PubMed · 15272326
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Y Z Zanganah. 2004-07-24. Incidental finding.. https://doi.org/10.1038/sj.bdj.4811502
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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.
BACKGROUND: Excessive blood may compromise gynecologic Papanicolaou (Pap) smears. Liquid-based cytologic techniques have been developed in part to address this problem. In the current study, conditions of excessive blood were simulated to compare the ability of two liquid-based systems, ThinPrep and SurePath, to satisfactorily process specimens in the presence of this potentially limiting factor. METHODS: Equal volumes of washed epithelial cells derived from pooled residues of liquid Pap vials were added to a series of ThinPrep and SurePath vials. Increasing volumes of freshly drawn, packed erythrocytes were added to the vials in progressive amounts from 50 microL or 100 microL up to 3000 microL. The vials were processed on their respective instruments according to U.S. Food and Drug Administration-approved procedures for a total of six test runs. The cellularity of the slides was measured by averaging epithelial cell counts in a total of five 40x fields. RESULTS: SurePath preparations were uncompromised by blood until aliquots from 1000 microL to 3000 microL were reached. The ThinPrep system invariably was overwhelmed by the first 50-microL or 100-microL aliquot of blood, with epithelial cell counts dropping immediately to near zero. CONCLUSIONS: The cell enrichment process of the SurePath system capably handled significantly greater amounts of potentially obscuring blood than the membrane filtration method of the ThinPrep system, which was compromised by as little as <or= 1 drop of packed erythrocytes (1 drop = 65 microL).
Echo-planar imaging (EPI) is widely used in functional MRI studies. It is well known that EPI quality is usually degraded by geometric distortions, when there exist susceptibility field inhomogeneities. EPI distortions may be corrected if the field maps are available. It is possible to estimate the susceptibility field gradients from the phase reconstruction of a single-TE EPI image, after a successful phase-unwrapping procedure. However, in regions affected by pronounced field gradients, the phase-unwrapping of a single-TE image may fail, and therefore the estimated field maps may be incorrect. It has been reported that the field inhomogeneity may be calculated more reliably from T2*-weighted images corresponding to multiple TEs. However, the multi-TE MRI field mapping increases the scan time. Furthermore, the measured field maps may be invalid if the subject's position changes during dynamic scans. To overcome the limitations in conventional field mapping approaches, a novel k-space energy spectrum analysis algorithm is developed, which quantifies the spatially dependent echo-shifting effect and the susceptibility field gradients directly from the k-space data of single-TE gradient-echo EPI. Using the k-space energy spectrum analysis, susceptibility field gradients can be reliably measured without phase-unwrapping, and EPI distortions can be corrected without extra field mapping scans or pulse sequence modification. The reported technique can be used to retrospectively improve the image quality of the previously acquired EPI and functional MRI data, provided that the complex-domain k-space data are still available.