Ogura Toshihiko, Sato Chikara
Neuroscience Research Institute and Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Umezono 1-1-4, Tsukuba, Ibaraki 305-8568, Japan.
J Struct Biol. 2004 Jun;146(3):344-58. doi: 10.1016/j.jsb.2004.01.007.
Single-particle analysis is a 3-D structure determining method using electron microscopy (EM). In this method, a large number of projections is required to create 3-D reconstruction. In order to enable completely automatic pickup without a matching template or a training data set, we established a brand-new method in which the frames to pickup particles are randomly shifted and rotated over the electron micrograph and, using the total average image of the framed images as an index, each frame reaches a particle. In this process, shifts are selected to increase the contrast of the average. By iterated shifts and further selection of the shifts, the frames are induced to shift so as to surround particles. In this algorithm, hundreds of frames are initially distributed randomly over the electron micrograph in which multi-particle images are dispersed. Starting with these frames, one of them is selected and shifted randomly, and acceptance or non-acceptance of its new position is judged using the simulated annealing (SA) method in which the contrast score of the total average image is adopted as an index. After iteration of this process, the position of each frame converges so as to surround a particle and the framed images are picked up. This method is the first unsupervised fully automatic particle picking method which is applicable to EM of various kinds of proteins, especially to low-contrasted cryo-EM protein images.
单颗粒分析是一种利用电子显微镜（EM）确定三维结构的方法。在这种方法中，需要大量投影来创建三维重建。为了在没有匹配模板或训练数据集的情况下实现完全自动拾取，我们建立了一种全新的方法，即在电子显微镜图像上随机移动和旋转用于拾取颗粒的帧，并以帧图像的总平均图像为指标，使每个帧定位到一个颗粒。在这个过程中，通过选择移动来增加平均值的对比度。通过反复移动和进一步选择移动，使帧围绕颗粒移动。在该算法中，最初在分散有多颗粒图像的电子显微镜图像上随机分布数百个帧。从这些帧开始，选择其中一个并随机移动，使用以总平均图像的对比度分数为指标的模拟退火（SA）方法判断其新位置是否被接受。经过这个过程的迭代，每个帧的位置收敛以围绕一个颗粒，从而拾取帧图像。该方法是第一种适用于各种蛋白质的电子显微镜，特别是低对比度冷冻电镜蛋白质图像的无监督全自动颗粒拾取方法。
