De Novo Seed plugins

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Seedax plugin

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class morphonet.plugins.DeNovoSeed.Seedax.Seedax

Bases: MorphoPlugin

This plugin generates seeds that can be used in other plugins (mainly watershed segmentation).

This plugin requires at least one selected object. On the selected object(s), the longest axis of the segmentation shape is computed, and then split in N segments of identical length (N being the number of seeds in parameter). Seeds are generated at the contact points of the segments.

Parameters:

number_of_seeds (int, default: 2) – The number of seeds to be generated by the plugin

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Seedero plugin

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class morphonet.plugins.DeNovoSeed.Seedero.Seedero

Bases: MorphoPlugin

This plugin generates seeds that can be used in other (mainly segmentation) algorithms.

This plugin requires at least one selected object. This plugin applies multiple erosion steps of each selected object, until objects can be separated into multiple unconnected parts. Then, a seed is placed at the barycenter of each individual eroded sub-part of the segmentation.

Parameters:

minimum_volume (int, default: 1000) – The minimal volume of each individual part that will be kept to generate a seed, after the erosion

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Seedin plugin

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class morphonet.plugins.DeNovoSeed.Seedin.Seedin

Bases: MorphoPlugin

This plugin generates seeds that can be used in other plugins (mainly watershed segmentation).

This plugin requires intensity image(s). Seeds are generated at the minimum intensity where no segmentation labels are found (in the background). If you have segmented images, the seeds will not be generated in segmentations.

Parameters:

  • sigma (int, default: 8) – The standard deviation for the Gaussian kernel when sigma>0, the plugin first applies a gaussian filter on the intensity image. (>=0)

  • h_minima_value (int, default: 2) – If using the H Minima method, determines the minimal depth of all extracted minima. (>=0)

  • method (string) – Method used to find local minima of intensity in the intensity image. H Minima method determine all minima of the image with depth >= h_minima_value Local minima method finds the local minima in the intensity image. The local minima are defined as connected sets of voxels with equal gray level (plateaus) strictly smaller than the gray levels of all voxels in the neighborhood.

  • membrane_channel (int , default: 0) – The desired channel to use as intensity images input

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Seedio plugin

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class morphonet.plugins.DeNovoSeed.Seedio.Seedio

Bases: MorphoPlugin

This plugin generates seeds that can be used in other plugins (mainly watershed segmentation). Users have to select objects (or label them) to generate seeds. Seeds are generated at the minima inside the selected object.

This plugin requires intensity image(s) and at least one selected object. Seeds are generated at the minimum image intensity inside the selected object(s) mask.

Parameters:

  • sigma (int, default: 8) – The standard deviation for the Gaussian kernel when sigma>0, the plugin first applies a gaussian filter on the intensity image. (scalar>=0)

  • h_minima_value (int, default: 2) – If using the H Minima method, determines the minimal depth of all extracted minima. (see https://scikit-image.org/docs/stable/api/skimage.morphology.html )

  • method (string) – Method used to find local minima of intensity in the intensity image. H Minima method determine all minima of the image with depth >= h_minima_value Local minima method finds the local minima in the intensity image. The local minima are defined as connected sets of voxels with equal gray level (plateaus) strictly smaller than the gray levels of all voxels in the neighborhood.

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Seedis plugin

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class morphonet.plugins.DeNovoSeed.Seedis.Seedis

Bases: MorphoPlugin

This plugin generates seeds that can be used in other plugins (mainly watershed segmentation).

This plugin requires at least one selected object. The plugin computes the distance to the border of the selected objects and then extracts the maxima. N seeds are generated at the maximal distance inside the selected object (N being the number of seeds to generate), if the distance (between seeds) is above the threshold given by the min_distance parameter (in voxels, not physical size).

Parameters:

  • nb_seeds (int, default: 2) – the number of seeds to generate in each object (> 1)

  • min_distance (int, default: 30) – The minimum allowed distance (number of voxels) separating peaks. To find the maximum number of peaks, use min_distance=1.