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ΔSCOPE: A new method to quantify 3D biological structures and identify differences in zebrafish forebrain development
Developmental Biology ( IF 2.7 ) Pub Date : 2019-12-24 , DOI: 10.1016/j.ydbio.2019.11.014
Morgan S Schwartz 1 , Jake Schnabl 2 , Mackenzie P H Litz 1 , Benjamin S Baumer 3 , Michael Barresi 4
Affiliation  

Research in the life sciences has traditionally relied on the analysis of clear morphological phenotypes, which are often revealed using increasingly powerful microscopy techniques analyzed as maximum intensity projections (MIPs). However, as biology turns towards the analysis of more subtle phenotypes, MIPs and qualitative approaches are failing to adequately describe these phenotypes. To address these limitations and quantitatively analyze the three-dimensional (3D) spatial relationships of biological structures, we developed the computational method and program called ΔSCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination). Our approach uses the fluorescent signal distribution within a 3D data set and reorients the fluorescent signal to a relative biological reference structure. This approach enables quantification and statistical analysis of spatial relationships and signal density in 3D multichannel signals that are positioned around a well-defined structure contained in a reference channel. We validated the application of ΔSCOPE by analyzing normal axon and glial cell guidance in the zebrafish forebrain and by quantifying the commissural phenotypes associated with abnormal Slit guidance cue expression in the forebrain. Despite commissural phenotypes which display disruptions to the reference structure, ΔSCOPE was able to detect subtle, previously uncharacterized changes in zebrafish forebrain midline crossing axons and glia. This method has been developed as a user-friendly, open source program. We propose that ΔSCOPE is an innovative approach to advancing the state of image quantification in the field of high resolution microscopy, and that the techniques presented here are of broad applications to the life science field.



中文翻译:

ΔSCOPE:一种量化3D生物结构并识别斑马鱼前脑发育差异的新方法

传统上,生命科学的研究依赖于清晰的形态表型的分析,这些形态表型通常是通过使用功能日益强大的显微镜技术(作为最大强度预测(MIP))来揭示的。然而,随着生物学转向更精细的表型分析,MIP和定性方法无法充分描述这些表型。为了解决这些局限性并定量分析生物结构的三维(3D)空间关系,我们开发了称为Δ范围(使用PCA考试的空间圆柱坐标方向的变化)。我们的方法使用3D数据集中的荧光信号分布,并将荧光信号重新定向为相对的生物学参考结构。这种方法可以对3D多通道信号中的空间关系和信号密度进行量化和统计分析,这些信号位于参考通道中定义良好的结构周围。我们验证了Δ通过分析斑马鱼前脑中的正常轴突和神经胶质细胞引导并量化与前脑中Slit引导提示异常表达相关的连合表型来进行范围分析。尽管连合表型对参考结构显示出破坏,ΔSCOPE能够检测出斑马鱼前脑中线交叉轴突和神经胶质细胞中细微的,以前没有特征的变化。此方法已开发为用户友好的开源程序。我们建议ΔSCOPE是一种创新的方法,可以提高高分辨率显微镜领域的图像量化状态,并且此处介绍的技术在生命科学领域具有广泛的应用。

更新日期:2020-03-30
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