PubMed · 10972593
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K Wiener. 2000. Potential for error from underfilling Glucometer Elite test strips.. https://doi.org/10.1046/j.1464-5491.2000.00311-6.x
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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.
PURPOSE: To investigate whether high-quality, relatively inexpensive, document and transparency scanners used as densitometers are sufficiently quantitative for routine quality assurance (QA). METHODS AND MATERIALS: The scanner we investigated used a linear amplifier, digitizing gray-scale images to 12-bit resolution with a user-selected spatial resolution of 0.170 mm(2) pixels. To reduce Newton's rings artifacts, the standard glass platen was replaced by glass with an antireflective coating. Conversion of reading to transmission was conducted by permanently placing a calibrated photographic step tablet on the scanner platen. After conversion to light transmission, a zero-phase two-dimensional Wiener filter was used to reduce pixel-to-pixel signal variation. Light-scatter artifacts were removed by deconvolution of a measured light-spread kernel. The light-spread kernel artifacts were significant along the scanner's detector axis, but were insignificant along the scanning axis. RESULTS: Pixel-to-pixel noise was better than 2% for optical densities, ranging from 0.4 to 2.0 and 0 to 2.7 for the unfiltered and filtered images, respectively. The document scanning system response was compared against a confocal scanning laser densitometer. A series of IMRT dose distribution and dose calibration film sets were scanned using the two scanners, and the measured dose was compared. The maximum mean and standard deviation of the measured dose difference between the document scanner and confocal scanner was 1.48% and 1.06%, respectively. CONCLUSION: While the document scanners are not as flexible as dedicated film densitometers, these results indicate that, using the intensity and scatter corrections, the system provides accurate and precise measurements up to an optical density of 2.0, sufficient for routine IMRT film QA. For some film types, this requires the reduction in monitor units to limit the dose delivered to the film. The user must be cautious that the delivered IMRT dose is scaled appropriately. This inexpensive and accurate system is being integrated into an automated QA program.
BACKGROUND: Cardiopulmonary resuscitation (CPR) creates artifacts on the ECG and, with automated defibrillators, a pause in CPR is mandatory during rhythm analysis. The rate of return of spontaneous circulation (ROSC) is reduced with increased duration of this hands-off interval in rats. We analyzed whether similar hands-off intervals in humans with ventricular fibrillation causes changes in the ECG predicting a lower probability of ROSC. METHODS AND RESULTS: The probability of ROSC after a shock was continually determined from ECG signal characteristics for up to 20 seconds of 634 such hands-off intervals in patients with ventricular fibrillation. In hands-off intervals with an initially high (40% to 100%) or median (25% to 40%) probability for ROSC, the probability was gradually reduced with time to a median of 8% to 11% after 20 seconds (P<0.001). In episodes with a low initial probability (0% to 25%; median, 5%), there was no further reduction with time. CONCLUSIONS: The interval between discontinuation of chest compressions and delivery of a shock should be kept as short as possible.