Segmentation correction Plugins

Delete plugin

_images/Delete.png
class morphonet.plugins.SegmentationCorrection.Delete.Delete

Bases: MorphoPlugin

This plugin removes any selected objects from the segmented images. Users can select objects at the current time point, or label any objects to delete at several time points. The background value (usually 0) will replace the object voxels inside the segmented image.

Parameters:

objects – The selected objects to apply deformation on MorphoNet

_images/Deli.png

Deli plugin

_images/Deli1.png
class morphonet.plugins.SegmentationCorrection.Deli.Deli

Bases: MorphoPlugin

This plugin remove objects under a certain volume in the segmented image. Please refer to the volume property to see the volume value for your segmented image.

Parameters:

  • minimum_volume (int, default: 20) – The threshold value of the volume (in number of voxels) allowed for the objects to be deleted (>=0)

  • time_points (string) – Current times : will only delete all objects at the current time point. All times : will delete all objects at all time points

  • association (string) – Determines how the deleted objects will be modified: Background : The dataset background value will replace the object label inside the segmented image. Closest object : The object to remove will be fused with the object sharing the most contact surface. Objects can be fused with the background.

  • segmentation_channel (int, default: 0) – The desired channel to perform the plugin

_images/Disco.png

Disco plugin

_images/Disco1.png
class morphonet.plugins.SegmentationCorrection.Disco.Disco

Bases: MorphoPlugin

This plugin can be used to split any object made up of several sub-objects that are not in contact with each other.

This plugin is applied on whole segmented images.

Parameters:

  • time_points (string) – Current times : will only split objects at the current time point. All times : will split objects for all the time points

  • temporal_links (bool) – Parameter to give new objects the temporal links of the previous objects.

_images/Fuse.png

Fuse plugin

_images/Fuse1.png
class morphonet.plugins.SegmentationCorrection.Fuse.Fuse

Bases: MorphoPlugin

This plugin performs the fusion of selected objects into a single one. If multiple objects are selected , they are fused together at the current time point. Else if objects are labeled it will apply a fusion between all objects sharing the same label (for each individual time points)

Parameters:

objects – The selected or labeled objects on MorphoNet

_images/Gaumi.png

Gaumi plugin

_images/Gaumi1.png
class morphonet.plugins.SegmentationCorrection.Gaumi.Gaumi

Bases: MorphoPlugin

This plugin calculates the gaussian mixture model probability distribution on selected objects in order to split

them into several objects which will replace the selected ones.

This plugin requires one or more selected objects.

Parameters:

  • objects – The selected or labeled objects on MorphoNet

  • n_components (int , default: 2) – The number of mixture components which correspond to the number of new objects to be created in each input object (>1)

  • method (string) – The method used to initialize the weights, the means and the precisions of the algorithms

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

Reference

This plugin use the Gaussian Mixture function in scikit-learn : https://scikit-learn.org/stable/modules/ generated/sklearn.mixture.GaussianMixture.html

_images/Splax.png

Splax plugin

_images/Splax1.png
class morphonet.plugins.SegmentationCorrection.Splax.Splax

Bases: MorphoPlugin

This plugin splits any selected objects in two new objects in the middle of one of the given image axes.

Parameters:

  • objects – The selected or labeled objects on MorphoNet

  • axis (string : X,Y OR Z) – axis chosen to split the objects, corresponding to axis in the image (independent of the rotation of the object in MorphoNet)

_images/CopyPaste.png

Copy-paste plugin

_images/CopyPaste1.png
class morphonet.plugins.SegmentationCorrection.CopyPaste.CopyPaste

Bases: MorphoPlugin

This plugin gives the possibility to copy an object (a segmented cell for example) and paste it at another time steps and/or another location.

This plugin requires one selected object. Once it is selected, activate the copy-paste mode in the Curate menu. Plugin controls in MorphoNet (make sure copy-paste mode is active in curate menu): * To copy a selected object, press C * To move a copy instance, put your mouse over it and press M * To delete a copy instance, put your mouse over it and press D * To scale a copy instance, put your mouse over it and press S , and then scroll with your mouse * To rotate a copy instance, put your mouse over it and press R , than move your mouse

Parameters:

  • objects – The selected objects to apply deformation on MorphoNet

  • copy_instances – List of copy instances to paste the selected object

_images/Match.png

Match plugin

_images/Match1.png
class morphonet.plugins.SegmentationCorrection.Match.Match

Bases: MorphoPlugin

This plugin allows you to match the elements of same object across several channels. It will give the selected objects a matching label in the segmented image. Can be used in batch by labeling objects together with label groups

This plugin requires selected objects on different channels.

Parameters:

objects – The selected or labeled objects on MorphoNet