ACME: automated cell morphology extractor for comprehensive reconstruction of cell membranes.
ACME: automated cell morphology extractor for comprehensive reconstruction of cell membranes.
复制标题
DOI：
10.1371/journal.pcbi.1002780
复制
发表时间：
2012
影响因子：
4.3
通讯作者：
Megason SG
中科院分区：
文献类型：
--
作者：
Mosaliganti KR;Noche RR;Xiong F;Swinburne IA;Megason SG
细胞形状、细胞迁移和细胞重排的量化对于解决发育生物学中的经典问题非常重要，例如模式形成和组织形态发生。表达荧光报告基因的转基因胚胎的延时显微成像是追踪体内形态发生变化和建立细胞谱系和命运图的首选方法。然而，人工步骤涉及的数千个假定的细胞分割已经成为这些技术应用的主要瓶颈，特别是在细胞膜上。细胞膜的分割虽然比细胞核分割更困难，但对于量化细胞形态变化和形态发生之间的关系是必要的。我们提出了一种新的全自动方法，首先重建膜信号，然后从3D膜图像中分割出细胞，即使在致密的组织中也是如此。该方法分为三个阶段：1)局部膜平面的检测，2)填补结构缺口的投票，3)区域分割。在斑马鱼神经外胚层和近轴中胚层的延时共聚焦和双光子图像上，我们通过与人类检测结果的比较，定量地证明了该算法的优越性能。我们还与在不同噪声条件下用荧光记者模拟成像过程生成的合成显微图像进行了比较。该方法的过分率和欠分割率都在5%左右。与专家手动分割相比，单个细胞的体积重叠始终超过84%。通过使用我们的软件(ACME)研究体节形成，我们能够高精度地分割接触细胞，并可靠地量化形态发生参数的变化，如细胞的形状和大小，以及上皮细胞和间充质细胞的排列。我们的软件已经在Windows、Mac和LINUX平台上进行了开发和测试，并在开放源码BSD许可(https://github.com/krm15/ACME).)下公开提供
The quantification of cell shape, cell migration, and cell rearrangements is important for addressing classical questions in developmental biology such as patterning and tissue morphogenesis. Time-lapse microscopic imaging of transgenic embryos expressing fluorescent reporters is the method of choice for tracking morphogenetic changes and establishing cell lineages and fate maps in vivo. However, the manual steps involved in curating thousands of putative cell segmentations have been a major bottleneck in the application of these technologies especially for cell membranes. Segmentation of cell membranes while more difficult than nuclear segmentation is necessary for quantifying the relations between changes in cell morphology and morphogenesis. We present a novel and fully automated method to first reconstruct membrane signals and then segment out cells from 3D membrane images even in dense tissues. The approach has three stages: 1) detection of local membrane planes, 2) voting to fill structural gaps, and 3) region segmentation. We demonstrate the superior performance of the algorithms quantitatively on time-lapse confocal and two-photon images of zebrafish neuroectoderm and paraxial mesoderm by comparing its results with those derived from human inspection. We also compared with synthetic microscopic images generated by simulating the process of imaging with fluorescent reporters under varying conditions of noise. Both the over-segmentation and under-segmentation percentages of our method are around 5%. The volume overlap of individual cells, compared to expert manual segmentation, is consistently over 84%. By using our software (ACME) to study somite formation, we were able to segment touching cells with high accuracy and reliably quantify changes in morphogenetic parameters such as cell shape and size, and the arrangement of epithelial and mesenchymal cells. Our software has been developed and tested on Windows, Mac, and Linux platforms and is available publicly under an open source BSD license (https://github.com/krm15/ACME).
登录
查看更多内容
影响因子：
3.7
作者：
Lin, G;Chawla, MK;Roysam, B
通讯作者：
Roysam, B
影响因子：
56.9
作者：
Olivier, Nicolas;Luengo-Oroz, Miguel A.;Beaurepaire, Emmanuel
通讯作者：
Beaurepaire, Emmanuel
影响因子：
4.6
作者：
Sarti, A;de Solórzano, CO;Malladi, R
通讯作者：
Malladi, R
影响因子：
10.6
作者：
Parvin, Bahram;Yang, Qing;Barcellos-Hoff, Mary Helen
通讯作者：
Barcellos-Hoff, Mary Helen
影响因子：
4.5
作者：
Loss, Leandro;Bebis, George;Skurikhin, Alexei
通讯作者：
Skurikhin, Alexei