PubMed · 7845765
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R L Gregory. 1994. Under the carpet.. https://doi.org/10.1068/p230741
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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: Patients who are misdiagnosed with ventricular tachycardia because of electrocardiographic artifact may be subjected to unnecessary procedures. The purpose of this study was to determine how often electrocardiographic artifact is misdiagnosed as ventricular tachycardia. METHODS: Physicians (n = 766) were surveyed with a case simulation that included a two-lead electrocardiographic monitor tracing of artifact simulating a wide-complex tachycardia. RESULTS: The rhythm strip was not recognized as artifact by 52 of the 55 internists (94%), 128 of the 221 cardiologists (58%), and 186 of the 490 electrophysiologists (38%). One hundred fifty-six of the 181 electrophysiologists (88%), 67 of the 126 cardiologists (53%), and 14 of the 15 internists (31%) who misdiagnosed the rhythm as ventricular tachycardia recommended an invasive procedure for further evaluation or therapy. CONCLUSIONS: This physician survey suggests that electrocardiographic artifact that mimics ventricular tachycardia may frequently result in patients being subjected to unnecessary invasive cardiac procedures. Physicians should include artifact in their differential diagnosis of wide complex tachycardias to minimize unneeded procedures.
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