Protocol for multicolor three-dimensional dSTORM data analysis using MATLAB-based script package Grafeo

Kalina Tamara Haas; Alexis Peaucelle

doi:10.1016/j.xpro.2021.100808

Protocol for multicolor three-dimensional dSTORM data analysis using MATLAB-based script package Grafeo

STAR Protoc. 2021 Sep 9;2(3):100808. doi: 10.1016/j.xpro.2021.100808. eCollection 2021 Sep 17.

Authors

Kalina Tamara Haas¹, Alexis Peaucelle¹

Affiliation

¹ Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France.

Abstract

This protocol describes the step-by-step analysis of the multicolor (one-, two-, or three-color) two- and three-dimensional dSTORM (direct STochastic Optical Reconstruction Microscopy) data using MATLAB-based script package Grafeo. Grafeo primarily uses pointillist data visualization and analysis frameworks, including the nearest neighbors, approach, Voronoi tessellation, Delaunay triangulation, Ripley's (K, L) and two-point correlation functions, and graph-based clustering. For complete details on the use and execution of this protocol, please refer to Peaucelle et al. (2020), Haas et al., 2018, Haas et al. (2020b).

Keywords: Bioinformatics; Biophysics; Developmental biology; Microscopy; Plant sciences.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cells, Cultured
Cluster Analysis
Computational Biology
Data Visualization*
Imaging, Three-Dimensional*
Software*