Visualization and analysis of 3D microscopic images

PLoS Comput Biol. 2012;8(6):e1002519. doi: 10.1371/journal.pcbi.1002519. Epub 2012 Jun 14.


In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / anatomy & histology
  • Caenorhabditis elegans / cytology
  • Caenorhabditis elegans / genetics
  • Computational Biology
  • Computer Simulation
  • Drosophila melanogaster / anatomy & histology
  • Gene Expression Profiling / statistics & numerical data
  • Imaging, Three-Dimensional / methods*
  • Imaging, Three-Dimensional / statistics & numerical data
  • Microscopy / methods*
  • Microscopy / statistics & numerical data