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Purpose: We introduce L2-regularized reconstruction algorithms with closed-form solutions that achieve dramatic computational speed-up relative to state of the art L1- and L2-based iterative algorithms while maintaining similar image quality for various applications in MRI reconstruction.
Materials And Methods: We compare fast L2-based methods to state of the art algorithms employing iterative L1- and L2-regularization in numerical phantom and in vivo data in three applications; (i) Fast Quantitative Susceptibility Mapping (QSM), (ii) Lipid artifact suppression in Magnetic Resonance Spectroscopic Imaging (MRSI), and (iii) Diffusion Spectrum Imaging (DSI). In all cases, proposed L2-based methods are compared with the state of the art algorithms, and two to three orders of magnitude speed up is demonstrated with similar reconstruction quality.
Results: The closed-form solution developed for regularized QSM allows processing of a three-dimensional volume under 5 s, the proposed lipid suppression algorithm takes under 1 s to reconstruct single-slice MRSI data, while the PCA based DSI algorithm estimates diffusion propagators from undersampled q-space for a single slice under 30 s, all running in Matlab using a standard workstation.
Conclusion: For the applications considered herein, closed-form L2-regularization can be a faster alternative to its iterative counterpart or L1-based iterative algorithms, without compromising image quality.
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http://dx.doi.org/10.1002/jmri.24365 | DOI Listing |
Adv Healthc Mater
September 2025
Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA.
Organ-on-chip (OOC) technologies, also called microphysiological systems (MPS), offer dynamic microenvironments that improve upon static culture systems, yet widespread adoption has been hindered by fabrication complexity, reliance on polydimethylsiloxane (PDMS), and limited modularity. Here, a modular MPS platform is presented, designed for ease of use, reproducibility, and broad applicability. The system comprises layered elastomeric inserts for dual monolayer cell culture, which is clamped within a reusable acrylic cassette for perfusion studies.
View Article and Find Full Text PDFNat Methods
September 2025
Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK.
Volume correlative light and electron microscopy (vCLEM) is a powerful imaging technique that enables the visualization of fluorescently labeled proteins within their ultrastructural context. Currently, vCLEM alignment relies on time-consuming and subjective manual methods. This paper presents CLEM-Reg, an algorithm that automates the three-dimensional alignment of vCLEM datasets by leveraging probabilistic point cloud registration techniques.
View Article and Find Full Text PDFNat Biotechnol
September 2025
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
The size of microbial sequence databases continues to grow beyond the abilities of existing alignment tools. We introduce LexicMap, a nucleotide sequence alignment tool for efficiently querying moderate-length sequences (>250 bp) such as a gene, plasmid or long read against up to millions of prokaryotic genomes. We construct a small set of probe k-mers, which are selected to efficiently sample the entire database to be indexed such that every 250-bp window of each database genome contains multiple seed k-mers, each with a shared prefix with one of the probes.
View Article and Find Full Text PDFJ Invest Dermatol
September 2025
Department of Dermatology and Allergology, Philipps University Marburg, Marburg, Germany. Electronic address:
Pemphigus vulgaris (PV) is an autoimmune blistering disorder, which is caused by the loss of desmosomal cell-cell adhesion, initiated by the binding of IgG antibodies against the desmosomal components desmoglein (Dsg)1 and Dsg3. Dsg3-reactive CD4 T helper (Th) cells, in particular follicular Th (Tfh) cells, play a central role in autoantibody production by Dsg3-specific B cells. In this study, we challenged the concept that distinct Dsg3-reactive CD4 T cell subsets are critical in PV pathogenesis utilizing phenotypical and functional state-of-the-art ex vivo assays.
View Article and Find Full Text PDFMethods
September 2025
School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China; Henan Key Laboratory of Big Data Analysis and Processing, Henan University, Kaifeng, Henan, China. Electronic address:
Genomic selection (GS) is a breeding technique that utilizes genomic markers to predict the genetic potential of crops and animals. This approach holds significant promise for accelerating the improvement of agronomic traits and addressing food security challenges. While traditional breeding methods based on statistical or machine learning techniques have been useful in predicting traits for some crops, they often fail to capture the complex interactions between genotypes and phenotypes.
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