Plugin type: 2dstack/filter

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 normaly 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.

Plugins:

byslice close dilate erode gauss label median mlv open regiongrow

byslice

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:

NameTypeDefaultDescription
filterfactory(required)2D filter to be applied. For supported plug-ins see Plugin type: 2dimage/filter

close

2D Stack morphological filter 'close'. Supported parameters are:

NameTypeDefaultDescription
shapefactory6nstructuring element. For supported plug-ins see Plugin type: 3dimage/shape

dilate

2D Stack morphological filter 'dilate'. Supported parameters are:

NameTypeDefaultDescription
shapefactory6nstructuring element. For supported plug-ins see Plugin type: 3dimage/shape

erode

2D Stack morphological filter 'erode'. Supported parameters are:

NameTypeDefaultDescription
shapefactory6nstructuring element. For supported plug-ins see Plugin type: 3dimage/shape

gauss

Gauss 2D fifo filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter (2*w+1)

label

Stack Label filter. Supported parameters are:

NameTypeDefaultDescription
mapstring(input,required)Mapfile to save label numbers that are joined
nfactory4n2D neighbourhood shape to define connectedness. For supported plug-ins see Plugin type: 2dimage/shape

median

median 2D fifo filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

mlv

Mean of Least Variance 2D stack image filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

open

2D Stack morphological filter 'open'. Supported parameters are:

NameTypeDefaultDescription
shapefactory6nstructuring element. For supported plug-ins see Plugin type: 3dimage/shape

regiongrow

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 allow 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:

NameTypeDefaultDescription
classint in [0, inf)2class to be segmented
depthint in [1, inf)10number of slices to keep during processing
lowfloat in (0, 1]0.5low threshold for acceptance probability
mapstring(input,required)seed class map
seedfloat in (0, 1]0.98threshold for seed probability

Plugin consumers:

mia-2dstackfilter