Protocol for Brain Magnetic Resonance Imaging and Extraction of Imaging‑Derived Phenotypes from the China Phenobank Project

Imaging-derived phenotypes(IDPs)have been increasingly used in population-based cohort studies in recent years.As widely reported,magnetic resonance imaging(MRI)is an important imaging modality for assessing the anatomical structure and function of the brain with high resolution and excellent soft-tissue contrast.The purpose of this article was to describe the imaging protocol of the brain MRI in the China Phenobank Project(CHPP).Each participant underwent a 30-min brain MRI scan as part of a 2-h whole-body imaging protocol in CHPP.The brain imaging sequences included T1-magnetization that prepared rapid gradient echo,T2 fuid-attenuated inversion-recovery,magnetic resonance angiography,difusion MRI,and resting-state functional MRI.The detailed descriptions of image acquisition,interpretation,and post-processing were provided in this article.The measured IDPs included volumes of brain subregions,cerebral vessel geometrical parameters,microstructural tracts,and function connectivity metrics.

An Image Skeletonization-Based Tool for Pollen Tube Morphology Analysis and Phenotyping

The mechanism underlying pollen tube growth involves diverse genes and molecular pathways. Alterations in the regulatory genes or pathways cause phenotypic changes reflected by cellular morphology, which can be captured using fluorescence microscopy. Determining and classifying pollen tube morphological phenotypes in such microscopic images is key to our understanding the involvement of genes and pathways. In this context, we propose a computational method to extract quantitative morphological features, and demonstrate that these features reflect morphological differences relevant to distinguish different defects of pollen tube growth. The corresponding software tool furthermore includes a novel semi-automated image segmentation approach, allowing to highly accurately identify the boundary of a pollen tube in a microscopic image.

Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight （R2 〉 0.92） and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response tonitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determina- tion of genomic regions associated with superior nutrient use efficiency.