Propagate segmentation Plugins

_images/Propa.png

Propa Plugin

_images/Propa1.png
class morphonet.plugins.PropagateSegmentation.Propa.Propa

Bases: MorphoPlugin

This plugin propagates labeled objects at the current time point through time.

It requires a segmentation, and labeled objects across several time points using labels. Optionally, it can work with intensity images as well.

It requires applying a specific label to the objects to propagate at the current time (named the source objects) And then label the corresponding objects on which to propagate at the next or previous time points (named the destination objects). The plugin can be executed Forward (source objects are at the beginning of the time range) or Backward (source objects are at the end of the time range). The source objects are eroded until they fit into destination objects at the next time point, and then a watershed is computed. The watershed algorith can be computed using an intensity image by checking the “use intensity” box. The new objects created by a watershed will replace the destination objects.

Parameters:

  • objects – The selected or labeled objects on MorphoNet

  • time_direction (string) – Forward : The first time point to be propagated is the lowest one. Backward : THe first time point to be propagated is the latest, and the propagation happens in backwards direction

  • use_intensity (bool) – Use intensity images for watershed

  • intensity_channel (int) – The selected or labeled objects on MorphoNet

_images/Prope.png

Prope Plugin

_images/Prope1.png
class morphonet.plugins.PropagateSegmentation.Prope.Prope

Bases: MorphoPlugin

This plugin propagates labeled objects at the current time point through time, filling empty space.

It requires a segmentation, an intensity image, and selected objects.

The selected object(s) (named the source objects) will be propagated Forward in time or Backward in time by choosing the appropriate time_direction parameter. The source objects are then copied to the segmentation of the next/previous time (the intersection with the rest of the segmentation is removed), and finally a watershed algorithm is applied, using the corresponding intensity image. New objects are created in the background of the segmentation.

Parameters:

  • objects – The selected or labeled objects on MorphoNet

  • time_direction (string) – Forward : The first time point to be propagated is the lowest one. Backward : THe first time point to be propagated is the latest, and the propagation happens in backwards direction