PubMed Health⌕ Search

PubMed · 11146491

Image-based ghost correction for interleaved EPI.

Abstract

A new image-based ghost correction technique is described for general interleaved EPI. This technique works reliably with both even- and odd-number interleaved EPI sequences. It estimates the phase distortions causing the ghosts as a general function of (x,y) even in the presence of a significant overlap of parent image and ghosts. If the phase distortion is assumed to be a function of x (frequency-encode direction) only, the new technique is similar to a recently published correction method for general interleaved EPI (Hennel. J Magn Reson 1998;134:206-213). However, that study concluded that the method for general interleaved EPI did not work. It showed that the SNRs of the edge pixels were too low to accurately estimate the phase distortion. The new technique utilizes not one, but many pixels in the image for estimating the phase distortion. The technique requires a user-defined ROI to outline the parent image and identify so-called eligible pixels for estimating the phase distortion. When all eligible pixels are used, the SNR of the phase distortion estimate is comparable to that obtained in single-shot EPI. This study provides the first examples of high-quality, image-based correction of multiple ghosts in general interleaved EPI. Magn Reson Med 45:96-108, 2001.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

M H Buonocore, D C Zhu. 2001. Image-based ghost correction for interleaved EPI.. https://doi.org/10.1002/1522-2594(200101)45%3A1%3C96%3A%3Aaid-mrm1014%3E3.0.co%3B2-j

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

Striping artifact removal in VisiumHD data through nuclear counts modeling.

MOTIVATION: 10x Genomics VisiumHD enables spatial transcriptomics at 2 µm × 2 µm resolution but exhibits slide-specific, non-periodic striping artifacts due to lane-width variability. These multiplicative row/column effects distort bin total counts and can bias downstream analyses. The state-of-the-art destriping approach is the normalization procedure used as a preprocessing step in bin2cell; it applies sequential high-quantile row- then column-wise normalization, which is asymmetric and can introduce edge effects/macro-stripes and distortions of large-scale total-count structure. RESULTS: We propose a statistical destriping approach that leverages nuclei segmentation from the co-registered H&E image. Assuming transcript abundance is constant within each nucleus, we model bin counts with a negative binomial distribution whose mean is a product of a nucleus-specific concentration and row- and column-specific stripe-factors reflecting lane-width variation. We fit all parameters in a generalized linear modeling framework with cross-validated regularization on stripe-factors and iterative dispersion estimation, and use the fitted parameters to correct the observed counts into a destriped image. On synthetic data with known ground truth, our method improves stripe-factor estimation accuracy and reduces error in corrected counts relative to bin2cell and bin2cell-derived baselines. Across four public VisiumHD slides, it consistently lowers striping intensity while substantially better preserving biological signal present in the large-scale global count structure and avoiding the artifacts introduced by other methods. AVAILABILITY AND IMPLEMENTATION: All source code and links to publicly available data used for this study are available at https://github.com/paolamalsot/destriping-GLM.

Artifacts↗

Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'.

Although it has been recognized that PCR amplification of mixed templates may generate sequence artifacts, the mechanisms of their formation, frequency and potential elimination have not been fully elucidated. Here evidence is presented for heteroduplexes as a major source of artifacts in mixed-template PCR. Nearly equal proportions of homoduplexes and heteroduplexes were observed after co-amplifying 16S rDNA from three bacterial genomes and analyzing products by constant denaturing capillary electrophoresis (CDCE). Heteroduplexes became increasingly prevalent as primers became limiting and/or template diversity was increased. A model exploring the fate of cloned heteroduplexes during MutHLS-mediated mismatch repair in the Escherichia coli host demonstrates that the diversity of artifactual sequences increases exponentially with the number of both variable nucleotides and of original sequence variants. Our model illustrates how minimization of heteroduplex molecules before cloning may reduce artificial genetic diversity detected during sequence analysis by clone screening. Thus, we developed a method to eliminate heteroduplexes from mixed-template PCR products by subjecting them to 'reconditioning PCR', a low cycle number re-amplification of a 10-fold diluted mixed-template PCR product. This simple modification to the protocol may ensure that sequence richness encountered in clone libraries more closely reflects genetic diversity in the original sample.

Artifacts↗