Using the EpiTools plugin for napari#

The following steps are part of the typical EpiTools workflow.

  1. Projection

The following video demonstrates how the projection step can be performed.

  1. Segmentation

The following video demonstrates how the segmentation step can be performed.

  1. Correcting Segmentation

If the segmentation output needs correction we would recommend the segment blobs and things with membranes plugin. This allows one to manually split and merge labels.

  1. Tracking

To perform tracking we would recommend the brack plugin.

  1. Correcting Tracking

This is not currently possible with EpiTools/btrack.

  1. Cell Statistics

EpiTools includes methods to extract a variety of statistics from the cells.

This video shows how to have a colour map for a given cell property, i.e. neighbours.

This video demonstrates how to export and save the cell statistics output.