Superpixel-ComBat modeling: A joint approach for harmonization and characterization of inter-scanner variability in T1-weighted images.

T1-weighted imaging holds wide applications in clinical and research settings; however, the challenge of inter-scanner variability arises when combining data across scanners, which impedes multi-site research. To address this, post-acquisition harmonization methods such as statistical or deep learning approaches have been proposed to unify cross-scanner images. Nevertheless, how inter-scanner variability manifests in images and derived measures, and how to harmonize it in an interpretable manner, remains underexplored.

NetBat: A network-driven harmonization method for structural connectivity.

As the practice of aggregating multi-site neuroimaging data has become more common, the field of neuroscience has increasingly recognized the importance of harmonization , or the removal of scanner effects from brain imaging data. While many harmonization methods exist, like ComBat and CovBat, few explicitly incorporate the network structure of the brain. Researchers studying structural connectivity are therefore not guaranteed to model the true underlying brain network.

MISPEL: A supervised deep learning harmonization method for multi-scanner neuroimaging data.

Large-scale data obtained from aggregation of already collected multi-site neuroimaging datasets has brought benefits such as higher statistical power, reliability, and robustness to the studies. Despite these promises from growth in sample size, substantial technical variability stemming from differences in scanner specifications exists in the aggregated data and could inadvertently bias any downstream analyses on it. Such a challenge calls for data normalization and/or harmonization frameworks, in addition to comprehensive criteria to estimate the scanner-related variability and evaluate the harmonization frameworks.

ComBat Harmonization: Empirical Bayes versus fully Bayes approaches.

Studying small effects or subtle neuroanatomical variation requires large-scale sample size data. As a result, combining neuroimaging data from multiple datasets is necessary. Variation in acquisition protocols, magnetic field strength, scanner build, and many other non-biologically related factors can introduce undesirable bias into studies.

Multi-scanner Harmonization of Paired Neuroimaging Data via Structure Preserving Embedding Learning.

Combining datasets from multiple sites/scanners has been becoming increasingly more prevalent in modern neuroimaging studies. Despite numerous benefits from the growth in sample size, substantial technical variability associated with site/scanner-related effects exists which may inadvertently bias subsequent downstream analyses. Such a challenge calls for a data harmonization procedure which reduces the scanner effects and allows the scans to be combined for pooled analyses.

A multi-scanner neuroimaging data harmonization using RAVEL and ComBat.

Modern neuroimaging studies frequently combine data collected from multiple scanners and experimental conditions. Such data often contain substantial technical variability associated with image intensity scale (image intensity scales are not the same in different images) and scanner effects (images obtained from different scanners contain substantial technical biases). Here we evaluate and compare results of data analysis methods without any data transformation (RAW), with intensity normalization using RAVEL, with regional harmonization methods using ComBat, and a combination of RAVEL and ComBat.

Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations.

Human microbiome data from genomic sequencing technologies is fast accumulating, giving us insights into bacterial taxa that contribute to health and disease. The predictive modeling of such microbiota count data for the classification of human infection from parasitic worms, such as helminths, can help in the detection and management across global populations. Real-world datasets of microbiome experiments are typically sparse, containing hundreds of measurements for bacterial species, of which only a few are detected in the bio-specimens that are analyzed.