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PubMed2005

Space-frequency quantiser design for ultrasound image compression based on minimum description length criterion.

The paper addresses the problem of how the spatial quantisation mode and subband adaptive uniform scalar quantiser can be jointly optimised in the minimum description length (MDL) framework for compression of ultrasound images. It has been shown that the statistics of wavelet coefficients in the medical ultrasound (US) image can be better approximated by the generalised Student t-distribution. By combining these statistics with the operational rate-distortion (RD) criterion, a space-frequency quantiser (SFQ) called the MDL-SFQ was designed, which used an efficient zero-tree quantisation technique for zeroing out the tree-structured sets of wavelet coefficients and an adaptive scalar quantiser to quantise the non-zero coefficients. The algorithm used the statistical 'variance of quantisation error' to achieve the different bit-rates ranging from near-lossless to lossy compression. Experimental results showed that the proposed coder outperformed the set partitioning in hierarchical trees (SPIHT) image coder both quantitatively and qualitatively. It yielded an improved compression performance of 1.01 dB over the best zero-tree based coder SPIHIT at 0.25 bits per pixel when averaged over five ultrasound images.

Algorithms↗
PubMed2000

Effect of CT digital image compression on detection of coronary artery calcification.

PURPOSE: To test the effect of digital compression of CT images on the detection of small linear or spotted high attenuation lesions such as coronary artery calcification (CAC). MATERIAL AND METHODS: Fifty cases with and 50 without CAC were randomly selected from a population that had undergone spiral CT of the thorax for screening lung cancer. CT image data were compressed using JPEG (Joint Photographic Experts Group) or wavelet algorithms at ratios of 10:1, 20:1 or 40:1. Five radiologists reviewed the uncompressed and compressed images on a cathode-ray-tube. Observer performance was evaluated with receiver operating characteristic analysis. RESULTS: CT images compressed at a ratio as high as 20:1 were acceptable for primary diagnosis of CAC. There was no significant difference in the detection accuracy for CAC between JPEG and wavelet algorithms at the compression ratios up to 20:1. CT images were more vulnerable to image blurring on the wavelet compression at relatively lower ratios, and "blocking" artifacts occurred on the JPEG compression at relatively higher ratios. CONCLUSION: JPEG and wavelet algorithms allow compression of CT images without compromising their diagnostic value at ratios up to 20:1 in detecting small linear or spotted high attenuation lesions such as CAC, and there was no difference between the two algorithms in diagnostic accuracy.

Adult↗
PubMed1997

Near-infrared spectroscopy for monitoring of tissue oxygenation of exercising skeletal muscle in a chronic compartment syndrome model.

Variations in the levels of muscle hemoglobin and of myoglobin oxygen saturation can be detected non-invasively with near-infrared spectroscopy. This technique could be applied to the diagnosis of chronic compartment syndrome, in which invasive testing has shown increased intramuscular pressure associated with ischemia and pain during exercise. We simulated chronic compartment syndrome in ten healthy subjects (seven men and three women) by applying external compression, through a wide inflatable cuff, to increase the intramuscular pressure in the anterior compartment of the leg. The tissue oxygenation of the tibialis anterior muscle was measured with near-infrared spectroscopy during gradual inflation of the cuff to a pressure of forty millimeters of mercury (5.33 kilopascals) during fourteen minutes of cyclic isokinetic dorsiflexion and plantar flexion of the ankle. The subjects exercised with and without external compression. The data on tissue oxygenation for each subject then were normalized to a scale of 100 per cent (the baseline value, or the value at rest) to 0 per cent (the physiological minimum, or the level of oxygenation achieved by exercise to exhaustion during arterial occlusion of the lower extremity). With external compression, tissue oxygenation declined at a rate of 1.4 +/- 0.3 per cent per minute (mean and standard error) during exercise. After an initial decrease at the onset, tissue oxygenation did not decline during exercise without compression. The recovery of tissue oxygenation after exercise was twice as slow with compression (2.5 +/- 0.6 minutes) than it was without the use of compression (1.3 +/- 0.2 minutes).

Adolescent↗
PubMed2006

Irreversible JPEG 2000 compression of abdominal CT for primary interpretation: assessment of visually lossless threshold.

To estimate the visually lossless threshold for Joint Photographic Experts Group (JPEG) 2000 compression of contrast-enhanced abdominal computed tomography (CT) images, 100 images were compressed to four different levels: a reversible (as negative control) and irreversible 5:1, 10:1, and 15:1. By alternately displaying the original and the compressed image on the same monitor, six radiologists independently determined if the compressed image was distinguishable from the original image. For each reader, we compared the proportion of the compressed images being rated distinguishable from the original images between the reversible compression and each of the three irreversible compressions using the exact test for paired proportions. For each reader, the proportion was not significantly different between the reversible (0-1%, 0/100 to 1/100) and irreversible 5:1 compression (0-3%). However, the proportion significantly increased with the irreversible 10:1 (95-99%) and 15:1 compressions (100%) versus reversible compression in all readers (P < 0.001); 100 and 95% of the 5:1 compressed images were rated indistinguishable from the original images by at least five of the six readers and all readers, respectively. Irreversibly 5:1 compressed abdominal CT images are visually lossless and, therefore, potentially acceptable for primary interpretation.

Contrast Media↗
PubMed2004

JPEG compression of stereoscopic digital images for the diagnosis of diabetic retinopathy via teleophthalmology.

BACKGROUND: Canada's vast size and remote rural communities represent a significant hurdle for successful monitoring and evaluation of diabetic retinopathy. Teleophthalmology may provide a solution to overcome this problem. We investigated the application of Joint Photographic Experts Group (PEG) compression to digital retinal images to determine whether JPEG compression could reduce file sizes while maintaining sufficient quality and detail to accurately diagnose diabetic retinopathy. METHODS: All 20 patients with type 2 diabetes mellitus assessed at a 1-day teleophthalmology clinic in northern Alberta were enrolled in the study. Following pupil dilation, seven 30 degrees fields of each fundus were digitally photographed at a resolution of 2008 x 3040 pixels and saved in uncompressed tagged image file format (TIFF). The files were compressed approximately 55x and 113x their original size using JPEG compression. A reviewer in Edmonton randomly viewed all original TIFF images along with the compressed JPEG images in a masked fashion for image quality and for specific diabetic retinal pathology in accordance with Early Treatment Diabetic Retinopathy Study standards. The level of diabetic retinopathy and recommendations for clinical follow-up were also recorded. Exact agreement and weighted kappa statistics, a measure of reproducibility, were calculated. RESULTS: Exact agreement between the compressed JPEG images and the TIFF images was high (75% to 100%) for all measured variables at both compression levels. Reproducibility was good to excellent at both compression levels for the identification of diabetic retinal abnormalities (K = 0.45-1), diagnosis of level of retinopathy (kappa = 0.73-1) and recommended follow-up (kappa = 0.64-1). INTERPRETATION: The application of JPEG compression at ratios of 55:1 and 113:1 did not significantly interfere with the identification of specific diabetic retinal pathology, diagnosis of level of retinopathy or recommended follow-up. These results indicate that JPEG compression at ratios as high as 113:1 has the potential to reduce storage requirements without interfering with the accurate and reproducible teleophthalmologic diagnosis of diabetic retinopathy. This pilot project demonstrates the potential for JPEG compression within a digital teleophthalmology viewing system.

Adult↗
PubMed2003

[Telemedicine in Ophthalmology: A Useful Tool in Store-and-Forward Counselling?].

Side by side with the progress in computers and imaging, telemedicine has already been used successfully in a large number of specialties of medicine. But high-quality images are not always suitable for transfer via modem because of their file size. The present experimental study was conducted to determine the effects of image compression by the JPEG algorithm on image quality and on the reliability of diagnosis after compression. Digital photographs of the retina were taken and the JPEG compressed images assessed by an experienced ophthalmologist. The present study showed a high reliability of diagnosis and a good agreement between the observations taken at the patient and at the computer. For this reason, JPEG image compression algorithm is suitable for reducing image size for producing high-quality images manageable for transmitting via modem in a store-and-forward teleophthalmological system.

Algorithms↗
PubMed2006

Piecewise parametric interpolation for temporal compression of multijoint movement trajectories.

Computer animation of sign language used by deaf individuals has been produced from 51 time-varying trajectories of the fingertips, the centers of rotation of the joints of the hands and arms, and facial landmarks. These trajectories are sampled at 1/5th the National Television Systems Committee (NTSC) video frame rate and interpolated using piecewise sequences of cubic Bezier splines. The resulting trajectories are used to control sparse, stick figure animations of sign language resulting in considerable spatiotemporal compression with intelligibility in the range of 90%. This method introduces an additional 5:1 compression in the temporal domain that has not been previously exploited, and is potentially useful in sign language telecommunication, multimedia presentations, and gesture recognition.

Arm↗
PubMed2004

Bayesian resolution enhancement of compressed video.

Super-resolution algorithms recover high-frequency information from a sequence of low-resolution observations. In this paper, we consider the impact of video compression on the super-resolution task. Hybrid motion-compensation and transform coding schemes are the focus, as these methods provide observations of the underlying displacement values as well as a variable noise process. We utilize the Bayesian framework to incorporate this information and fuse the super-resolution and post-processing problems. A tractable solution is defined, and relationships between algorithm parameters and information in the compressed bitstream are established. The association between resolution recovery and compression ratio is also explored. Simulations illustrate the performance of the procedure with both synthetic and nonsynthetic sequences.

Algorithms↗
PubMed2006

Wavelet-domain approximation and compression of piecewise smooth images.

The wavelet transform provides a sparse representation for smooth images, enabling efficient approximation and compression using techniques such as zerotrees. Unfortunately, this sparsity does not extend to piecewise smooth images, where edge discontinuities separating smooth regions persist along smooth contours. This lack of sparsity hampers the efficiency of wavelet-based approximation and compression. On the class of images containing smooth C2 regions separated by edges along smooth C2 contours, for example, the asymptotic rate-distortion (R-D) performance of zerotree-based wavelet coding is limited to D(R) (< or = 1/R, well below the optimal rate of 1/R2. In this paper, we develop a geometric modeling framework for wavelets that addresses this shortcoming. The framework can be interpreted either as 1) an extension to the "zerotree model" for wavelet coefficients that explicitly accounts for edge structure at fine scales, or as 2) a new atomic representation that synthesizes images using a sparse combination of wavelets and wedgeprints--anisotropic atoms that are adapted to edge singularities. Our approach enables a new type of quadtree pruning for piecewise smooth images, using zerotrees in uniformly smooth regions and wedgeprints in regions containing geometry. Using this framework, we develop a prototype image coder that has near-optimal asymptotic R-D performance D(R) < or = (log R)2 /R2 for piecewise smooth C2/C2 images. In addition, we extend the algorithm to compress natural images, exploring the practical problems that arise and attaining promising results in terms of mean-square error and visual quality.

Algorithms↗
PubMed2026

Optimizing sparse and skew hashing: faster k-mer dictionaries.

MOTIVATION: Representing a set of k-mers-strings of length k-in small space under fast lookup queries is a fundamental requirement for several applications in Bioinformatics. A data structure based on sparse and skew hashing (SSHash) was recently proposed for this purpose (Pibiri 2022): it combines good space effectiveness with fast lookup and streaming queries. It is also order-preserving, i.e. consecutive k-mers (sharing a prefix-suffix overlap of length k-1) are assigned consecutive hash codes which helps compressing satellite data typically associated with k-mers, like abundances and color sets in colored De Bruijn graphs. RESULTS: We study the problem of accelerating queries under the sparse and skew hashing indexing paradigm, without compromising its space effectiveness. We propose a refined data structure with less complex lookups and fewer cache misses. We give a simpler and faster algorithm for streaming lookup queries. The refined architecture translates to substantial performance gains, outperforming the original version of SSHash in both index construction speed and query efficiency. Compared to indexes with similar capabilities and based on the Burrows-Wheeler transform, like SBWT and FMSI, SSHash is significantly faster to build and query. SSHash is competitive in space with the fast (and default) modality of SBWT when both k-mer strands are indexed. While larger than FMSI, it is also more than one order of magnitude faster to query. AVAILABILITY AND IMPLEMENTATION: The SSHash software is available at https://github.com/jermp/sshash, and also distributed via Bioconda. A benchmark of data structures for k-mer sets is available at https://github.com/jermp/kmer_sets_benchmark. The datasets used in this article are described and available at https://zenodo.org/records/17582116.

Algorithms↗
PubMed1999

Extraspinal bone and soft-tissue tumors as a cause of sciatica. Clinical diagnosis and recommendations: analysis of 32 cases.

STUDY DESIGN: Between 1982 and 1997, the authors treated 32 patients with sciatica who subsequently were found to have a tumor along the extraspinal course of the sciatic nerve. SUMMARY OF BACKGROUND DATA: Extraspinal compression of the sciatic nerve by a tumor is a rare cause of sciatica. Signs and symptoms overlap those of the more common causes of sciatica (i.e., herniated disc and spinal stenosis). OBJECTIVE: To characterize the unique clinical presentation of these patients and to formulate guidelines that may lead to early diagnosis. METHODS: All pertinent clinical data and studies were reviewed retrospectively, and standard demographic data were collected for analysis. RESULTS: These patients typically sought treatment for an insidious onset of sciatic pain that was constant, progressive, and unresponsive to change in position or bed rest. The mean time to final diagnosis was 11.9 months (median, 6 months). Seventeen patients were able to locate their pain to a specific point along the extraspinal course of the sciatic pain, and a mass was noted in 13 patients. Eighteen of these tumors were in the pelvis, 10 in the thigh, and 4 in the popliteal fossa and calf. CONCLUSIONS: A high index of clinical suspicion is the key to early diagnosis of bone or soft-tissue tumors as a cause of sciatica; special attention should be given to pain pattern, physical examination of the entire course of the sciatic nerve, and selection of proper imaging studies. Routine anteroposterior plain radiography of the pelvis as part of the initial imaging screening process is recommended.

Bone Neoplasms↗
PubMed2004

Influence of lossy compression on eye movement signals.

Eye movements considered in our research are physiological signals that are measured in otoneurological balance tests. They are also investigated in other areas of medicine and in psychology. When great amounts of signals are measured in clinical and research work, signal compression is of great use in storing measurements for later investigations. In this research we assessed the influence of lossy compression on medically interesting parameter values that are computed from eye movement signals. We found that high compression ratios with bit rates lower than 1.5 bits per sample on signals with an original resolution of 13 bits per sample produced results without significant changes to the medical parameters values.

Data Compression↗
PubMed2006

Varying complexity in tree-structured image distribution models.

Probabilistic models of image statistics underlie many approaches in image analysis and processing. An important class of such models have variables whose dependency graph is a tree. If the hidden variables take values on a finite set, most computations with the model can be performed exactly, including the likelihood calculation, training with the EM algorithm, etc. Crouse et al. developed one such model, the hidden Markov tree (HMT). They took particular care to limit the complexity of their model. We argue that it is beneficial to allow more complex tree-structured models, describe the use of information theoretic penalties to choose the model complexity, and present experimental results to support these proposals. For these experiments, we use what we call the hierarchical image probability (HIP) model. The differences between the HIP and the HMT models include the use of multivariate Gaussians to model the distributions of local vectors of wavelet coefficients and the use of different numbers of hidden states at each resolution. We demonstrate the broad utility of image distributions by applying the HIP model to classification, synthesis, and compression, across a variety of image types, namely, electrooptical, synthetic aperture radar, and mammograms (digitized X-rays). In all cases, we compare with the HMT.

Algorithms↗
PubMed2006

Compression of surface EMG signals with algebraic code excited linear prediction.

Despite the interest in long timescale recordings of surface electromyographic (EMG) signals, only a few studies have focused on EMG compression. In this paper we investigate a lossy coding technique for surface EMG signals that is based on the algebraic code excited linear prediction (ACELP) paradigm, widely used for speech signal coding. The algorithm was adapted to the EMG characteristics and tested on both simulated and experimental signals. The coding parameters selected led to a compression ratio of 87.3%. For simulated signals, the mean square error in signal reconstruction and the percentage error in average rectified value after compression were 11.2% and 4.90%, respectively. For experimental signals, they were 6.74% and 3.11%. The mean power spectral frequency and third-order power spectral moment were estimated with relative errors smaller than 1.23% and 8.50% for simulated signals, and 3.74% and 5.95% for experimental signals. It was concluded that the proposed coding scheme could be effectively used for high rate and low distortion compression of surface EMG signals. Moreover, the method is characterized by moderate complexity (approximately 20 million instructions/s) and an algorithmic delay smaller than 160 samples (approximately 160ms).

Adult↗
PubMed2002

Linear modes of gene expression determined by independent component analysis.

MOTIVATION: The expression of genes is controlled by specific combinations of cellular variables. We applied Independent Component Analysis (ICA) to gene expression data, deriving a linear model based on hidden variables, which we term 'expression modes'. The expression of each gene is a linear function of the expression modes, where, according to the ICA model, the linear influences of different modes show a minimal statistical dependence, and their distributions deviate sharply from the normal distribution. RESULTS: Studying cell cycle-related gene expression in yeast, we found that the dominant expression modes could be related to distinct biological functions, such as phases of the cell cycle or the mating response. Analysis of human lymphocytes revealed modes that were related to characteristic differences between cell types. With both data sets, the linear influences of the dominant modes showed distributions with large tails, indicating the existence of specifically up- and downregulated target genes. The expression modes and their influences can be used to visualize the samples and genes in low-dimensional spaces. A projection to expression modes helps to highlight particular biological functions, to reduce noise, and to compress the data in a biologically sensible way.

Algorithms↗
PubMed2002

Robust region of interest coding for improved sign language telecommunication.

More than 500,000 deaf people in North America use American Sign Language or a similar signed system as a first language. Long-distance communication of this visually based medium is hampered by its incompatibility with audio and text telecommunication systems. Movements associated with signed languages require a more consistent and higher frame rate than is available with residential video telephony. New video compression standards (JPEG 2000 and MPEG-4) allow optional region of interest coding in which areas within a frame can be assigned different levels of compression. This paper presents a novel skin color segmentation approach that identifies the hands and face each video frame. This method is robust in terms of variations in skin pigmentation in a single subject, in skin pigmentation across a population of potential users, subject clothing, and image background. Specifying these critical regions of interest to the compression algorithm maintains high visual quality in the regions of the hands and face, while allowing very lossy, high compression of the remainder of the video frame. This reduces the coded representation of each frame, and offers a potential increase in the frame rate for telecommunication.

Algorithms↗
PubMed2006

JPEG2000 compression of thin-section CT images of the lung: effect of compression ratio on image quality.

PURPOSE: To assess retrospectively the effect of the Joint Photographic Experts Group 2000 (JPEG2000) compression ratio on the quality of thin-section computed tomographic (CT) images. MATERIALS AND METHODS: In this institutional review board-approved investigation (protocol 238/2004), thin-section CT images were subjected to irreversible JPEG2000 compression by using five compression ratios (3:1, 5:1, 7:1, 9:1, and 11:1). Three radiologists independently evaluated 60 thin-section CT images, of various diseases, that were obtained with single-detector (weighted dose index, 14.4 mGy) and multidetector (weighted dose index, 9.8 mGy) CT. Toggling between the original and compressed images, readers had to identify the original image by using a forced-choice two-alternative model and to subjectively rank the quality of what they believed to be the compressed image. To assess the reader's ability to distinguish the compressed from the original image, a binomial test was used. Bonferroni correction was applied for all multiple tests. RESULTS: Images compressed with a ratio of 3:1 were not distinguishable from original images (P > .2 for all readers). With use of the 5:1 ratio, minor differences in appearance between the compressed and original images were seen by one of the three readers. With use of higher compression ratios (>/=7:1), all readers (P < .001) recognized the original image. The quality of more than 90% of the images compressed with a 7:1 or higher ratio was substantially degraded. Single-detector and multidetector CT results were not significantly different. CONCLUSION: The highest ratio that yielded visually lossless compression of thin-section CT images was 3:1. With the 5:1 ratio, there was minor image quality loss, while use of higher compression ratios (>/=7:1) caused substantial degradation of image quality and potential loss of diagnostic information.

Adult↗
PubMed1999

Movement-related variation in forces under compression stockings.

OBJECTIVES: Compression therapy is widely used in the treatment of venous leg ulcers, but the efficacy of this treatment is variable. Assessment of variation in compression forces associated with movement may help to elucidate the mechanism of action of compression therapy. The aim of this study was to develop and apply a system to investigate forces under compression stockings during movement. METHOD: Three sensors were placed on the medial aspect of the left leg on six healthy volunteers to monitor forces under class 2 (Continental European classification) compression stockings. Data were recorded during dorsiflexion and plantar flexion of the left foot and also during short periods of walking. RESULTS: Changes in pressure were observed, associated with dorsiflexion and plantar flexion of the foot. These changes were dependent on sensor position. Changes in pressure during walking were also position-dependent and of variable duration. CONCLUSIONS: The system enables forces associated with compression therapy to be examined during movement and may thus be of value in further understanding its mechanism of action. Foot movement can be associated with clear changes in pressure under compression stockings and rapid changes in pressure may occur during walking.

Adult↗