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PubMed2003

Is digital image compression acceptable within diabetic retinopathy screening?

AIMS: The National Screening Committee (NSC), whilst recommending the use of digital mydriatic retinal photography for diabetic retinopathy screening, has not yet accepted the use of digitally compressed images for grading. By greatly reducing the file size, however, compression of images is invaluable for storage and for its rapid transmission across computer networks. We undertook a study to compare the different levels of JPEG compression with the original bit-mapped image to determine whether there was any loss of clinical detail following compression. METHODS: Three hundred and thirty images were analysed in this study. These images had been captured from 66 eyes consecutively photographed in a diabetic retinopathy screening programme, using a Sony DXC-950 P 3CCD colour video camera mounted on a Canon CR6-45NMf fundus camera. Single 45 degrees macula-centred images were taken from each eye. The images were compressed using the JPEG algorithm within Adobe Photoshop (version 4.0) and then displayed with a Sony Trinitron colour monitor. Four different levels of compression were used, JPEG-1, JPEG-2, JPEG-3, JPEG-4, and an objective analysis was undertaken using 'lesion counts'. The compressed images were assessed separately and blindly and the results compared with their original BMP images. RESULTS: Eight BMP images could not be evaluated (five right eye and three left eye). A total of 290 images were therefore used in the final evaluation. All the JPEG-1 images with file sizes between 16 and 24 kb were found to be 'pixelated', while the JPEG-4 images (66-107 kb) appeared similar to the original BMP (1.3 Mb) images. Both JPEG-2 and JPEG-3 images had significantly lower counted lesions than the BMP images. CONCLUSIONS: From our findings we can conclude that only some degree of image compression (compression ratios of 1 : 20 to 1 : 12) with file sizes of 66-107 kb is permissible using JPEG format, whereas the images obtained after higher compression ratios may not be suitable for diabetic retinopathy screening.

Adult↗
PubMed2006

Semi-regular representation and progressive compression of 3-D dynamic mesh sequences.

We propose an algorithm that represents three-dimensional dynamic objects with a semi-regular mesh sequence and compresses the sequence using the spatiotemporal wavelet transform. Given an irregular mesh sequence, we construct a semi-regular mesh structure for the first frame and then map it to subsequent frames based on the hierarchical motion estimation. The regular structure of the resulting mesh sequence facilitates the application of advanced coding schemes and other signal processing techniques. To encode the mesh sequence compactly, we develop an embedded coding scheme, which supports signal-to-noise ratio and temporal scalability modes. Simulation results demonstrate that the proposed algorithm provides significantly better compression performance than the static mesh coder, which encodes each frame independently.

Algorithms↗
PubMedDate not supplied

A comparison of JPEG and FIF compression of color medical images for dermatology.

Dermatologists were shown digitized images of skin lesions compressed by Joint Photographic Expert Group (JPEG) and fractal image format (FIF) algorithms and asked to make a diagnostic assessment and rate the image quality in displaying the features necessary for that assessment. Dermatologists performance in the diagnostic assessment was not affected by the level of compression (up to 40X) using either algorithm, but ratings of image quality for all compressed images were significantly lower than for uncompressed images and for the original photographic slides. There were no significant differences in dermatologists' performance or ratings between the two compression algorithms.

Algorithms↗
PubMedDate not supplied

Wavelet-based progressive compression scheme for triangle meshes: wavemesh.

This paper proposes a new lossy to lossless progressive compression scheme for triangular meshes, based on a wavelet multiresolution theory for irregular 3D meshes. Although remeshing techniques obtain better compression ratios for geometric compression, this approach can be very effective when one wants to keep the connectivity and geometry of the processed mesh completely unchanged. The simplification is based on the solving of an inverse problem. Optimization of both the connectivity and geometry of the processed mesh improves the approximation quality and the compression ratio of the scheme at each resolution level. We show why this algorithm provides an efficient means of compression for both connectivity and geometry of 3D meshes and it is illustrated by experimental results on various sets of reference meshes, where our algorithm performs better than previously published approaches for both lossless and progressive compression.

Algorithms↗
PubMed2026

RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.

MOTIVATION: Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this problem. In particular, run-length Burrows-Wheeler transform (RLBWT) based compressed full text indexes have seen wide development and adoption. However, the construction of these RLBWT-based compressed full text indexes is still computationally expensive, sometimes prohibitively so, even for current dataset sizes. RESULTS: Therefore, we present algorithms for the construction of RLBWT-based compressed full text indexes and their supporting data structures in compressed space. The algorithms have a space complexity of O(r) words and run in O(n) time for repetitive datasets, where r is the number of runs in the BWT, n is the length of the text, and repetitive datasets implies nr∈Ω(log n). We provide the first algorithm to compute LCP-related information for repetitive datasets in optimal time and O(r) space, greatly reducing memory requirements. The key idea behind this algorithm is the utilization of r samples of the inverse suffix array at regular intervals. For example, on the Human Pangenome Reference Consortium Release 2 dataset, this reduces peak memory from 2135 GiB to 170 GiB (12.6x reduction) compared to the previous best method (pfp-thresholds). AVAILABILITY AND IMPLEMENTATION: The implementation is available at https://github.com/ucfcbb/TeraTools.

Algorithms↗
PubMed2006

3-band motion-compensated temporal structures for scalable video coding.

Recent breakthroughs in motion-compensated temporal wavelet filtering have finally enabled implementation of highly efficient scalable and error-resilient video codecs. These new wavelet codecs provide numerous advantages over nonscalable conventional solutions techniques based on motion-compensated prediction, such as no recursive predictive loop, separation of noise and sampling artifacts from the content through use of longer temporal filters, removal of long range as well as short range temporal redundancies, etc. Moreover, these wavelet video coding schemes can provide flexible spatial, temporal, signal-to-noise ratio and complexity scalability with fine granularity over a large range of bit rates, while maintaining a very high coding efficiency. However, most motion-compensated wavelet video schemes are based on classical two-band decompositions that offer only dyadic factors of temporal scalability. In this paper, we propose a three-band temporal structure that extends the concept of motion-compensated temporal filtering (MCTF) that was introduced in the classical lifting framework. These newly introduced structures provide higher temporal scalability flexibility, as well as improved compression performance compared with dyadic Haar MCTF.

Algorithms↗
PubMed2002

[ECG signal compression based on best basis of wavelet packets].

The paper reports a kind of new compression method of ECG signal. The method is realized by means of wavelet packets transform based on best basis performed by Shanon-Weaker entropy criterion. The result of simulation shows that this is an efficient compression method characterized by larger compression ratio and less loss, and the original signal can be recovered well.

Algorithms↗
PubMed1996

Quantitative DNA ploidy analysis of breast carcinoma: a study of the effects of joint photographer experts group (JPEG) compression on DNA ploidy images.

Telepathology usage in the past has typically been a qualitative procedure rather than a quantitative measurement. DNA ploidy using image analysis has been favorably compared to DNA ploidy analysis by flow cytometry in numerous publications. A step from DNA ploidy analysis using conventional image analysis to DNA ploidy analysis using stored images allows DNA ploidy analysis by image cytometry to become a powerful tool in telepathology. Remote DNA ploidy analysis using stored images has an impact on the field of pathology, as not every hospital or laboratory can afford to perform this type of specialized testing. However, images have large data files and require lengthy transmission times over communication systems to other computers. Joint Photographer Experts Group (JPEG) compression is a computer algorithm that allows the file size of an image to be reduced in order to decrease transmission times to another computer. A study was initiated to investigate the effects of JPEG compression on images of Feulgen stained breast tumor touch preps and the resulting DNA ploidy histograms.

Animals↗
PubMed2001

ECG data reduction method for medical telemetry systems.

In current medical practice, all transmitters used for monitoring an ECG send data continuously. If transmission could be limited to only the ECG data that requires the attention of a technician, the likelihood of interference and power consumption would be reduced considerably. In this paper, we propose a new ECG telemetry system. The transmitter has a simple ECG analyzer and it only transmits data when abnormal waveforms are detected. As part of this system, we propose a simple algorithm to detect an abnormal ECG. The algorithm is composed of a baseline drift canceller (utilizing a moving average calculation), a waveform detector (using a modified second order derivative) and an ECG analyzer. In order to test the effectiveness and feasibility of the algorithm, computer simulations (with a MIT-BIH ECG database) and experiments (with microprocessor-based hardware) were performed. The results of the simulations show that the detection performance and data compression performance of the algorithm are adequate. The results of the experiment show that the algorithm even performs adequately when used with microprocessor-based hardware that is of limited size or limited power consumption.

Algorithms↗
PubMed2004

A perceptual evaluation of JPEG 2000 image compression for digital mammography: contrast-detail characteristics.

In this investigation the effect of JPEG 2000 compression on the contrast-detail (CD) characteristics of digital mammography images was studied using an alternative forced choice (AFC) technique. Images of a contrast-detail phantom, acquired using a clinical full-field digital mammography system, were compressed using a commercially available software product (JPEG 2000). Data compression was achieved at ratios of 1:1, 10:1, 20:1, and 30:1 and the images were reviewed by seven observers on a high-resolution display. Psychophysical detection characteristics were first computed by fitting perception data using a maximum-likelihood technique from which CD curves were derived at 50%, 62.5%, and 75% threshold levels. Statistical analysis indicated no significant difference in the perception of mean disk thickness up to 20:1 compression except for disk diameter of 1 mm. All other compression combinations exhibited significant degradation in CD characteristics.

Algorithms↗
PubMed2005

Lossless compression based on inter-frame coding for MDCT.

Many images are generated by medical equipment and the number of images to be stored increases yearly. To cope with the large digital storage and transmission requirements, data compression techniques have been studied. In the present study, grayscale data (2 bytes/pixel) were divided into high bytes and low bytes, and then the original medical images were also divided into high byte (1byte/pixel format) and low byte (1byte/pixel format) images. Inter-frame coding with and without division into high and low byte images was applied to MDCT images. Prediction (inter-frame) coding is a very common method to compress sequence images. The division process can be added to inter-frame coding easily. The compression ratio of the archived file produced by application of Lemple-Ziv compression and prediction coding with the division process was 0.39 at 700 images.

Algorithms↗
PubMed2003

Lossy compression of eye movement and auditory brainstem response signals.

Eye movement and auditory brainstem response signals recorded for balance and hearing investigations were used as a medical test battery for several types of lossy compression techniques. These signals are associated with the function of the ears. The former signals are used to assess the balance problems (especially vertigo) of a subject and the latter his or her hearing problems. New technique is also presented based on successive approximation quantization. The effect of information loss on medical parameters computed from the signals in the course of compression was evaluated for brainstem response signals. It is important to ensure that lossy compression techniques of these biomedical signals do not impair medical parameter values computed from the signals.

Algorithms↗
PubMed2001

Compression of echocardiographic scan line data using wavelet packet transform.

An efficient compression strategy is indispensable for digital echocardiography. Previous work has suggested improved results utilizing wavelet transforms in the compression of 2D echocardiographic images. Set partitioning in hierarchical trees (SPIHT) was modified to compress echocardiographic scanline data based on the wavelet packet transform. A compression ratio of at least 94:1 resulted in preserved image quality.

Algorithms↗
PubMedDate not supplied

The formal specification of an electrocardiogram compressor.

Remote telemonitoring of physiological parameters is being used increasingly both for medical research and for clinical management. However, the technique entails the collection of large volumes of information for transmission and storage which necessitates efficient means of data compression. This paper presents a simple mathematical model of the lossy compression of physiological signals. The model is developed in a top-down style making design decisions progressively. First a general model of lossy compression is developed and some lemmas presented. Then the model is refined to take advantage of inherent cyclicity in many types of physiological signal. Finally the model is specialized to the compression of electrocardiograms. An algorithm is described for implementing the model. The algorithm is a table-based method capable of achieving very low output bit rates (50 bps) with reasonable fidelity. This compares favourably with the results obtained by other workers and holds promise for further evaluation. The generality of the model should ultimately allow a coherent approach to the compression of the various types of physiological signal currently being recorded.

Algorithms↗
PubMed2006

Efficient transmission of compressed data for remote volume visualization.

One of the goals of telemedicine is to enable remote visualization and browsing of medical volumes. There is a need to employ scalable compression schemes and efficient client-server models to obtain interactivity and an enhanced viewing experience. First, we present a scheme that uses JPEG2000 and JPIP (JPEG2000 Interactive Protocol) to transmit data in a multi-resolution and progressive fashion. The server exploits the spatial locality offered by the wavelet transform and packet indexing information to transmit, in so far as possible, compressed volume data relevant to the clients query. Once the client identifies its volume of interest (VOI), the volume is refined progressively within the VOI from an initial lossy to a final lossless representation. Contextual background information can also be made available having quality fading away from the VOI. Second, we present a prioritization that enables the client to progressively visualize scene content from a compressed file. In our specific example, the client is able to make requests to progressively receive data corresponding to any tissue type. The server is now capable of reordering the same compressed data file on the fly to serve data packets prioritized as per the client's request. Lastly, we describe the effect of compression parameters on compression ratio, decoding times and interactivity. We also present suggestions for optimizing JPEG2000 for remote volume visualization and volume browsing applications. The resulting system is ideally suited for client-server applications with the server maintaining the compressed volume data, to be browsed by a client with a low bandwidth constraint.

Algorithms↗
PubMed2005

Fourier-transform method of data compression and temporal fringe pattern analysis.

Temporal fringe pattern analysis is invaluable in studies of transient phenomena but necessitates large data storage for two essential sets of data, i.e., fringe pattern intensity and deformation phase. We describe a compression scheme based on the Fourier-transform method for temporal fringe data storage that permits retrieval of both the intensity and the deformation phase. When the scheme was used with simulated temporal wavefront interferometry intensity fringe patterns, a high compression ratio of 10.77 was achieved, with a significant useful data ratio of 0.859. The average root-mean-square error in phase value restored was a low 0.0015 rad. With simulated temporal speckle interferometry intensity fringe patterns, the important paremeters varied with the modulation cutoff value applied. For a zero modulation cutoff value, the ratio of data points and the compression ratio values obtained were roughly the same as in wavelength interferometry, albeit the average root-mean-square error in the phase value restored was far higher. By increasing the modulation cutoff value we attained significant reduction and increase in the ratio of data points and the compression ratio, respectively, whereas the average root-mean-square error in the restored phase values was reduced only slightly.

Algorithms↗
PubMed2002

The efficient computation of position-specific match scores with the fast fourier transform.

Historically, in computational biology the fast Fourier transform (FFT) has been used almost exclusively to count the number of exact letter matches between two biosequences. This paper presents an FFT algorithm that can compute the match score of a sequence against a position-specific scoring matrix (PSSM). Our algorithm finds the PSSM score simultaneously over all offsets of the PSSM with the sequence, although like all previous FFT algorithms, it still disallows gaps. Although our algorithm is presented in the context of global matching, it can be adapted to local matching without gaps. As a benchmark, our PSSM-modified FFT algorithm computed pairwise match scores. In timing experiments, our most efficient FFT implementation for pairwise scoring appeared to be 10 to 26 times faster than a traditional FFT implementation, with only a factor of 2 in the acceleration attributable to a previously known compression scheme. Many important algorithms for detecting biosequence similarities, e.g., gapped BLAST or PSIBLAST, have a heuristic screening phase that disallows gaps. This paper demonstrates that FFT algorithms merit reconsideration in these screening applications.

Algorithms↗