Diagnostic Compression of Biomedical Volumes

In this work we deal with lossy compression of biomedical volumes. By force of circumstances, diagnostic compression is bound to a subjective judgment. However, with respect to the algorithms, there is a need to shape the coding methodology so as to highlight beyond compression three important factors: the medical data, the specic usage and the particular end-user. Biomedical volumes may have very dierent characteristics which derive from imaging modality, resolution and voxel aspect ratio. Moreover, volumes are usually viewed slice by slice on a lightbox, according to dierent cutting direction (typically one of the three voxel axes). We will see why and how these aspects impact on the choice of the coding algorithm and on a possible extension of 2D well known algorithms to more ecient 3D versions. Cross-correlation between reconstruction error and signal is a key aspect to keep into account; we suggest to apply a non uniform quantization to wavelet coefficients in order to reduce slice PSNR variation. Once a good neutral coding for a certain volume is obtained, non uniform quantization can also be made space variant in order to reach more objective quality on Volumes of Diagnostic Interest (VoDI), which in turns can determine the diagnostic quality of the entire data set

Cyclostationary error analysis and filter properties in a 3D wavelet coding framework

The reconstruction error due to quantization of wavelet subbands can be modeled as a cyclostationary process because of the linear periodically shift variant property of the inverse wavelet transform. For N-dimensional data, N-dimensional reconstruction error power cyclostationary patterns replicate on the data sample lattice. For audio and image coding applications this fact is of little practical interest since the decoded data is perceived in its wholeness, the error power oscillations on single data elements cannot be seen or heard and a global PSNR error measure is often used to represent the reconstruction quality. A different situation is the one of 3D data (static volumes or video sequences) coding, where decoded data are usually visualized by plane sections and the reconstruction error power is commonly measured by a PSNR[n] sequence, with n representing either a spatial slicing plane (for volumetric data) or the temporal reference frame (for video). In this case, the cyclostationary oscillations on single data elements lead to a global PSNR[n] oscillation and this effect may become a relevant concern. In this paper we study and describe the above phenomena and evaluate their relevance in concrete coding applications. Our analysis is entirely carried out in the original signal domain and can easily be extended to more than three dimensions. We associate the oscillation pattern with the wavelet filter properties in a polyphase framework and we show that a substantial reduction of the oscillation amplitudes can be achieved under a proper selection of the basis functions. Our quantitative model is initially made under high-resolution conditions and then qualitatively extended to all coding rates for the wide family of bit-plane quantization-based coding techniques. Finally, we experimentally validate the proposed models and we perform a subjective evaluation of the visual relevance of the PSNR[n] fluctuations in the cases of medical volumes and video coding

Multi-view alignment with database of features for an improved usage of high-end 3D scanners

The usability of high-precision and high-resolution 3D scanners is of crucial importance due to the increasing demand of 3D data in both professional and general-purpose applications. Simplified, intuitive and rapid object modeling requires effective and automated alignment pipelines capable to trace back each independently acquired range image of the scanned object into a common reference system. To this end, we propose a reliable and fast feature-based multiple-view alignment pipeline that allows interactive registration of multiple views according to an unchained acquisition procedure. A robust alignment of each new view is estimated with respect to the previously aligned data through fast extraction, representation and matching of feature points detected in overlapping areas from different views. The proposed pipeline guarantees a highly reliable alignment of dense range image datasets on a variety of objects in few seconds per million of points

Progressive contour coding in the wavelet domain

This paper presents a new wavelet-based image contour coding technique, suitable for representing either shapes or generic contour maps. Starting from a contour map (e.g. a segmentation map or the result of a contour extraction operator), this is first converted in a one-dimensional signal. Coordinate jumps among different contour extremities are converted, if under a suitable threshold, into signal discontinuities which can be compactly represented in the wavelet domain. Otherwise, the exceeding discontinuities are coded as side information. This side information is minimized by an optimized contour segment sequencing. The obtained 1D signal is decomposed and coded in the wavelet domain by using a 1D version of an improved implementation of the SPIHT algorithm. This technique can efficiently code every kind of 2D contour map, from one to many unconnected contour segments. It guarantees a fully embedded progressive coding, state-of-art coding performance, good approximation capabilities for both open and closed contours, and visually graceful degradation at low bit-rates

Adaptive dilation analysis for wavelet coding with EMDC

The Embedded Morphological Dilation Coding (EMDC) algorithm, recently proposed by the author of this work, implements a direct coding of the wavelet coefficients significance map that is based on the action of a new kind of multiresolution binary (bit-plane) morphological operator. EMDC actually includes the most part of existing morphological wavelet codecs, it produces a fully progressive bitstream with low complexity and has demonstrated competitive coding performances. A peculiar feature of EMDC is the adaptive and the extended connectivity nature of the morphological analysis of the subband coefficients. In this paper we give a detailed description of this feature and quantify the related performance improvements. We conclude that the considered pattern analysis and coding technique allow an increased reduction of the data redundancy and fills the gap between existing morphological dilation techniques and state-of-the-art wavelet coders

A robust pipeline for rapid feature-based pre-alignment of dense range scans

Aiming at reaching an interactive and simplified usage of high-resolution 3D acquisition systems, this paper presents a fast and automated technique for pre-alignment of dense range images. Starting from a multi-scale feature point ex- traction and description, a processing chain composed by feature matching and correspondence searching, ranking grouping and skimming is performed to select the most re- liable correspondences over which the correct alignment is estimated. Pre-alignment is obtained in few seconds per million point images on a off-the-shelf PC architecture. The experimental setup aimed to demonstrate the system behav- ior with respect to a set of concurrent requirements and the obtained performance are significant in the perspective of a fast, robust and unconstrained 3D object reconstruction

High-Performance Embedded Morphological Wavelet Coding

Morphological analysis can be applied in wavelet domain to analyze and represent the position of significant coefficients. New operators have to be introduced which are able to exploit both the multiresolution and the filter bank peculiarities of the subband representation of visual information. In this paper an efficient morphological wavelet coder is proposed. The clustering trend of significant coefficients is captured by a new kind of multi resolution binary dilation operator. The layered and adaptive nature of this subband dilation makes it possible for the coding technique to produce an embedded bit-stream with a modest computational cost and state-of-the-art Rate-Distortion performance. Morphological wavelet coding appears promising because the localized analysis of wavelet coefficient clusters is adequate to capture intrinsic patterns of the source which can have substantial benefits for perceptual or even object-based reconstruction quality concerns. Here we test the performance of our algorithm and compare the effects of different wavelet filters. We obtain state of the art coding performance and good perceptual results both for 2D and 3D images, with a new technique that seems to be well suited for further developments

Performance Evidence of Software Proposal for Wavelet Video Coding Exploration Group

The document m13416 presents the encoding performance of the wavelet scalable video codec developed by aceMedia consortium. The codec architecture, concerning the encoding schemes (t+2D, 2D+t+2D, etc.) that can be realized, are basically the same allowed in the current MSRA VidWav scalable video coding model. The main differences can be found in the fundamental tools, such as Motion Estimation, Entropy Encoder, etc., used to implement a given encoding architecture. The evaluation of the proposed technology and its performance will be useful for improving the current VidWav reference scalable video codec

Spatial–Spectral Evidence of Glare Influence on Hyperspectral Acquisitions

Glare is an unwanted optical phenomenon which affects imaging systems with optics. This paper presents for the first time a set of hyperspectral image (HSI) acquisitions and measurements to verify how glare affects acquired HSI data in standard conditions. We acquired two ColorCheckers (CCs) in three different lighting conditions, with different backgrounds, different exposure times, and different orientations. The reflectance spectra obtained from the imaging system have been compared to pointwise reference measures obtained with contact spectrophotometers. To assess and identify the influence of glare, we present the Glare Effect (GE) index, which compares the contrast of the grayscale patches of the CC in the hyperspectral images with the contrast of the reference spectra of the same patches. We evaluate, in both spatial and spectral domains, the amount of glare affecting every hyperspectral image in each acquisition scenario, clearly evidencing an unwanted light contribution to the reflectance spectra of each point, which increases especially for darker pixels and pixels close to light sources or bright patche

Improving SPIHT-based Compression of Volumetric Medical Data

Volumetric medical data (CT,MR) are useful tools for diagnostic investigation however their usage may be made diffcult because of the amount of data to store or because of the duration of communication over a limited capacity channel. In order to code such information sources we present a progressive three dimensional image compression algorithm based on zerotree wavelet coder with arithmetic coding. We make use of a 3D separable biorthogonal wavelet transform and we extend the zerotree SPIHT algorithm to three dimensions. Moreover we propose some improvements to the SPIHT encoder in order to obtain a better rate distortion performance without increasing the computational complexity. Finally we propose an efficient context-based adaptive arithmetic coding which eliminates high order redundancy. The results obtained on progressive coding of a test CT volume are better than those presented in recent similar works both for the mean PSNR on the whole volume and for the PSNR homogeneity between various slices