Map Manager is software to annotate and analyze 3D image stack time-series

Main features

  • Track 3D annotations in time-series images.
  • Automatically aligns images and annotations across timepoints.
  • Works with any in vivo, ex vivo, and fixed tissue image volumes.


  • Easily analyze the dynamics of annotations.
  • Detailed spine intensity analysis.
  • Powerful trajectory analysis.

Getting started



All code and documentation written by Robert Cudmore.