PubMed · 9411788
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R A Kerr. 1997-12-05. Putative Martian microbes called microscopy artifacts.. https://doi.org/10.1126/science.278.5344.1706
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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.
Even in the absence of an experimental effect, functional magnetic resonance imaging (fMRI) time series generally demonstrate serial dependence. This colored noise or endogenous autocorrelation typically has disproportionate spectral power at low frequencies, i.e., its spectrum is (1/f)-like. Various pre-whitening and pre-coloring strategies have been proposed to make valid inference on standardised test statistics estimated by time series regression in this context of residually autocorrelated errors. Here we introduce a new method based on random permutation after orthogonal transformation of the observed time series to the wavelet domain. This scheme exploits the general whitening or decorrelating property of the discrete wavelet transform and is implemented using a Daubechies wavelet with four vanishing moments to ensure exchangeability of wavelet coefficients within each scale of decomposition. For (1/f)-like or fractal noises, e.g., realisations of fractional Brownian motion (fBm) parameterised by Hurst exponent 0 < H < 1, this resampling algorithm exactly preserves wavelet-based estimates of the second order stochastic properties of the (possibly nonstationary) time series. Performance of the method is assessed empirically using (1/f)-like noise simulated by multiple physical relaxation processes, and experimental fMRI data. Nominal type 1 error control in brain activation mapping is demonstrated by analysis of 13 images acquired under null or resting conditions. Compared to autoregressive pre-whitening methods for computational inference, a key advantage of wavelet resampling seems to be its robustness in activation mapping of experimental fMRI data acquired at 3 Tesla field strength. We conclude that wavelet resampling may be a generally useful method for inference on naturally complex time series.
This investigation evaluated metallic surgical instruments for magnetic resonance (MR) safety in association with a 1.5-Tesla/64-MHz MR system. Seven different instruments (mallet, bone punch, curette, Weil-Blakesley ethmoid forceps, suction cannula, septum speculum, and Kocher-Langenbeck retractor; Aesculap, Inc. (South San Francisco, CA) were tested for magnetic field interactions, heating, and generation of artifacts by using previously described techniques. Heating was evaluated for the septum speculum and Kocher-Langenbeck retractor by using a special gel-filled phantom and a fluoroptic thermometer to record temperatures immediately before and during MRI performed at a whole-body averaged SAR of 1.3 W/kg. Artifacts were assessed with the instruments placed inside of a gel-filled phantom and performing MRI using T1-weighted spin-echo and gradient-echo pulse sequences. Magnetic field interactions were relatively minor (deflection angles, 0 to 7 degrees; torque, 0 to +1), the highest temperature changes were < or = +0.8 degrees C, and the artifacts should not create substantial problems considering the "intended use" for these instruments. The findings of the MR safety tests indicated that the seven different metallic surgical instruments (Aesculap, Inc.) would be safe and acceptable for use in interventional MRI procedures performed with MR systems with static magnetic fields of 1.5 T or less. J. Magn. Reson. Imaging 2001;13:152-157.