PubMed · 12958510
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Joanne Edwards, John M S Bartlett. 2003. Mutation and polymorphism detection: a technical overview.. https://doi.org/10.1385/1-59259-384-4%3A287
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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).
Nine observers reviewed a previously assembled library of 320 chest computed radiography (CR) images. Observers participated in four sessions, reading a different 1/4 of the sample on each of four liquid crystal displays: a 2-megapixel (MP) consumer color display, a 2-MP business color display, a 2-MP medical-grade gray display, and a 3-MP gray display. Each display was calibrated according to the DICOM Part 14 standard. The viewing application required observer log-in, then randomized the order of the subsample seen on the display, and timed the responses of the observer to render a 1-5 judgment on the absence or presence of ILD on chest CRs. Selections of 1-2 were considered negative, 3 was indeterminate, and 4-5 were positive. The order of viewing sessions was also randomized for each observer. The experiment was conducted under controlled lighting, temperature, and sound conditions to mimic conditions typically found in a patient examination room. Lighting was indirect, and illuminance at the display face was 195 +/- 8% lux and was monitored over the course of the experiment. The average observer sensitivity for the 2 MP color consumer, 2 MP business color, 2 MP gray, and 3 MP gray displays were 83.7%, 84.1%, 85.5%, and 86.7%, respectively. The only pairwise significant difference was between the 2-MP consumer color and the 2-MP gray (P = 0.05). Effect of order within a session was not significant (P = 0.21): period 1 (84.3%), period 2 (86.2%), period 3 (85.4%), period 4 (84.1%). Observer specificity for the various displays was not statistically significant (P = 0.21). Finally, a timing analysis showed no significant difference between the displays for the user group (P = 0.13), ranging from 5.3 s (2 MP color business) to 5.9 s (3 MP Gray). There was, however, a reduction in time over the study that was significant (P < 0.001) for all users; the group average decreased from 6.5 to 4.7 s per image. Physical measurements of the resolution, contrast, and noise properties of the displays were acquired. Most notably, the noise of the displays varied by 3.5x between the lowest and highest noise displays. Differences in display noise were indicative of observer performance. However, the large difference in the magnitude of the noise was not predictive of the small difference (3%) in the observer sensitivity for various displays. This is likely because detection of interstitial lung disease is limited by "anatomical noise" rather than display or x-ray image noise.