Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, Germany.
Centre for Organismal Studies, COS, Heidelberg University, Im Neunheimer Feld 230, Heidelberg, Germany.
Sci Rep. 2018 Nov 8;8(1):16531. doi: 10.1038/s41598-018-34848-z.
Vertebrate models provide indispensable paradigms to study development and disease. Their analysis requires a quantitative morphometric study of the body, organs and tissues. This is often impeded by pigmentation and sample size. X-ray micro-computed tomography (micro-CT) allows high-resolution volumetric tissue analysis, largely independent of sample size and transparency to visual light. Importantly, micro-CT data are inherently quantitative. We report a complete pipeline of high-throughput 3D data acquisition and image analysis, including tissue preparation and contrast enhancement for micro-CT imaging down to cellular resolution, automated data processing and organ or tissue segmentation that is applicable to comparative 3D morphometrics of small vertebrates. Applied to medaka fish, we first create an annotated anatomical atlas of the entire body, including inner organs as a quantitative morphological description of an adult individual. This atlas serves as a reference model for comparative studies. Using isogenic medaka strains we show that comparative 3D morphometrics of individuals permits identification of quantitative strain-specific traits. Thus, our pipeline enables high resolution morphological analysis as a basis for genotype-phenotype association studies of complex genetic traits in vertebrates.
脊椎动物模型为研究发育和疾病提供了不可或缺的范例。对它们的分析需要对身体、器官和组织进行定量形态计量学研究。这通常受到色素沉着和样本大小的限制。X 射线微计算机断层扫描（micro-CT）允许对组织进行高分辨率的体积分析，在很大程度上不受样本大小和可见光透明度的影响。重要的是，micro-CT 数据本质上是定量的。我们报告了一个完整的高通量 3D 数据采集和图像分析流水线，包括组织准备和对比增强，以实现高达细胞分辨率的 micro-CT 成像、自动数据处理以及适用于小型脊椎动物比较 3D 形态计量学的器官或组织分割。我们将其应用于斑马鱼，首先创建了整个身体的注释解剖图谱，包括内部器官，作为成年个体的定量形态描述。该图谱作为比较研究的参考模型。使用同基因的斑马鱼品系，我们表明个体的比较 3D 形态计量学可以识别定量的品系特异性特征。因此，我们的流水线能够进行高分辨率形态分析，作为脊椎动物复杂遗传特征的基因型-表型关联研究的基础。
