Non-rigid landmark-based large-scale image registration in 3-D reconstruction of mouse and rat kidney nephrons
Non-rigid landmark-based large-scale image registration in 3-D reconstruction of mouse and rat kidney nephrons
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DOI：
10.1016/j.micron.2014.10.002
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发表时间：
2015-01-01
期刊：
影响因子：
2.4
通讯作者：
Andreasen, Arne
中科院分区：
文献类型：
--
作者：
Zhang, Yan-Ling;Chang, Shi-Jie;Andreasen, Arne
背景：连续的组织切片会受到机械变形的影响，从而影响三维物体的重建。我们已经纠正了这样的文物与非刚性的地标为基础的方法，尊重组织块中的原始几何形状。该方法在小鼠和大鼠肾脏的半薄连续切片的大规模配准中得到了验证，并在FFPE切片上进行了测试。目的：在小鼠和大鼠肾脏的这项研究中，我们测量并表征了在制备2.5 μ m厚Epon切片时引入的变形，然后通过基于地标的非刚性变换（NRT）消除它们。我们从三个小鼠肾脏和三个大鼠肾脏获得了2.5 μ m厚的Epon连续切片，用于肾单位小管的三维重建。首先，来自3000个连续小鼠和13，000个连续大鼠切片的图像经历经典的刚性配准（CRR），并且测量和索引失真。对切片图像进行进一步的NRT，以补偿变形。所使用的NRT是一种经典的交互式基于地标的方法。通过比较变换后图像的几何形状与相应的块图像来验证NRT的质量。结果：经过CRR后，2.5 μ m厚的切片发生了高达2%的线性变形，管状长度被高估了高达1.5倍，并且最难从一个切片追踪到另一个切片。额外的NRT后，图像的几何形状反映了原来的几何形状在块中，管的长度不再高估，和NRT高度促进跟踪的tubular system.Conclusions：NRT促进了跟踪的肾小管系统在肾脏，跟踪，否则将是最困难的执行。NRT对小鼠和大鼠肾脏的节段性和空间性肾单位组织产生了大量的新知识。(C)2014作者爱思唯尔有限公司出版
Background: Serial histological sections are suffering from mechanical distortions that disturb the reconstruction of 3-D objects. We have corrected such artifacts with a non-rigid landmark-based method that respects the original geometry in the tissue block. The method is exemplified on a large scale in the registration of semi-thin serial sections of the mouse and rat kidneys, and has been tested on FFPE-sections.Aim: In this study of mouse and rat kidneys, we have measured and characterized the deformations introduced in the preparation of 2.5-mu m-thick Epon sections and then eliminated them by a landmark-based non-rigid transformation (NRT).Methods: We obtained 2.5-mu m-thick serial Epon sections from three mouse kidneys and three rat kidneys for 3-D reconstruction of the nephron tubules. First, the images from 3000 serial mouse and 13,000 serial rat sections underwent a classic rigid registration (CRR), and the distortions were measured and indexed. The section images underwent a further NRT in order to compensate for the deformations. The NRT used is a classic interactive landmark-based approach. The quality of the NRT was verified by comparing the geometry of the transformed images with corresponding block images.Results: After CRR, the 2.5-mu m-thick sections had a linear deformation of up to 2%, the tubular lengths were overestimated with up to 1.5x, and it was most difficult to trace the tubules from section to section. After the additional NRT, the geometry of the images reflected the original geometry in the block, the tubular lengths were no longer overestimated, and the NRT highly facilitated the tracing of the tubular system.Conclusions: NRT has facilitated the tracing of the tubular system in kidneys, a tracing, which would otherwise have been most difficult to perform. NRT has yielded substantial new knowledge to segmental and spatial nephron organization in the mouse and rat kidneys. (C) 2014 The Authors. Published by Elsevier Ltd.