PubMed · 10663055
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R Hauser. 2000. [Computer-aided 3D-navigation systems-a plea for an error model].. https://doi.org/10.1007/s001060050014
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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: The ThinPrep Processor has gained popularity as a collection and preparation technique for fine-needle aspiration biopsy (FNAB). Specific cytologic criteria to evaluate ThinPrep preparation (TP) may differ from those of conventional preparation (CP). The authors retrospectively reviewed the quality, cytologic features, and pitfalls of TP versus CP in thyroid FNABs and addressed the cytomorphologic criteria used to evaluate TP specimens. METHODS: Thyroid FNABs received between January 1996-July 1999 were identified from the computer files of the Department of Pathology, University of Michigan (Ann Arbor, MI). Histologic correlation and clinical follow-up were reviewed. The cytology slides were reevaluated for cellularity, cellular preservation, artifacts, background material, architectural integrity, cytoplasmic details, and nuclear details by two observers. RESULTS: Of the 209 thyroid FNABs performed during the study period, TP and CP prepared 127 and 82 cases respectively. Histologic correlation was available in 68 (33%) cases (32 TP and 36 CP). Overall sensitivity was 80% and specificity was 98%. The sensitivity of CP versus TP was 87% and 70%, respectively. Thyroid FNABs prepared by TP, as compared with CP, were characterized by the following: The TP slide 1) allowed assessment of the overall specimen cellularity but not individual passes of an FNAB, 2) contained only "hard" colloid that appeared dense, markedly fragmented, or in droplets, 3) showed crowded, tight, tissue clusters with loss of cellular preservation, especially in the larger aggregates, 4) demonstrated more cell shrinkage, 5) showed increased disruption of the cytoplasm and numerous naked nuclei, 6) occasionally gave nucleoli a more prominent appearance, and 7) was less likely to show nuclear grooves and "pseudoinclusions" in papillary carcinoma. CONCLUSIONS: This study concluded that cytologic features used to evaluate thyroid FNABs prepared by CP may need to be modified when using TP. Awareness of the above-described findings and further studies to evaluate TP are essential to avoid potential diagnostic pitfalls.
The binding of oligodeoxynucleotides modified with adenine 2'-O-methyl riboside, 2,6-diaminopurine 2'-O-methyl riboside, cytosine 2'-O-methyl riboside, 2,6-diaminopurine deoxyriboside or 5-bromodeoxyuridine was studied with a microarray containing all possible (4096) polyacrylamide-bound hexadeoxynucleotides (a generic microchip). The generic microchip was manufactured by using reductive immobilization of aminooligonucleotides in the activated copolymer of acrylamide, bis-acrylamide and N-(2,2-dimethoxyethyl) acrylamide. The binding of the fluorescently labeled modified octanucleotides to the array was analyzed with the use of both melting profiles and the fluorescence distribution at selected temperatures. Up to three substitutions of adenosines in the octamer sequence by adenine 2'-O-methyl ribosides (A(m)), 2,6-diaminopurine 2'-O-methyl ribosides (D(m)) or 2,6-diaminopurine deoxyribosides (D) resulted in increased mismatch discrimination measured at the melting temperature of the corresponding perfect duplex. The stability of complexes formed by 2'-O-methyl-adenosine-modified oligodeoxynucleotides was slightly decreased with every additional substitution, yielding approximately 4 degrees C of total loss in melting temperature for three modifications, as followed from microchip thermal denaturation experiments. 2,6-Diaminopurine 2'-O-methyl riboside modifications led to considerable duplex stabilization. The cytosine 2'-O-methyl riboside and 5-bromodeoxyuridine modifications generally did not change either duplex stability or mismatch resolution. Denaturation experiments conducted with selected perfect duplexes on microchips and in solution showed similar results on thermal stabilities. Some hybridization artifacts were observed that might indicate the formation of parallel DNA.