Graph-based transforms based on prediction inaccuracy modeling for pathology image coding

Digital pathology images are multi giga-pixel color images that usually require large amounts of bandwidth to be transmitted and stored. Lossy compression using intra - prediction offers an attractive solution to reduce the storage and transmission requirements of these images. In this paper, we evaluate the performance of the Graph - based Transform (GBT) within the context of block - based predictive transform coding. To this end, we introduce a novel framework that eliminates the need to signal graph information to the decoder to recover the coefficients. This is accomplished by computing the GBT using predicted residual blocks, which are predicted by a modeling approach that employs only the reference samples and information about the prediction mode. Evaluation results on several pathology images, in terms of the energy preserved and MSE when a small percentage of the largest coefficients are used for reconstruction, show that the GBT can outperform the DST and DCT

Prediction-based coding with rate control for lossless region of interest in pathology imaging

Online collaborative tools for medical diagnosis produced from digital pathology images have experimented an increase in demand in recent years. Due to the large sizes of pathology images, rate control (RC) techniques that allow an accurate control of compressed file sizes are critical to meet existing bandwidth restrictions while maximizing retrieved image quality. Recently, some RC contributions to Region of Interest (RoI) coding for pathology imaging have been presented. These encode the RoI without loss and the background with some loss, and focus on providing high RC accuracy for the background area. However, none of these RC contributions deal efficiently with arbitrary RoI shapes, which hinders the accuracy of background definition and rate control. This manuscript presents a novel coding system based on prediction with a novel RC algorithm for RoI coding that allows arbitrary RoIs shapes. Compared to other methods of the state of the art, our proposed algorithm significantly improves upon their RC accuracy, while reducing the compressed data rate for the RoI by 30%. Furthermore, it offers higher quality in the reconstructed background areas, which has been linked to better clinical performance by expert pathologists. Finally, the proposed method also allows lossless compression of both the RoI and the background, producing data volumes 14% lower than coding techniques included in DICOM, such as HEVC and JPEG-LS

Mosaic-Based Color-Transform Optimization for Lossy and Lossy-to-Lossless Compression of Pathology Whole-Slide Images

Altres ajuts: This work has been funded by the EU Marie Curie CIG Programme under Grant PIMCO, the Engineering and Physical Sciences Research Council (EPSRC), UKThe use of whole-slide images (WSIs) in pathology entails stringent storage and transmission requirements because of their huge dimensions. Therefore, image compression is an essential tool to enable efficient access to these data. In particular, color transforms are needed to exploit the very high degree of inter-component correlation and obtain competitive compression performance. Even though the state-of-the-art color transforms remove some redundancy, they disregard important details of the compression algorithm applied after the transform. Therefore, their coding performance is not optimal. We propose an optimization method called mosaic optimization for designing irreversible and reversible color transforms simultaneously optimized for any given WSI and the subsequent compression algorithm. Mosaic optimization is designed to attain reasonable computational complexity and enable continuous scanner operation. Exhaustive experimental results indicate that, for JPEG 2000 at identical compression ratios, the optimized transforms yield images more similar to the original than the other state-of-the-art transforms. Specifically, irreversible optimized transforms outperform the Karhunen-Loève Transform in terms of PSNR (up to 1.1 dB), the HDR-VDP-2 visual distortion metric (up to 3.8 dB), and the accuracy of computer-aided nuclei detection tasks (F1 score up to 0.04 higher). In addition, reversible optimized transforms achieve PSNR, HDR-VDP-2, and nuclei detection accuracy gains of up to 0.9 dB, 7.1 dB, and 0.025, respectively, when compared with the reversible color transform in lossy-to-lossless compression regimes

DPCM-based edge prediction for lossless screen content coding in HEVC

Screen content sequences are ubiquitous type of video data in numerous multimedia applications like video conferencing, remote education, and cloud gaming. These sequences are characterized for depicting a mix of computer generated graphics, text, and camera-captured material. Such a mix poses several challenges, as the content usually depicts multiple strong discontinuities, which are hard to encode using current techniques. Differential pulse code modulation (DPCM)-based intra-prediction has shown to improve coding efficiency for these sequences. In this paper we propose sample-based edge and angular prediction (SEAP), a collection of DPCM-based intra-prediction modes to improve lossless coding of screen content. SEAP is aimed at accurately predicting regions depicting not only camera-captured material, but also those depicting strong edges. It incorporates modes that allow selecting the best predictor for each pixel individually based on the characteristics of the causal neighborhood of the target pixel. We incorporate SEAP into HEVC intra-prediction. Evaluation results on various screen content sequences show the advantages of SEAP over other DPCM-based approaches, with bit-rate reductions of up to 19.56% compared to standardized RDPCM. When used in conjunction with the coding tools of the screen content coding extensions, SEAP provides bit-rate reductions of up to 8.63% compared to RDPCM

Graph based transforms for block-based predictive transform coding

Orthogonal transforms are the key aspects of the encoding and decoding process in many state-of-the-art compression systems. The transforms in blockbased predictive transform coding (PTC) is essential for improving coding performance, as it allows decorrelating the signal in the form of transform coefficients. Recently, the Graph-Based Transform (GBT), has been shown to attain promising results for data decorrelation and energy compaction especially for block-based PTC. However, in order to reconstruct a frame for GBT using block-based PTC, extra-information is needed to be signalled into the bitstream, which may lead to an increased overhead. Additionally, the same graph should be available at the reconstruction stage to compute the inverse GBT of each block. In this thesis, we propose a set of a novel class of GBTs to enhance the performance of transform. These GBTs adopt several methods to address the issue of the availability of the same graph at the decoder while reconstructing video frames. Our methods to predict the graph can be categorized in two types: non-learning-based approaches and deep learning (DL) based prediction. For the first type our method uses reference samples and template-based strategies for reconstructing the same graph. For our next strategies we learn the graphs so that the information needed to compute the inverse transform is common knowledge between the compression and reconstruction processes. Finally, we train our model online to avoid the amount, quality, and relevance of the training data. Our evaluation is based on all the possible classes of HEVC videos, consist of class A to F/Screen content based on their varied resolution and characteristics. Our experimental results show that the proposed transforms outperforms the other non-trainable transforms, such as DCT and DCT/DST, which are commonly employed in current video codecs in terms of compression and reconstruction quality

Piecewise mapping in HEVC lossless intra-prediction coding

The lossless intra-prediction coding modality of the High Efficiency Video Coding (HEVC) standard provides high coding performance while following frame-by-frame basis access to the coded data. This is of interest in many professional applications such as medical imaging, automotive vision and digital preservation in libraries and archives. Various improvements to lossless intra-prediction coding have been proposed recently, most of them based on sample-wise prediction using Differential Pulse Code Modulation (DPCM). Other recent proposals aim at further reducing the energy of intra-predicted residual blocks. However, the energy reduction achieved is frequently minimal due to the difficulty of correctly predicting the sign and magnitude of residual values. In this paper, we pursue a novel approach to this energy-reduction problem using piecewise mapping (pwm) functions. Specifically, we analyze the range of values in residual blocks and apply accordingly a pwm function to map specific residual values to unique lower values. We encode appropriate parameters associated with the pwm functions at the encoder, so that the corresponding inverse pwm functions at the decoder can map values back to the same residual values. These residual values are then used to reconstruct the original signal. This mapping is, therefore, reversible and introduces no losses. We evaluate the pwm functions on 4×4 residual blocks computed after DPCM-based prediction for lossless coding of a variety of camera-captured and screen content sequences. Evaluation results show that the pwm functions can attain maximum bit-rate reductions of 5.54% and 28.33% for screen content material compared to DPCM-based and block-wise intra-prediction, respectively. Compared to IntraBlock Copy, piecewise mapping can attain maximum bit-rate reductions of 11.48% for camera-captured material

Visual Saliency Estimation Via HEVC Bitstream Analysis

Abstract Since Information Technology developed dramatically from the last century 50's, digital images and video are ubiquitous. In the last decade, image and video processing have become more and more popular in biomedical, industrial, art and other fields. People made progress in the visual information such as images or video display, storage and transmission. The attendant problem is that video processing tasks in time domain become particularly arduous. Based on the study of the existing compressed domain video saliency detection model, a new saliency estimation model for video based on High Efficiency Video Coding (HEVC) is presented. First, the relative features are extracted from HEVC encoded bitstream. The naive Bayesian model is used to train and test features based on original YUV videos and ground truth. The intra frame saliency map can be achieved after training and testing intra features. And inter frame saliency can be achieved by intra saliency with moving motion vectors. The ROC of our proposed intra mode is 0.9561. Other classification methods such as support vector machine (SVM), k nearest neighbors (KNN) and the decision tree are presented to compare the experimental outcomes. The variety of compression ratio has been analysis to affect the saliency

Contributions to Medical Image Segmentation and Signal Analysis Utilizing Model Selection Methods

This thesis presents contributions to model selection techniques, especially based on information theoretic criteria, with the goal of solving problems appearing in signal analysis and in medical image representation, segmentation, and compression.The field of medical image segmentation is wide and is quickly developing to make use of higher available computational power. This thesis concentrates on several applications that allow the utilization of parametric models for image and signal representation. One important application is cell nuclei segmentation from histological images. We model nuclei contours by ellipses and thus the complicated problem of separating overlapping nuclei can be rephrased as a model selection problem, where the number of nuclei, their shapes, and their locations define one segmentation. In this thesis, we present methods for model selection in this parametric setting, where the intuitive algorithms are combined with more principled ones, namely those based on the minimum description length (MDL) principle. The results of the introduced unsupervised segmentation algorithm are compared with human subject segmentations, and are also evaluated with the help of a pathology expert.Another considered medical image application is lossless compression. The objective has been to add the task of image segmentation to that of image compression such that the image regions can be transmitted separately, depending on the region of interest for diagnosis. The experiments performed on retinal color images show that our modeling, in which the MDL criterion selects the structure of the linear predictive models, outperforms publicly available image compressors such as the lossless version of JPEG 2000.For time series modeling, the thesis presents an algorithm which allows detection of changes in time series signals. The algorithm is based on one of the most recent implementations of the MDL principle, the sequentially normalized maximum likelihood (SNML) models.This thesis produces contributions in the form of new methods and algorithms, where the simplicity of information theoretic principles are combined with a rather complex and problem dependent modeling formulation, resulting in both heuristically motivated and principled algorithmic solutions

Image Processing Using FPGAs

This book presents a selection of papers representing current research on using field programmable gate arrays (FPGAs) for realising image processing algorithms. These papers are reprints of papers selected for a Special Issue of the Journal of Imaging on image processing using FPGAs. A diverse range of topics is covered, including parallel soft processors, memory management, image filters, segmentation, clustering, image analysis, and image compression. Applications include traffic sign recognition for autonomous driving, cell detection for histopathology, and video compression. Collectively, they represent the current state-of-the-art on image processing using FPGAs