These filters work on a stack of 2D images in a 3D manner by interpreting the images of the stack as slices of a 3D image. For spacial filters with a fixed filter width that is small compared to the number of slices the filter is applied in a true 3D manner. For other filters, that would normally require to work on the whole image domain at once, the image filter is only applied to a subset of the images at a time which results in a quasi-3D processing that may require additional post-processing.
byslice close dilate erode gauss label median mlv open regiongrow
Runs a filter on a per slice basis. In essence, this is a wrapper that makes it possible to add pure 2D filters to the stack filter pipeline without ducplicating the implementation.. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| filter | factory | (required) | 2D filter to be applied. For supported plug-ins see Plugin type: 2dimage/filter |
2D Stack morphological filter 'close'. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
2D Stack morphological filter 'dilate'. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
2D Stack morphological filter 'erode'. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
Gauss 2D fifo filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| w | int in [1, inf) | 1 | filter width parameter (2*w+1) |
Stack Label filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| map | string | (input,required) | Mapfile to save label numbers that are joined |
| n | factory | 4n | 2D neighbourhood shape to define connectedness. For supported plug-ins see Plugin type: 2dimage/shape |
median 2D fifo filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| w | int in [1, inf) | 1 | filter width parameter |
Mean of Least Variance 2D stack image filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| w | int in [1, inf) | 1 | filter width parameter |
2D Stack morphological filter 'open'. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
Run a region-growing filter on a stack of images that comprise a 3D image. The region growing is based on class probabilities obtained from a c-means classification of the pixel intensities. One seed thresh is use to initiate a region, and another (lower) threshold is used to stop the region growing. By holding a number of 3D slices in the working memory to permit the region to grow "backwards " in the stack a Quasi-3D processing is achieved. However, with complex structures the region growing may not properly be segmented.. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| class | int in [0, inf) | 2 | class to be segmented |
| depth | int in [1, inf) | 10 | number of slices to keep during processing |
| low | float in (0, 1] | 0.5 | low threshold for acceptance probability |
| map | string | (input,required) | seed class map |
| seed | float in (0, 1] | 0.98 | threshold for seed probability |