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¶
License & Copyright¶
Please see the description file distributed with this Plugin
DREAM.3D Mailing Lists¶
If you need more help with a Filter, please consider asking your question on the DREAM.3D Users Google group!