Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.
Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.
Bioinformatics. 2018 Sep 1;34(17):3004-3012. doi: 10.1093/bioinformatics/bty200.
Single-molecule localization microscopy (SMLM) can play an important role in integrated structural biology approaches to identify, localize and determine the 3D structure of cellular structures. While many tools exist for the 3D analysis and visualization of crystal or cryo-EM structures little exists for 3D SMLM data, which can provide unique insights but are particularly challenging to analyze in three dimensions especially in a dense cellular context.
We developed 3DClusterViSu, a method based on 3D Voronoi tessellations that allows local density estimation, segmentation and quantification of 3D SMLM data and visualization of protein clusters within a 3D tool. We show its robust performance on microtubules and histone proteins H2B and CENP-A with distinct spatial distributions. 3DClusterViSu will favor multi-scale and multi-resolution synergies to allow integrating molecular and cellular levels in the analysis of macromolecular complexes.
3DClusterViSu is available under http://cbi-dev.igbmc.fr/cbi/voronoi3D.
Supplementary figures are available at Bioinformatics online.
单分子定位显微镜（SMLM）可以在综合结构生物学方法中发挥重要作用，用于识别、定位和确定细胞结构的 3D 结构。虽然有许多工具可用于晶体或冷冻电镜结构的 3D 分析和可视化，但对于 3D SMLM 数据几乎没有，3D SMLM 数据可以提供独特的见解，但在三维空间中分析特别具有挑战性，特别是在密集的细胞环境中。
我们开发了 3DClusterViSu，这是一种基于 3D Voronoi 细分的方法，允许对 3D SMLM 数据进行局部密度估计、分割和量化，并在 3D 工具中可视化蛋白质簇。我们展示了它在微管和组蛋白 H2B 和 CENP-A 上的稳健性能，它们具有不同的空间分布。3DClusterViSu 将有利于多尺度和多分辨率的协同作用，以允许在分析大分子复合物时整合分子和细胞水平。
3DClusterViSu 可在 http://cbi-dev.igbmc.fr/cbi/voronoi3D 下获得。
补充图可在生物信息学在线获得。
