Automated tracing of neurites from light microscopy stacks of images.
Automated tracing of neurites from light microscopy stacks of images.
复制标题
DOI：
10.1007/s12021-011-9121-2
复制
发表时间：
2011-09
期刊：
影响因子：
3
通讯作者：
Stepanyants A
中科院分区：
文献类型：
--
作者：
Chothani P;Mehta V;Stepanyants A
大规模的神经回路重建过程的自动化是神经科学领域最重要的挑战之一。在这项研究中，我们研究的方法，从三维光学显微镜（LM）堆栈图像的电路重建。我们展示了一个理想的重建过程的最小错误率如何取决于标记的神经突的密度，从而产生了基于LM的神经回路研究方法的根本限制。电路重建过程通常涉及与神经元标记和成像以及随后的图像预处理和神经突追踪相关的步骤。在这项研究中，我们专注于最后一步-从已经预处理的图像堆栈中检测神经突的痕迹。我们的自动跟踪算法作为神经回路跟踪器软件包的一部分实现，包括以下主要步骤。首先，对图像堆栈进行滤波以增强标记的神经突。第二，神经突的中心线检测和优化。最后，最佳轨迹的各个分支被合并成基于成本最小化方法的树。成本函数考虑了分支方向、它们的端点之间的距离、合并结构的曲率及其强度。该算法能够连接由于不完美的标记而出现断裂的分支，并且可以解决由于光学显微镜的有限分辨率而出现分支融合的情况。Neural Circuit Tracer软件旨在自动整合ImageJ插件和MatLab编写的函数，与手动跟踪相比，速度大约提高了10倍。
Automating the process of neural circuit reconstruction on a large-scale is one of the foremost challenges in the field of neuroscience. In this study we examine the methodology for circuit reconstruction from three-dimensional light microscopy (LM) stacks of images. We show how the minimal error-rate of an ideal reconstruction procedure depends on the density of labeled neurites, giving rise to the fundamental limitation of an LM based approach for neural circuit research. Circuit reconstruction procedures typically involve steps related to neuron labeling and imaging, and subsequent image pre-processing and tracing of neurites. In this study, we focus on the last step – detection of traces of neurites from already pre-processed stacks of images. Our automated tracing algorithm, implemented as part of the Neural Circuit Tracer software package, consists of the following main steps. First, image stack is filtered to enhance labeled neurites. Second, centerline of the neurites is detected and optimized. Finally, individual branches of the optimal trace are merged into trees based on a cost minimization approach. The cost function accounts for branch orientations, distances between their end-points, curvature of the merged structure, and its intensity. The algorithm is capable of connecting branches which appear broken due to imperfect labeling and can resolve situations where branches appear to be fused due the limited resolution of light microscopy. The Neural Circuit Tracer software is designed to automatically incorporate ImageJ plug-ins and functions written in MatLab and provides roughly a 10-fold increases in speed in comparison to manual tracing.
登录
查看更多内容
影响因子：
16.2
作者：
Holtmaat, AJGD;Trachtenberg, JT;Svoboda, K
通讯作者：
Svoboda, K
影响因子：
3
作者：
Cannon, RC;Turner, DA;Wheal, HV
通讯作者：
Wheal, HV
DOI：
10.1109/tpami.2004.44
发表时间：
2004-08-01
影响因子：
23.6
作者：
Jacob, M;Unser, M
通讯作者：
Unser, M
影响因子：
4.3
作者：
Bohland JW;Wu C;Barbas H;Bokil H;Bota M;Breiter HC;Cline HT;Doyle JC;Freed PJ;Greenspan RJ;Haber SN;Hawrylycz M;Herrera DG;Hilgetag CC;Huang ZJ;Jones A;Jones EG;Karten HJ;Kleinfeld D;Kötter R;Lester HA;Lin JM;Mensh BD;Mikula S;Panksepp J;Price JL;Safdieh J;Saper CB;Schiff ND;Schmahmann JD;Stillman BW;Svoboda K;Swanson LW;Toga AW;Van Essen DC;Watson JD;Mitra PP
通讯作者：
Mitra PP
影响因子：
19.5
作者：
KASS, M;WITKIN, A;TERZOPOULOS, D
通讯作者：
TERZOPOULOS, D