents

Page layout analysis has been extensively studied since the 1980`s, particularly after computers began to be used for document storage or database units. For efficient document storage and retrieval from a database, a paper document would be transformed into its electronic version. Algorithms and methodologies are used for document image analysis in order to segment a scanned document into different regions such as text, image or line regions. To contribute a novel approach in the field of page layout analysis and classification, this algorithm is developed for both RGB space and grey-scale scanned documents without requiring any specific document types, and scanning techniques. In this thesis, a page classification algorithm is proposed which mainly applies wavelet transform, Markov random field (MRF) and Hough transform to segment text, photo and strong edge/ line regions in both color and gray-scale scanned documents. The algorithm is developed to handle both simple and complex page layout structures and contents (text only vs. book cover that includes text, lines and/or photos). The methodology consists of five modules. In the first module, called pre-processing, image enhancements techniques such as image scaling, filtering, color space conversion or gamma correction are applied in order to reduce computation time and enhance the scanned document. The techniques, used to perform the classification, are employed on the one-fourth resolution input image in the CIEL*a*b* color space. In the second module, the text detection module uses wavelet analysis to generate a text-region candidate map which is enhanced by applying a Run Length Encoding (RLE) technique for verification purposes. The third module, photo detection, initially uses block-wise segmentation which is based on basis vector projection technique. Then, MRF with maximum a-posteriori (MAP) optimization framework is utilized to generate photo map. Next, Hough transform is applied to locate lines in the fourth module. Techniques for edge detection, edge linkages, and line-segment fitting are used to detect strong-edges in the module as well. After those three classification maps are obtained, in the last module a final page layout map is generated by using K-Means. Features are extracted to classify the intersection regions and merge into one classification map with K-Means clustering. The proposed technique is tested on several hundred images and its performance is validated by utilizing Confusion Matrix (CM). It shows that the technique achieves an average of 85% classification accuracy rate in text, photo, and background regions on a variety of scanned documents like articles, magazines, business-cards, dictionaries or newsletters etc. More importantly, it performs independently from a scanning process and an input scanned document (RGB or gray-scale) with comparable classification quality

Deep point-based scene labeling with depth mapping and geometric patch feature encoding

This paper presents a deep CNN approach for point-based semantic scene labeling. This is challenging because 3D point clouds do not have a canonical domain and can have complex geometry and substantial variation of sampling densities. We propose a novel framework where the convolution operator is defined on depth maps around sampled points, which captures characteristics of local surface regions. We introduce Depth Mapping (DM) and Reverse Depth Mapping (RDM) operators to transform between the point domain and the depth map domain. Our depth map based convolution is computationally efficient, robust to scene scales and sampling densities, and can capture rich surface characteristics. We further propose to augment each point with feature encoding of the local geometric patches resulted from multi-method through patch pooling network (PPN). The patch features provide complementary information and are fed into our classification network to achieve semantic segmentation

Auto-completion of contours in sketches, maps and sparse 2D images based on topological persistence.

We design a new fast algorithm to automatically complete closed contours in a finite point cloud on the plane. The only input can be a scanned map with almost closed curves, a hand-drawn artistic sketch or any sparse dotted image in 2D without any extra parameters. The output is a hierarchy of closed contours that have a long enough life span (persistence) in a sequence of nested neighborhoods of the input points. We prove theoretical guarantees when, for a given noisy sample of a graph in the plane, the output contours geometrically approximate the original contours in the unknown graph

Consistent Density Scanning and Information Extraction From Point Clouds of Building Interiors

Over the last decade, 3D range scanning systems have improved considerably enabling the designers to capture large and complex domains such as building interiors. The captured point cloud is processed to extract specific Building Information Models, where the main research challenge is to simultaneously handle huge and cohesive point clouds representing multiple objects, occluded features and vast geometric diversity. These domain characteristics increase the data complexities and thus make it difficult to extract accurate information models from the captured point clouds. The research work presented in this thesis improves the information extraction pipeline with the development of novel algorithms for consistent density scanning and information extraction automation for building interiors. A restricted density-based, scan planning methodology computes the number of scans to cover large linear domains while ensuring desired data density and reducing rigorous post-processing of data sets. The research work further develops effective algorithms to transform the captured data into information models in terms of domain features (layouts), meaningful data clusters (segmented data) and specific shape attributes (occluded boundaries) having better practical utility. Initially, a direct point-based simplification and layout extraction algorithm is presented that can handle the cohesive point clouds by adaptive simplification and an accurate layout extraction approach without generating an intermediate model. Further, three information extraction algorithms are presented that transforms point clouds into meaningful clusters. The novelty of these algorithms lies in the fact that they work directly on point clouds by exploiting their inherent characteristic. First a rapid data clustering algorithm is presented to quickly identify objects in the scanned scene using a robust hue, saturation and value (H S V) color model for better scene understanding. A hierarchical clustering algorithm is developed to handle the vast geometric diversity ranging from planar walls to complex freeform objects. The shape adaptive parameters help to segment planar as well as complex interiors whereas combining color and geometry based segmentation criterion improves clustering reliability and identifies unique clusters from geometrically similar regions. Finally, a progressive scan line based, side-ratio constraint algorithm is presented to identify occluded boundary data points by investigating their spatial discontinuity