Straightening Caenorhabditis elegans images
Straightening Caenorhabditis elegans images
复制标题
DOI：
10.1093/bioinformatics/btm569
复制
发表时间：
2008-01-15
期刊：
影响因子：
5.8
通讯作者：
Myers, Eugene W.
中科院分区：
文献类型：
--
作者：
Peng, Hanchuan;Long, Fuhui;Myers, Eugene W.
动机：秀丽隐杆线虫，一种在土壤中发现的蛔虫，是一种被广泛研究的模式生物，成年时约有1000个细胞。制作秀丽隐杆线虫的高分辨率荧光图像以揭示生物学见解正在成为常规，这激发了先进计算工具的开发，用于分析所产生的图像堆栈。例如，蠕虫的身体通常在图像中明显弯曲。因此，必须拉直蠕虫，如果他们要比较下一个典型的coordinate system.Results：我们开发了一个蠕虫矫直算法（WSA），restacks切割平面正交的骨干模型的anteriorposterior轴的蠕虫。我们制定的骨干作为一个参数三次样条定义的一系列控制点。我们开发了两种自动确定控制点位置的方法。我们的实验方法表明，我们的方法有效地拉直2D和3D蠕虫图像。
Motivation: Caenorhabditis elegans, a roundworm found in soil, is a widely studied model organism with about 1000 cells in the adult. Producing high-resolution fluorescence images of C.elegans to reveal biological insights is becoming routine, motivating the development of advanced computational tools for analyzing the resulting image stacks. For example, worm bodies usually curve significantly in images. Thus one must straighten the worms if they are to be compared under a canonical coordinate system.Results: We develop a worm straightening algorithm (WSA) that restacks cutting planes orthogonal to a backbone that models the anteriorposterior axis of the worm. We formulate the backbone as a parametric cubic spline defined by a series of control points. We develop two methods for automatically determining the locations of the control points. Our experimental methods show that our approaches effectively straighten both 2D and 3D worm images.