Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 11146491

Image-based ghost correction for interleaved EPI.

M H Buonocore·D C Zhu
View original source ↗Export metadata ↓

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

ArtifactsBrainComputer SimulationEcho-Planar ImagingHumansPhantoms, ImagingJournal Article

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

PubMed2026

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↗
PubMed2001

In vitro replication slippage by DNA polymerases from thermophilic organisms.

Replication slippage of DNA polymerases is a potential source of spontaneous genetic rearrangements in prokaryotic and eukaryotic cells. Here we show that different thermostable DNA polymerases undergo replication slippage in vitro, during single-round replication of a single-stranded DNA template carrying a hairpin structure. Low-fidelity polymerases, such as Thermus aquaticus (Taq), high-fidelity polymerases, such as Pyrococcus furiosus (Pfu) and a highly thermostable polymerase from Pyrococcus abyssi (Pyra exo(-)) undergo slippage. Thermococcus litoralis DNA polymerase (Vent) is also able to slip; however, slippage can be inhibited when its strand-displacement activity is induced. Moreover, DNA polymerases that have a constitutive strand-displacement activity, such as Bacillus stearothermophilus DNA polymerase (Bst), do not slip. Polymerases that slip during single-round replication generate hairpin deletions during PCR amplification, with the exception of Vent polymerase because its strand-displacement activity is induced under these conditions. We show that these hairpin deletions occurring during PCR are due to replication slippage, and not to a previously proposed process involving polymerization across the hairpin base.

Artifacts↗