Quantitative imaging of collective cell migration during Drosophila gastrulation: multiphoton microscopy and computational analysis

Nat Protoc. 2009;4(10):1397-412. doi: 10.1038/nprot.2009.130. Epub 2009 Sep 10.


This protocol describes imaging and computational tools to collect and analyze live imaging data of embryonic cell migration. Our five-step protocol requires a few weeks to move through embryo preparation and four-dimensional (4D) live imaging using multi-photon microscopy, to 3D cell tracking using image processing, registration of tracking data and their quantitative analysis using computational tools. It uses commercially available equipment and requires expertise in microscopy and programming that is appropriate for a biology laboratory. Custom-made scripts are provided, as well as sample datasets to permit readers without experimental data to carry out the analysis. The protocol has offered new insights into the genetic control of cell migration during Drosophila gastrulation. With simple modifications, this systematic analysis could be applied to any developing system to define cell positions in accordance with the body plan, to decompose complex 3D movements and to quantify the collective nature of cell migration.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Movement*
  • Cell Survival
  • Cytological Techniques*
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / cytology*
  • Drosophila melanogaster / embryology*
  • Drosophila melanogaster / metabolism
  • Gastrulation*
  • Image Processing, Computer-Assisted / methods*
  • Membrane Transport Proteins / genetics
  • Membrane Transport Proteins / metabolism
  • Microscopy, Fluorescence, Multiphoton / methods*
  • Zebrafish / embryology
  • Zebrafish / genetics
  • Zebrafish / metabolism


  • Drosophila Proteins
  • Membrane Transport Proteins
  • klar protein, Drosophila