Detection of the optimal neuron traces in confocal microscopy images.
Detection of the optimal neuron traces in confocal microscopy images.
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DOI：
10.1016/j.jneumeth.2008.11.008
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发表时间：
2009-03-30
影响因子：
3
通讯作者：
Stepanyants, Armen
中科院分区：
文献类型：
--
作者：
Vasilkoski, Zlatko;Stepanyants, Armen
神经回路的定量分析方法依赖于在三维 (3D) 上精确重建的大型神经元数据集。由于神经元乔木的复杂性，必须使用自动化算法生成重建神经元的大型数据集。在这里，我们尝试自动化从稀疏标记的 3D 共焦显微镜图像堆栈中进行神经元追踪的过程。我们的算法涉及两个步骤。第一步，对堆栈中神经突的分割图像进行体素编码。连续编码的波前的强度中心连接成分支结构，代表神经突的粗迹。在第二步中，使用改进的活动轮廓方法对该轨迹进行优化，该方法倾向于最大化沿轨迹的强度，同时保持其处于张力下。为了评估算法的性能，我们使用了神经元的手动重建并将其转换为人工强度图像堆栈。使用开发的算法对这些图像进行追踪，并与相应的手动追踪进行定量比较。最佳迹线平均比手动迹线短 6.0%。长度的减少是由于最佳轨迹的平滑度造成的，与手动轨迹相比，最佳轨迹是由较短的线段构建而成，因此曲折程度减少了 3.3%。最佳迹线与手动迹线之间的平均距离为0.14 μm，对应分支点之间的平均距离为2.2 μm，说明迹线之间具有良好的一致性。
Quantitative methods of analysis of neural circuits rely on large datasets of neurons reconstructed accurately in three dimensions (3D). Due to the complexity of neuronal arbors, large datasets of reconstructed neurons must be generated with automated algorithms. Here, we attempted to automate the process of neuron tracing from sparsely labeled 3D stacks of confocal microscopy images. Our algorithm involves two steps. In the first step, the segmented image of neurites in the stack is voxel-coded. Centers of intensity of consecutively coded wave fronts are connected into a branched structure, which represents a coarse trace of the neurites. In the second step, this trace is optimized with the modified active contour method, which tends to maximize the intensity along the trace while keeping it under tension. To assess the performance of the algorithm we used manual reconstructions of neurons and converted them into artificial stacks of intensity images. These images were traced using the developed algorithm and quantitatively compared to the corresponding manual traces. The optimal traces were on average 6.0% shorter than the manual traces. This reduction in length resulted from the smoothness of the optimal traces, which, in comparison to the manual ones, were built out of shorter segments, and, as a result, were 3.3% less tortuous. The average distance between the optimal and the manual traces was 0.14 μm, and the average distance between their corresponding branch-points was 2.2 μm, illustrating good agreement between the traces.
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