Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Organismal phenotypes frequently involve multiple organ systems. Histology
is a powerful way to detect cellular and tissue phenotypes, but is largely
descriptive and subjective. To determine how synchrotron-based X-ray
micro-tomography (micro-CT) can yield 3-dimensional whole-organism images
suitable for quantitative histological phenotyping, we scanned whole
zebrafish, a small vertebrate model with diverse tissues, at ~1 micron
voxel resolutions. Using micro-CT optimized for cellular characterization
(histo-tomography), brain nuclei can be computationally segmented and
assigned to brain regions. Shape and volume can be computed for
populations of nuclei, motor neurons and red blood cells. Computed cell
density revealed striking individual phenotypic variation. Unlike
histology, histo-tomography allows the detection of phenotypes that
require millimeter scale context in multiple planes. We expect the
computational and visual insights into 3D tissue architecture provided by
histo-tomography to be useful for reference atlases, hypothesis
generation, comprehensive organismal screens, and diagnostics.

生物体表型往往涉及多个器官系统。组织学（Histology）是检测细胞与组织表型的有力方法，但在很大程度上具有描述性与主观性。为明确基于同步辐射的X射线显微断层扫描（synchrotron-based X-ray micro-tomography，micro-CT）如何生成适用于定量组织学表型分析的三维全生物图像，我们对斑马鱼（一种具有多样组织的小型脊椎动物模型）进行了扫描，体素分辨率约为1微米。利用针对细胞表征优化的显微断层扫描（histo-tomography，即组织断层扫描），可通过计算对脑核进行分割并将其分配至不同脑区。能够计算核群、运动神经元及红细胞的形态与体积。计算得出的细胞密度揭示了显著的个体表型变异。与组织学不同，组织断层扫描可检测需要多平面毫米级背景的表型。我们期望，组织断层扫描所提供的三维组织结构的计算与视觉洞察，能为参考图谱、假设生成、全面生物筛选及诊断提供帮助。