A decay-modeled compressed sensing reconstruction approach for non-Cartesian hyperpolarized 129Xe MRI.

PURPOSE: Hyperpolarized 129Xe MRI benefits from non-Cartesian acquisitions that sample k-space efficiently and rapidly. However, their reconstructions are complex and burdened by decay processes unique to hyperpolarized gas. Currently used gridded reconstructions are prone to artifacts caused by magnetization decay and are ill-suited for undersampling. We present a compressed sensing (CS) reconstruction approach that incorporates magnetization decay in the forward model, thereby producing images with increased sharpness and contrast, even in undersampled data. METHODS: Radio-frequency, T1, and T 2 * $$ {\mathrm{T}}_2^{\ast } $$ decay processes were incorporated into the forward model and solved using iterative methods including CS. The decay-modeled reconstruction was validated in simulations and then tested in 2D/3D-spiral ventilation and 3D-radial gas-exchange MRI. Quantitative metrics including apparent-SNR and sharpness were compared between gridded, CS, and twofold undersampled CS reconstructions. Observations were validated in gas-exchange data collected from 15 healthy and 25 post-hematopoietic-stem-cell-transplant participants. RESULTS: CS reconstructions in simulations yielded images with threefold increases in accuracy. CS increased sharpness and contrast for ventilation in vivo imaging and showed greater accuracy for undersampled acquisitions. CS improved gas-exchange imaging, particularly in the dissolved-phase where apparent-SNR improved, and structure was made discernable. Finally, CS showed repeatability in important global gas-exchange metrics including median dissolved-gas signal ratio and median angle between real/imaginary components. CONCLUSION: A non-Cartesian CS reconstruction approach that incorporates hyperpolarized 129Xe decay processes is presented. This approach enables improved image sharpness, contrast, and overall image quality in addition to up-to threefold undersampling. This contribution benefits all hyperpolarized gas MRI through improved accuracy and decreased scan durations.

Appropriate pancreatic phase image acquisition by free-breathing dynamic contrast-enhanced pancreatic MRI using stack-of-stars radial sampling and Compressed SENSE.

PURPOSE: To evaluate the feasibility of a free-breathing sequence (4D FreeBreathing) combined with Compressed SENSE in dynamic contrast-enhanced pancreatic MRI and compare it with a breath-holding sequence (eTHRIVE). METHOD: Patients who underwent pancreatic MRI, either eTHRIVE or 4D FreeBreathing, from April 2022 to November 2023 were included in this retrospective study. Two radiologists, who were unaware of the scan sequence, independently and randomly reviewed the images at the precontrast, pancreatic, portal venous, and equilibrium phases and assigned confidence scores for motion and streaking artifacts, pancreatic sharpness, and overall image quality using a 5-point scale. Furthermore, the radiologists assessed the appropriateness of the scan timing of the pancreatic phase. Mann-Whitney U and Fisher's exact tests were conducted to compare the confidence scores and adequacy of the pancreatic phase scan timing between eTHRIVE and 4D FreeBreathing. RESULTS: Overall, 48 patients (median age, 71 years; interquartile range, 64-77 years; 24 women) were included. Among them, 20 patients (42%) were scanned using 4D FreeBreathing. The 4D FreeBreathing showed moderate streaking artifact but improved motion artifact (P <.001-.17) at all phases. Pancreatic sharpness and overall image quality were almost comparable between two sequences (P = .17-.96). All 20 examinations in 4D FreeBreathing showed appropriate pancreatic phase images, but only 16 (57%; P <.001 for reviewer 1) and 18 (64%; P = .003 for reviewer 2) examinations showed it in eTHRIVE. CONCLUSION: The use of 4D FreeBreathing combined with Compressed SENSE was feasible in pancreatic MRI and provided appropriate pancreatic phase images in all examinations.

A new efficient referential genome compression technique for FastQ files.

Hospitals and medical laboratories create a tremendous amount of genome sequence data every day for use in research, surgery, and illness diagnosis. To make storage comprehensible, compression is therefore essential for the storage, monitoring, and distribution of all these data. A novel data compression technique is required to reduce the time as well as the cost of storage, transmission, and data processing. General-purpose compression techniques do not perform so well for these data due to their special features: a large number of repeats (tandem and palindrome), small alphabets, and highly similar, and specific file formats. In this study, we provide a method for compressing FastQ files that uses a reference genome as a backup without sacrificing data quality. FastQ files are initially split into three streams (identifier, sequence, and quality score), each of which receives its own compression technique. A novel quick and lightweight mapping mechanism is also presented to effectively compress the sequence stream. As shown by experiments, the suggested methods, both the compression ratio and the compression/decompression duration of NGS data compressed using RBFQC, are superior to those achieved by other state-of-the-art genome compression methods. In comparison to GZIP, RBFQC may achieve a compression ratio of 80-140% for fixed-length datasets and 80-125% for variable-length datasets. Compared to domain-specific FastQ file referential genome compression techniques, RBFQC has a compression and decompression speed (total) improvement of 10-25%.

Lossy Image Compression in a Preclinical Multimodal Imaging Study.

The growing use of multimodal high-resolution volumetric data in pre-clinical studies leads to challenges related to the management and handling of the large amount of these datasets. Contrarily to the clinical context, currently there are no standard guidelines to regulate the use of image compression in pre-clinical contexts as a potential alleviation of this problem. In this work, the authors study the application of lossy image coding to compress high-resolution volumetric biomedical data. The impact of compression on the metrics and interpretation of volumetric data was quantified for a correlated multimodal imaging study to characterize murine tumor vasculature, using volumetric high-resolution episcopic microscopy (HREM), micro-computed tomography (µCT), and micro-magnetic resonance imaging (µMRI). The effects of compression were assessed by measuring task-specific performances of several biomedical experts who interpreted and labeled multiple data volumes compressed at different degrees. We defined trade-offs between data volume reduction and preservation of visual information, which ensured the preservation of relevant vasculature morphology at maximum compression efficiency across scales. Using the Jaccard Index (JI) and the average Hausdorff Distance (HD) after vasculature segmentation, we could demonstrate that, in this study, compression that yields to a 256-fold reduction of the data size allowed to keep the error induced by compression below the inter-observer variability, with minimal impact on the assessment of the tumor vasculature across scales.

Compressive Sensing of Medical Images Based on HSV Color Space.

Recently, compressive sensing (CS) schemes have been studied as a new compression modality that exploits the sensing matrix in the measurement scheme and the reconstruction scheme to recover the compressed signal. In addition, CS is exploited in medical imaging (MI) to support efficient sampling, compression, transmission, and storage of a large amount of MI. Although CS of MI has been extensively investigated, the effect of color space in CS of MI has not yet been studied in the literature. To fulfill these requirements, this article proposes a novel CS of MI based on hue-saturation value (HSV), using spread spectrum Fourier sampling (SSFS) and sparsity averaging with reweighted analysis (SARA). An HSV loop that performs SSFS is proposed to obtain a compressed signal. Next, HSV-SARA is proposed to reconstruct MI from the compressed signal. A set of color MIs is investigated, such as colonoscopy, magnetic resonance imaging of the brain and eye, and wireless capsule endoscopy images. Experiments were performed to show the superiority of HSV-SARA over benchmark methods in terms of signal-to-noise ratio (SNR), structural similarity (SSIM) index, and measurement rate (MR). The experiments showed that a color MI, with a resolution of 256×256 pixels, could be compressed by the proposed CS at MR of 0.1, and could be improved in terms of SNR being 15.17% and SSIM being 2.53%. The proposed HSV-SARA can be a solution for color medical image compression and sampling to improve the image acquisition of medical devices.

GVC: efficient random access compression for gene sequence variations.

BACKGROUND: In recent years, advances in high-throughput sequencing technologies have enabled the use of genomic information in many fields, such as precision medicine, oncology, and food quality control. The amount of genomic data being generated is growing rapidly and is expected to soon surpass the amount of video data. The majority of sequencing experiments, such as genome-wide association studies, have the goal of identifying variations in the gene sequence to better understand phenotypic variations. We present a novel approach for compressing gene sequence variations with random access capability: the Genomic Variant Codec (GVC). We use techniques such as binarization, joint row- and column-wise sorting of blocks of variations, as well as the image compression standard JBIG for efficient entropy coding. RESULTS: Our results show that GVC provides the best trade-off between compression and random access compared to the state of the art: it reduces the genotype information size from 758 GiB down to 890 MiB on the publicly available 1000 Genomes Project (phase 3) data, which is 21% less than the state of the art in random-access capable methods. CONCLUSIONS: By providing the best results in terms of combined random access and compression, GVC facilitates the efficient storage of large collections of gene sequence variations. In particular, the random access capability of GVC enables seamless remote data access and application integration. The software is open source and available at https://github.com/sXperfect/gvc/ .

Use of Full-quality DICOM Images Compared to Minimally Compressed Mammograms in JPEG Format for Radiology Training: A Study From Radiologist and Radiographer Perspectives.

BACKGROUND: Running online training in mammography interpretation poses a challenge to radiologists and reporting radiographers due to the large size of digital mammograms in DICOM format and limited bandwidth capabilities of the users for image transmission. This study aims to compare image quality between the full-quality with minimal compressed JPEG and DICOM format of mammograms on a diagnostic monitor through the evaluation of radiologists and radiographers. METHODS: Twelve participants including six radiologists and six radiographers participated as observers in this study. The observers viewed 60 2D digital mammography screening cases (22 cancer and 38 normal cases) in DICOM and minimal compressed JPEG formats on a 5MP diagnostic monitor. A 5-point Likert scale was provided for observers to compare the quality of mammograms between the two formats, with text anchors indicating to one image being significantly better, slightly better or of equal quality in terms of technical and diagnostic aspects. Nonparametric descriptive statistics were used to evaluate the ratings of radiologists and radiographers in different characteristics of mammograms of two image formats. RESULTS: The DICOM and JPEG images were statistically equivalent through ratings from radiographers in brightness, contrast, dynamic range, sharpness, no significant distortion, no significant noise, and background homogeneity in all mammograms. Similarly, most radiologists rated DICOM and JPEG images clinically and statistically equivalent with respect to difficulty of interpretation, brightness, contrast, dynamic range, sharpness, the appearance of Cooper's ligaments, visibility of subtle microcalcifications, visibility of structures at the margins of the breast. Normal cases were marginally favored by radiologists in DICOM format (ranging from 0.4% to 5.3%) while cancer cases in JPEG (ranging from 0.8% to 7.6%) received slightly higher rating. CONCLUSIONS: Findings showed that baseline full-quality with minimal compression JPEG was equivalent to the DICOM format of full-field digital mammograms which suggests that this type of JPEG could be used for online training and education in radiology.

Compression of images of dermatological manifestations of paucisymptomatic COVID-19 patients through periodic principal components / Compresión de imágenes de manifestaciones dermatológicas de pacientes paucisintomáticos de COVID-19 mediante componentes principales periódicos

Introduction: The management of medical images has been gaining followers based on the advantages it offers for the diagnosis of diseases, which, like COVID-19, present with clinical manifestations that can be captured in the form of images. Objective: Take advantage of the quasi-periodicity of the principal components (PCs) in the decomposition into PCs of medical images, which represent dermatological manifestations in paucisymptomatic patients of COVID-19. Methods: Here, a set of photos was taken of one of the most frequent patterns in COVID-19, the maculopapular pattern, characterized by an erythmatopapular rash, and compression of one of the medical images was performed. Said compression was carried out in different ways: (1) using two PCs, (2) using both a periodic PC and a non-periodic PC, (3) using two periodic PCs, (4) using a single PC, and (5) using a single periodic PC. Result: The results of this research proved that it is possible to work with acceptable reconstructions of compressed images in the field of dermatology, without losing the quality and characteristics that allow to reach a correct diagnosis. In addition, this achievement permits to correctly classify many diseases without fear of being wrong. Conclusion: With the method presented, the use of a robust medical image compression technique that could be very useful in the field of health is proposed. The images allow the diagnosis of diseases such as COVID-19 in paucisymptomatic patients, understanding them allows minimizing their weight without losing quality, which facilitates their use and storage.

Introducción: El empleo de imágenes médicas en el diagnóstico de enfermedades ha ido ganando adeptos. Un ejemplo es la COVID-19 que cursa con manifestaciones clínicas dermatológicas. Objetivo: Aprovechar la cuasi-periodicidad de los componentes principales de la descomposición en imágenes médicas, que representan manifestaciones dermatológicas en pacientes paucisintomáticos de COVID-19. Métodos: Se tomó un conjunto de fotografías de uno de los patrones más frecuentes en la COVID-19 (el patrón maculopapular), caracterizado por un exantema eritematopapular, y se realizó la compresión de una de las imágenes médicas. Dicha compresión se realizó de diferentes formas: (1) usando dos componentes principales, (2) usando tanto un componente principal periódico como no periódico, (3) dos componentes principales periódicos, (4) un único componente principal, y (5) un solo componente principal periódico. Resultados: Es posible trabajar con reconstrucciones aceptables de imágenes comprimidas en el campo de la dermatología, sin perder la calidad y características que permitan llegar a un diagnóstico correcto. Además, este logro permite clasificar correctamente muchas enfermedades sin miedo a equivocarse. Conclusiones: Con el método presentado se propone el uso de una técnica robusta de compresión de imágenes médicas que podría ser de gran utilidad en el campo de la salud. Las imágenes permiten el diagnóstico de enfermedades como la COVID-19 en pacientes paucisintomáticos, con cuya compresión se minimiza su peso sin perder la calidad, lo que facilita su uso y almacenamiento.

Parameterized syncmer schemes improve long-read mapping.

MOTIVATION: Sequencing long reads presents novel challenges to mapping. One such challenge is low sequence similarity between the reads and the reference, due to high sequencing error and mutation rates. This occurs, e.g., in a cancer tumor, or due to differences between strains of viruses or bacteria. A key idea in mapping algorithms is to sketch sequences with their minimizers. Recently, syncmers were introduced as an alternative sketching method that is more robust to mutations and sequencing errors. RESULTS: We introduce parameterized syncmer schemes (PSS), a generalization of syncmers, and provide a theoretical analysis for multi-parameter schemes. By combining PSS with downsampling or minimizers we can achieve any desired compression and window guarantee. We implemented the use of PSS in the popular minimap2 and Winnowmap2 mappers. In tests on simulated and real long-read data from a variety of genomes, the PSS-based algorithms, with scheme parameters selected on the basis of our theoretical analysis, reduced unmapped reads by 20-60% at high compression while usually using less memory. The advantage was more pronounced at low sequence identity. At sequence identity of 75% and medium compression, PSS-minimap had only 37% as many unmapped reads, and 8% fewer of the reads that did map were incorrectly mapped. Even at lower compression and error rates, PSS-based mapping mapped more reads than the original minimizer-based mappers as well as mappers using the original syncmer schemes. We conclude that using PSS can improve mapping of long reads in a wide range of settings.

Simultaneous compression and speckle reduction of clinical breast and fetal ultrasound images using rate-fidelity optimized coding.

Medical ultrasound images are inherently noised with speckle noise, which may interfere with Computer Aided Diagnostics (CAD) tasks, such as automatic segmentation. A compression and speckle de-noising method is proposed and tested on real clinical breast and fetal ultrasound images. The proposed algorithm is based on the optimization of quantization coefficients when applying Wavelet representation on the image, where the optimization is held such that a pre-defined mathematical fidelity criterion with respect to a desired de-speckled image is obtained. The proposed algorithm yields effective speckle reduction whilst preserving the edges in the images, with a reduced computational burden compared to other existing state-of-the-art methods, such as Optimal Bayesian Non-Local Means (OBNLM). In addition, the images are simultaneously compressed to a target bit-rate. The proposed algorithm is evaluated using both objective mathematical fidelity criteria (such as Structural Similarity and Edge Preserve) as well as subjective radiologists tests. The experimental results demonstrate the ability of the proposed method to achieve de-speckled images with compression ratios of approximately 30:1, whilst obtaining competitive subjective as well as objective fidelity measures with respect to the desired de-speckled images.

Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences.

BACKGROUND: Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available. FINDINGS: We systematically benchmarked 430 settings of 48 compressors (including 29 specialized sequence compressors and 19 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA, and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 27 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/), which allows custom visualizations to be built for selected subsets of benchmark results. CONCLUSION: We found that modern compressors offer a large improvement in compactness and speed compared to gzip. Our benchmark allows compressors and their settings to be compared using a variety of performance measures, offering the opportunity to select the optimal compressor on the basis of the data type and usage scenario specific to a particular application.

Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations.

BACKGROUND: Unsupervised compression algorithms applied to gene expression data extract latent or hidden signals representing technical and biological sources of variation. However, these algorithms require a user to select a biologically appropriate latent space dimensionality. In practice, most researchers fit a single algorithm and latent dimensionality. We sought to determine the extent by which selecting only one fit limits the biological features captured in the latent representations and, consequently, limits what can be discovered with subsequent analyses. RESULTS: We compress gene expression data from three large datasets consisting of adult normal tissue, adult cancer tissue, and pediatric cancer tissue. We train many different models across a large range of latent space dimensionalities and observe various performance differences. We identify more curated pathway gene sets significantly associated with individual dimensions in denoising autoencoder and variational autoencoder models trained using an intermediate number of latent dimensionalities. Combining compressed features across algorithms and dimensionalities captures the most pathway-associated representations. When trained with different latent dimensionalities, models learn strongly associated and generalizable biological representations including sex, neuroblastoma MYCN amplification, and cell types. Stronger signals, such as tumor type, are best captured in models trained at lower dimensionalities, while more subtle signals such as pathway activity are best identified in models trained with more latent dimensionalities. CONCLUSIONS: There is no single best latent dimensionality or compression algorithm for analyzing gene expression data. Instead, using features derived from different compression models across multiple latent space dimensionalities enhances biological representations.

Quantitative Assessment of the Effects of Compression on Deep Learning in Digital Pathology Image Analysis.

PURPOSE: Deep learning (DL), a class of approaches involving self-learned discriminative features, is increasingly being applied to digital pathology (DP) images for tasks such as disease identification and segmentation of tissue primitives (eg, nuclei, glands, lymphocytes). One application of DP is in telepathology, which involves digitally transmitting DP slides over the Internet for secondary diagnosis by an expert at a remote location. Unfortunately, the places benefiting most from telepathology often have poor Internet quality, resulting in prohibitive transmission times of DP images. Image compression may help, but the degree to which image compression affects performance of DL algorithms has been largely unexplored. METHODS: We investigated the effects of image compression on the performance of DL strategies in the context of 3 representative use cases involving segmentation of nuclei (n = 137), segmentation of lymph node metastasis (n = 380), and lymphocyte detection (n = 100). For each use case, test images at various levels of compression (JPEG compression quality score ranging from 1-100 and JPEG2000 compression peak signal-to-noise ratio ranging from 18-100 dB) were evaluated by a DL classifier. Performance metrics including F1 score and area under the receiver operating characteristic curve were computed at the various compression levels. RESULTS: Our results suggest that DP images can be compressed by 85% while still maintaining the performance of the DL algorithms at 95% of what is achievable without any compression. Interestingly, the maximum compression level sustainable by DL algorithms is similar to where pathologists also reported difficulties in providing accurate interpretations. CONCLUSION: Our findings seem to suggest that in low-resource settings, DP images can be significantly compressed before transmission for DL-based telepathology applications.

Evaluation of video compression methods for cone-beam computerized tomography.

PURPOSE: Cone-beam computerized tomography (CBCT) is routinely performed for verification of patient position in radiotherapy. It produced a large amount of data which require a method to compress them for efficient storage. In this study three video compression algorithms were introduced and their performance was evaluated based on real patient data. MATERIALS AND METHODS: At first CBCT images in multiple sets of a patient were transferred from reconstruction workstation or exported from treatment planning system. Then CBCT images were sorted according to imaging time (time-prioritized sequence) or imaging location (location-prioritized sequence). Next, this sequence was processed by a video compression algorithm and resulted in a movie. Three representative video compression algorithms (Motion JPEG 2000, Motion JPEG AVI, and MPEG-4) were employed and their compression performance was evaluated based on the CBCT data of 30 patients. RESULTS: Among three video compression algorithms, Motion JPEG 2000 has the least compression ratio since it is a lossless compression algorithm. Motion JPEG AVI and MPEG-4 have higher compression ratios than Motion JPEG 2000 but come with certain image losses. For MPEG-4, location-prioritized sequences show higher compression ratio than time-prioritized sequences. Based on the results achieved on the clinical target verification application, the registration accuracy of CBCT after decompression was comparable to that of the original CBCT. CONCLUSIONS: Video compression algorithms could provide a higher compression ratio comparing to static image compression algorithm. Although the loss of CBCT image due to compression its impact on registration accuracy of patient positioning is almost negligible. Video compression method is an effective way to substantially reduce the size of CBCT images for storage.

Accelerated positive contrast MRI of interventional devices using parallel compressed sensing imaging.

Susceptibility-based magnetic resonance imaging (MRI) method can image small MR-compatible devices with positive contrast. However, the relatively long data acquisition time required by the method hinders its practical applications. This study presents a parallel compressive sensing technique with a modified fast spin echo to accelerate data acquisition for the susceptibility-based positive contrast MRI. The method integrates the generalized autocalibrating partially parallel acquisitions and the compressive sensing techniques in the reconstruction algorithm. MR imaging data acquired from several phantoms containing interventional devices such as biopsy needles, stent, and brachytherapy seeds, used for validating the proposed technique. The results show that it can speed up data acquisition by a factor of about five while preserving the quality of the positive contrast images.

Compressed Sensing-Sensitivity Encoding (CS-SENSE) Accelerated Brain Imaging: Reduced Scan Time without Reduced Image Quality.

BACKGROUND AND PURPOSE: Compressed sensing-sensitivity encoding is a promising MR imaging acceleration technique. This study compares the image quality of compressed sensing-sensitivity encoding accelerated imaging with conventional MR imaging sequences. MATERIALS AND METHODS: Patients with known, treated, or suspected brain tumors underwent compressed sensing-sensitivity encoding accelerated 3D T1-echo-spoiled gradient echo or 3D T2-FLAIR sequences in addition to the corresponding conventional acquisition as part of their clinical brain MR imaging. Two neuroradiologists blinded to sequence and patient information independently evaluated both the accelerated and corresponding conventional acquisitions. The sequences were evaluated on 4- or 5-point Likert scales for overall image quality, SNR, extent/severity of artifacts, and gray-white junction and lesion boundary sharpness. SNR and contrast-to-noise ratio values were compared. RESULTS: Sixty-six patients were included in the study. For T1-echo-spoiled gradient echo, image quality in all 5 metrics was slightly better for compressed sensing-sensitivity encoding than conventional images on average, though it was not statistically significant, and the lower bounds of the 95% confidence intervals indicated that compressed sensing-sensitivity encoding image quality was within 10% of conventional imaging. For T2-FLAIR, image quality of the compressed sensing-sensitivity encoding images was within 10% of the conventional images on average for 3 of 5 metrics. The compressed sensing-sensitivity encoding images had somewhat more artifacts (P = .068) and less gray-white matter sharpness (P = .36) than the conventional images, though neither difference was significant. There was no significant difference in the SNR and contrast-to-noise ratio. There was 25% and 35% scan-time reduction with compressed sensing-sensitivity encoding for FLAIR and echo-spoiled gradient echo sequences, respectively. CONCLUSIONS: Compressed sensing-sensitivity encoding accelerated 3D T1-echo-spoiled gradient echo and T2-FLAIR sequences of the brain show image quality similar to that of standard acquisitions with reduced scan time. Compressed sensing-sensitivity encoding may reduce scan time without sacrificing image quality.

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

The 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.

Compressed-Sensing MP2RAGE sequence: Application to the detection of brain metastases in mice at 7T.

PURPOSE: To develop a Compressed Sensing (CS)-MP2RAGE sequence to drastically shorten acquisition duration and then detect and measure the T1 of brain metastases in mice at 7 T. METHODS: The encoding trajectory of the standard Cartesian MP2RAGE sequence has been modified (1) to obtain a variable density Poisson disk under-sampling distribution along the ky -kz plane, and (2) to sample the central part of the k-space exactly at TI1 and TI2 inversion times. In a prospective study, the accuracy of the T1 measurements was evaluated on phantoms containing increasing concentrations of gadolinium. The CS acceleration factors were increased to evaluate their influence on the contrast and T1 measurements of brain metastases in vivo. Finally, the 3D T1 maps were acquired with at 4-fold increased spatial resolution. The volumes and T1 values of the metastases were measured while using CS to reduce scan time. RESULTS: The implementation of the CS-encoding trajectory did not affect the T1 measurements in vitro. Accelerating the acquisition by a factor of 2 did not alter the contrast or the T1 values of the brain metastases. 3D T1 maps could be obtained in < 1 min using a CS factor of 6. Increasing the spatial resolution enabled more accurately measurement of the metastasis volumes while maintaining an acquisition duration below 5 min. CONCLUSION: The CS-MP2RAGE sequence could be of great interest in oncology to either rapidly obtain mouse brain 3D T1 maps or to increase the spatial resolution with no penalty on the scan duration.

Cartesian MR fingerprinting in the eye at 7T using compressed sensing and matrix completion-based reconstructions.

PURPOSE: To explore the feasibility of MR Fingerprinting (MRF) to rapidly quantify relaxation times in the human eye at 7T, and to provide a data acquisition and processing framework for future tissue characterization in eye tumor patients. METHODS: In this single-element receive coil MRF approach with Cartesian sampling, undersampling is used to shorten scan time and, therefore, to reduce the degree of motion artifacts. For reconstruction, approaches based on compressed sensing (CS) and matrix completion (MC) were used, while their effects on the quality of the MRF parameter maps were studied in simulations and experiments. Average relaxation times in the eye were measured in 6 healthy volunteers. One uveal melanoma patient was included to show the feasibility of MRF in a clinical context. RESULTS: Simulation results showed that an MC-based reconstruction enables large undersampling factors and also results in more accurate parameter maps compared with using CS. Experiments in 6 healthy volunteers used a reduction in scan time from 7:02 to 1:16 min, producing images without visible loss of detail in the parameter maps when using the MC-based reconstruction. Relaxation times from 6 healthy volunteers are in agreement with values obtained from fully sampled scans and values in literature, and parameter maps in a uveal melanoma patient show clear difference in relaxation times between tumor and healthy tissue. CONCLUSION: Cartesian-based MRF is feasible in the eye at 7T. High undersampling factors can be achieved by means of MC, significantly shortening scan time and increasing patient comfort, while also mitigating the risk of motion artifacts.

Pathological image compression for big data image analysis: Application to hotspot detection in breast cancer.

In this paper, we propose a pathological image compression framework to address the needs of Big Data image analysis in digital pathology. Big Data image analytics require analysis of large databases of high-resolution images using distributed storage and computing resources along with transmission of large amounts of data between the storage and computing nodes that can create a major processing bottleneck. The proposed image compression framework is based on the JPEG2000 Interactive Protocol and aims to minimize the amount of data transfer between the storage and computing nodes as well as to considerably reduce the computational demands of the decompression engine. The proposed framework was integrated into hotspot detection from images of breast biopsies, yielding considerable reduction of data and computing requirements.