Multi-Array EM/MPM

Group (Subgroup)

Reconstruction (Segmentation)

Description

This Filter performs the EM/MPM algorithm on a selected number of Atribute Arrays, representing grayscale images, that all belong to the same Cell Attribute Matrix. The user may select any number of Attribute Arrays to segment. The Select/Deselect All button can used to automatically select all Attribute Arrays in a given Attribute Matrix. The segmented images will be stored into a newly created Cell Attribute Matrix where the name of each output array will be the a user defined prefix plus the original name of the input array. For information regarding the operation of the EM/MPM algorithm and the meaning of the parameters, please refer to the documentation for the EM/MPM Filter.

This Filter contains an additional option to use the last mu (mean) and sigma (variance) values calculated on the current array as the initialization values for the next Attribute Array to process. Using this can help the EM/MPM algorithm achieve subjectively "better" segmentations by starting the algorithm at values that should be close to the ending values. This option should only be used if all of the images are "similar" to one another (e.g., a montage/tiled data set or a 3D stack of images). If the input Attribute Arrays are qualitatively different, using this option can have negative effects on the accuracy of the final segmented images.

Input Parameters

Name Type Description
Number of Classes int32_t The number of classes in which to segment the image
Exchange Energy float The value of the exchange energy
Histogram Loops (EM) int32_t The number of histogram loops (EM) to perform
Segmentation Loops (MPM) int32_t The number of segmentation loops (MPM) to perform
Use Simulated Annealing bool Apply the simulated annealing process
Use Gradient Penalty bool Use a penalty to gradients when segmenting
Gradient Penalty (Beta E) float The penalty to apply for gradients. Only needed if Use Gradient Penalty is checked
Use Curvature Penalty bool Use a penalty for curvature
Curvature Penalty float The penalty to use for curvatures. Only needed if Use Curvature Penalty is checked
R Max float The max radius for the curvature penalty. Only needed if Use Curvature Penalty is checked
EM Loop Delay int32_t The number of EM Loops to delay before applying the curvature penalty. Only needed if Use Curvature Penalty is checked
Use 1-Based Values bool Use 1-based values instead of 0-based values
Use Mu/Sigma from Previous Image as Initialization for Current Image bool Whether to use the calculated mu/sigma from the previous segmented image as the starting point for the next image segmentation. May help reduce computation time
Output Array Name Prefix String Prefix to apply to the output segmented arrays

Required Geometry

Image

Required Objects

Kind Default Name Type Component Dimensions Description
Cell Attribute Arrays None uint8_t (1) 8 bit grayscale images to segment. The user may select any number of arrays to segment

Created Objects

Kind Default Name Type Component Dimensions Description
Cell Attribute Arrays None uint8_t (1) Unsigned 8 bit array representing the value of the class that the Cell was segmented into. An output array is created for each segmented input array and placed in a new Cell Attribute Matrix that the user may name

Example Pipelines

Please see the description file distributed with this Plugin

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