OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics
OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics
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DOI：
10.1093/bioinformatics/btaa096
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发表时间：
2020-05-15
期刊：
影响因子：
5.8
通讯作者：
Newton, Paul K.
中科院分区：
文献类型：
--
作者：
Hasnain, Zaki;Fraser, Andrew K.;Newton, Paul K.
摘要：类器官模型系统概括了哺乳动物组织的关键特征，并使高通量实验成为可能。然而，这些实验的影响可能受到手动、非标准化、静态或定性表型分析的限制。OrgDyn是一个开源和模块化的管道，使用基于特征和模型的方法对2D类器官轮廓图像的时间序列进行量化。我们的管道包括（i）几何和信号处理特征提取，（ii）降维以区分动态路径，（iii）时间序列聚类以识别类器官的相干组，以及（iv）使用点分布模型来解释时间形状变化的动态建模。OrgDyn可以表征、聚类和建模定义不同最终形状的独特动力学路径之间的差异，从而实现组织发育和疾病分子基础的定量分析。
A Summary: Organoid model systems recapitulate key features of mammalian tissues and enable high throughput experiments. However, the impact of these experiments may be limited by manual, non-standardized, static or qualitative phenotypic analysis. OrgDyn is an open-source and modular pipeline to quantify organoid shape dynamics using a combination of feature- and model-based approaches on time series of 2D organoid contour images. Our pipeline consists of (i) geometrical and signal processing feature extraction, (ii) dimensionality reduction to differentiate dynamical paths, (iii) time series clustering to identify coherent groups of organoids and (iv) dynamical modeling using point distribution models to explain temporal shape variation. OrgDyn can characterize, cluster and model differences among unique dynamical paths that define diverse final shapes, thus enabling quantitative analysis of the molecular basis of tissue development and disease.