Sazzed Salim, Scheible Peter, He Jing, Wriggers Willy
Department of Computer Science, Old Dominion University, Norfolk, VA 23529.
Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529.
Proceedings (IEEE Int Conf Bioinformatics Biomed). 2021 Dec;2021:2553-2559. doi: 10.1109/bibm52615.2021.9669318.
We propose a fast, dynamic programming-based framework for tracing actin filaments in 3D maps of subcellular components in cryo-electron tomography. The approach can identify high-density filament segments in various orientations, but it takes advantage of the arrangement of actin filaments within cells into more or less tightly aligned bundles. Assuming that the tomogram can be rotated such that the filaments can be oriented to be directed in a dominant direction (i.e., the , , or axis), the proposed framework first identifies local seed points that form the origin of candidate filament segments (CFSs), which are then grown from the seeds using a fast dynamic programming algorithm. The CFS length can be tuned to the nominal resolution of the tomogram or the separation of desired features, or it can be used to restrict the curvature of filaments that deviate from the overall bundle direction. In subsequent steps, the CFSs are filtered based on backward tracing and path density analysis. Finally, neighboring CFSs are fused based on a collinearity criterion to bridge any noise artifacts in the 3D map that would otherwise fractionalize the tracing. We validate our proposed framework on simulated tomograms that closely mimic the features and appearance of experimental maps.
我们提出了一种基于动态规划的快速框架，用于在冷冻电子断层扫描的亚细胞成分三维图中追踪肌动蛋白丝。该方法可以识别各种方向上的高密度丝段，但它利用了细胞内肌动蛋白丝排列成或多或少紧密排列的束这一特点。假设断层扫描图像可以旋转，使得丝能够定向到一个主导方向（即x、y或z轴），所提出的框架首先识别形成候选丝段（CFS）起点的局部种子点，然后使用快速动态规划算法从种子点开始生长。CFS的长度可以调整到断层扫描图像的标称分辨率或所需特征的间距，或者它可以用于限制偏离整体束方向的丝的曲率。在后续步骤中，基于反向追踪和路径密度分析对CFS进行滤波。最后，基于共线性标准融合相邻的CFS，以弥合三维图中否则会使追踪碎片化的任何噪声伪影。我们在紧密模拟实验图像特征和外观的模拟断层扫描图像上验证了我们提出的框架。
