Segmentation from Seeds Plugins

_images/Wata.png

Wata plugin

_images/Wata1.png
class morphonet.plugins.SegmentationFromSeeds.Wata.Wata

Bases: MorphoPlugin

This plugin creates new objects using a watershed algorithm from seed generated using a plugin or placed in the MorphoNet Viewer.

This plugin requires seeds and a segmented image. The watershed algorithm generates new objects using the segmentation image for each seed, and limits each new object to fit inside a bounding box of the user-defined box_size size (in voxels). If the new generated objects are under the volume threshold defined by the user, the object is not created.

Parameters:

  • minimum_volume (int, default: 1000) – The minimal volume (in number of voxels) allowed for the new objects to be created (>=0)

  • box_size (int, default: 50) – Boundaries (in number of voxel) of working area around a seed to generate a new object

  • seeds – List of seeds added on the MorphoNet Window

  • segmentation_channel (int, default: 0) – The desired channel to create the object in

_images/Wati.png

Wati plugin

_images/Wati1.png
class morphonet.plugins.SegmentationFromSeeds.Wati.Wati

Bases: MorphoPlugin

This plugin creates new objects using a watershed algorithm from seed generated or placed in the MorphoNet Viewer.

It requires intensity images and at least one seed.

The watershed algorithm generates new objects using the intensity image, and the segmented image (if it exists) to limit new objects. If the new generated objects are under the volume threshold defined by the user, they are not created.

Parameters:

  • sigma (int, default: 2) – The standard deviation for the Gaussian kernel when sigma>0, the plugin first applies a gaussian filter on the intensity image. (>=0)

  • minimum_volume (int, default: 1000) – The minimal volume (in number of voxels) allowed for the new objects to be created (>=0)

  • box_size (int, default: 50) – Boundaries (in number of voxel) of working area around a seed to generate a new object (>=0)

  • seeds – List of seeds added on the MorphoNet Window

  • membrane_channel (int, default: 0) – The desired channel of the intensity images used for segmentation

  • segmentation_channel (int, default: 0) – The desired channel for the new segmentation

_images/Watio.png

Watio plugin

_images/Watio1.png
class morphonet.plugins.SegmentationFromSeeds.Watio.Watio

Bases: MorphoPlugin

This plugin creates new objects using a watershed algorithm from seed generated using a plugin or manually placed in the MorphoNet Viewer inside selected object.

This plugin requires an intensity image, seeds and selected objects. The watershed algorithm generates new objects using the intensity image and replaces the selected objects. If the new generated objects are under the volume threshold defined by the user, the object is not created.

Parameters:

  • sigma (int, default: 2) – The standard deviation for the Gaussian kernel when sigma>0, the plugin first applies a gaussian filter on the intensity image. (>=0)

  • minimum_volume (int, default: 1000) – The minimal volume (in number of voxels) allowed for the new objects to be created (>=0)

  • seeds – List of seeds added on the MorphoNet Window

  • membrane_channel (int, default: 0) – The desired channel of the intensity images used for segmentation

_images/Wato.png

Wato plugin

_images/Wato1.png
class morphonet.plugins.SegmentationFromSeeds.Wato.Wato

Bases: MorphoPlugin

This plugin creates new objects using a watershed algorithm from seed generated using a plugin or placed in the MorphoNet Viewer inside selected segmented objects. It does not require intensity images. The watershed algorithm generates new objects based on the segmentation image for each seed and replaces the selected objects. If the new generated objects are under the volume threshold defined by the user, they are not created.

Parameters:

  • minimum_volume (int, default: 1000) – The minimal volume (in number of voxels) allowed for the new objects to be created (>=0)

  • seeds – List of seeds added on the MorphoNet Window

  • rescale_with_voxel (bool, default: True) – Rescale segmentation depending on voxel size, useful for low resolution images