17 Jun 2020

Cell Detection and Tracking 2020.2

Simple workflow for tracking cell nuclei in a 3D Time Series.

20-02-2020 11-27-37

This Xtra shows how to perform cell tracking throughout a time series.

It contains:

  • A python script module for enhancing the center of cell nuclei, using a Scale-Space Laplacian on Gaussian filter implemented using the scipy package,
  • An IVP recipe for performing the detection step easily,
  • A presentation with slides explaining the steps to apply the recipe on the full time series, generating the tracks, measuring statistics and visualizing the results, and a few projects to directly access intermediate or final results.

It relies on the dataset that is proposed in the installation folder of Amira tutorial/tracking.