PubMed Health⌕ Search

PubMed · 10232521

Improved three-dimensional GRASE imaging with the SORT phase-encoding strategy.

Abstract

The phase-encoding strategy plays a critical role in determining the quality of gradient- and spin-echo (GRASE) images. Phase-encoding methods developed for two-dimensional GRASE imaging strive to achieve a balance between artifacts from T2-dependent signal amplitude modulations and off-resonance-dependent signal phase shifts, although no current method provides smooth and nonperiodic evolutions for both of these signal changes. In three-dimensional GRASE imaging, the use of two phase-encoding directions presents the opportunity for improved phase-encoding strategies. In this report a phase-encoding strategy for three-dimensional GRASE, termed SORT, is described; this strategy separates off-resonance and T2 effects, mapping one along each of the two phase-encoding directions. Thus, off-resonance-induced artifacts can be minimized while eliminating T2-dependent periodic signal modulations and allowing complete flexibility in the selection of echo time. The performance of the SORT phase-encoding method for T2-weighted GRASE imaging was compared with that of existing methods based on calculated point spread functions and simulated images. The predicted performance of SORT phase encoding was verified experimentally using T2-weighted three-dimensional GRASE imaging of the brain. Generally artifact-free images were obtained even in the presence of fat, susceptibility interfaces, and a wide range of T2 values.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

J P Mugler. 1999. Improved three-dimensional GRASE imaging with the SORT phase-encoding strategy.. https://doi.org/10.1002/(sici)1522-2586(199904)9%3A4%3C604%3A%3Aaid-jmri15%3E3.0.co%3B2-1

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↗

The cell in absence of aggregation artifacts.

Eduard Kellenberger understood that the conventional resin-embedding, he helped to develop (Ryter, A., Kellenberger, E., 1958. L'inclusion au polyester pour l'ultramicrotomie. J. Ultrastruct. Res. , 2, 200-214), was prone to aggregation artifacts (Kellenberger, E., 1987. The response to biological macromolecules and supramolecular structures to the physics of specimen cryo-preparation. In: Steinbrecht, R.A., Zierold, K. (Eds.), Cryo-techniques in Biological Electron Microscopy, Springer, Berlin, pp. 35-63). He was instrumental in developing various methods to overcome this limitation, for instance, by using low temperature-embedding and partially hydrophilic resins (Carlemalm, E., Garavito, R.M., Villiger, W., 1982. Resin development for electron microscopy and an analysis of embedding at low temperature. J. Microstruct., 126, 123-143; Villiger,W., 1993. Low temperature-embedding with Lowicryl resins. In: Robards, A.W., Wilson, A.J. (Eds.), Procedures in electron microscopy, Wiley, Chichester, UK, pp. 16:7.3-16:7.6). In principle, cryo-electron microscopy of vitreous sections is free of any aggregation artifact since the material remains fully hydrated and is free of chemical fixation or staining. The method is technically difficult still, but recent progress has made it amenable to routine practical applications. We compare here electron microscopical aspects of Zea mays meristem cells prepared by: (1) conventional resin-embedding and sectioning; (2) low temperature-embedding and sectioning of freeze substituted samples; and (3) cryo-sections of vitrified samples. The appearance of the extra-cellular space, the cytoplasm and the nucleoplasm are very different in conditions (1) and (3). They appear as compact, irregular and well delineated structures in conventional resin sections, whereas they are more diffuse and homogeneous in the vitreous sections. In the resin sections, the material seems to form a complex matrix, whereas it looks more like a thick soup in the vitreous sample. Low temperature-embedding (condition 2) shows an intermediate appearance. We suggest that regardless of the difference due to staining and different sectioning conditions, the other image differences are the consequence of aggregation artifacts in the resin-embedded specimens.

Artifacts↗

Comparison of transthoracic echocardiography with second harmonic imaging with transesophageal echocardiography in the detection of right to left shunts.

We compared the use of transthoracic echocardiography with second harmonic imaging after a peripheral intravenous injection of an agitated saline solution with transesophageal echocardiography (TEE) in the detection of right to left shunts at the cardiac and pulmonary level. Second harmonic mode transthoracic echocardiography and TEE are equally sensitive in detecting right to left shunts in patients undergoing a daily routine TEE.

Artifacts↗