These plug-ins provide 2D image filters. Unless otherwise noted, they take a gray scale image of abitrary pixel type as input, process it and return the result as newly created image. Filters can be chained by specifying more then one filter description concated with the '+' sign. for example bandpass:min=10,max=20+median:w=3+convert:repn=ushort:map=copy' will create a filter chain that first runs a bandpass, then a median filter and a conversion to unsigned short values by a plain copy.
adaptmed admean aniso bandpass binarize close combiner convert crop dilate distance downscale erode gauss gradnorm invert kmeans label labelmap load mask mean median mlv ngfnorm noise open pruning regiongrow sandp scale selectbig sepconv shmean sort-label sws tee thinning thresh transform ws
2D image adaptive median filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
w | int | 2 | half filter width in [0, 2147483647] |
An adaptive mean filter that works like a normal mean filter, if the intensity variation within the filter mask is lower then the intensity variation in the whole image, that the uses a special formula if the local variation is higher then the image intensity variation.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
w | int | 1 | half filter width in [0, 2147483647] |
2D Anisotropic image filter. Supported parameters are:
Name | Type | Default | Description | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
epsilon | float | 1 | iteration change threshold in [0.001, 100] | ||||||||||
iter | int | 100 | number of iterations in [1, 10000] | ||||||||||
k | float | -1 | k the noise threshold (<=0 -> adaptive) in [0, 100] | ||||||||||
n | set | 8 | neighbourhood Supported values are:(4, 8, ) | ||||||||||
psi | dict | tuckey |
|
intensity bandpass filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
max | float | 3.40282e+38 | maximum of the band in [-3.40282e+38, 3.40282e+38] |
min | float | 0 | minimum of the band in [-3.40282e+38, 3.40282e+38] |
image binarize filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
max | float | 3.40282e+38 | maximum of accepted range in [0, 3.40282e+38] |
min | float | 0 | minimum of accepted range in [0, 3.40282e+38] |
morphological close. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
hint | set | black | a hint at the main image content Supported values are:(black, white, ) |
shape | factory | [sphere:r=2] | structuring element. For supported plug-ins see Plugin type: 2dimage/shape |
Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
image | io | (input,required) | second image that is needed in the combiner. For supported file types see Plugin type: 2dimage/io |
op | factory | (required) | Image combiner to be applied to the images. For supported plug-ins see Plugin type: 2dimage/combiner |
reverse | bool | 0 | reverse the order in which the images passed to the combiner |
image pixel format conversion filter. Supported parameters are:
Name | Type | Default | Description | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
a | float | 1 | linear conversion parameter a in [-3.40282e+38, 3.40282e+38] | ||||||||||||||||||||||||
b | float | 0 | linear conversion parameter b in [-3.40282e+38, 3.40282e+38] | ||||||||||||||||||||||||
map | dict | opt |
| ||||||||||||||||||||||||
repn | dict | ubyte |
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Crop a region of an image, the region is always clamped to the original image size.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
end | streamable | [[-1,-1]] | end of crop region |
start | streamable | [[0,0]] | start of crop region |
2d image stack dilate filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
hint | set | black | a hint at the main image content Supported values are:(black, white, ) |
shape | factory | [sphere:r=2] | structuring element. For supported plug-ins see Plugin type: 2dimage/shape |
2D image distance filter, evaluates the distance map for a binary mask.. (This plug-in doesn't take parameters)
Downscale the input image by using a given block size to define the downscale factor. Prior to scaling the image is filtered by a smoothing filter to eliminate high frequency data and avoid aliasing artifacts.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
b | 2dbounds | [[1,1]] | blocksize |
bx | uint | 1 | blocksize in x direction in [1, 2147483647] |
by | uint | 1 | blocksize in y direction in [1, 2147483647] |
kernel | factory | gauss | smoothing filter kernel to be applied, the size of the filter is estimated based on the blocksize.. For supported plug-ins see Plugin type: 1d/spacialkernel |
2d image stack erode filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
hint | set | black | a hint at the main image content Supported values are:(black, white, ) |
shape | factory | [sphere:r=2] | structuring element. For supported plug-ins see Plugin type: 2dimage/shape |
isotropic 2D gauss filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
w | int | 1 | filter width parameter in [0, 2147483647] |
2D image to gradient norm filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
normalize | bool | 0 | Normalize the gradient norms to range [0,1]. |
2D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
c | int | 3 | number of classes in [2, 255] |
Label connected components in a binary 2D image.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
n | factory | 4n | Neighborhood mask to describe connectivity.. For supported plug-ins see Plugin type: 2dimage/shape |
2D image filter to remap label id's.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
map | string | (input,required) | Label mapping file |
Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
file | io | (input,required) | name of the input file to load from.. For supported file types see Plugin type: 2dimage/io |
2D masking, one of the two input images must by of type bit.. Supported parameters are:
Name | Type | Default | Description | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
fill | dict | min |
| ||||||||
input | io | (input,required) | second input image file name. For supported file types see Plugin type: 2dimage/io | ||||||||
inverse | bool | 0 | set to true to use the inverse of the mask for masking |
2D image mean filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
w | int | 0 | half filter width in [0, 2147483647] |
2D image median filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
w | int | 0 | half filter width in [0, 2147483647] |
Mean of Least Variance 2D image filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
w | int | 1 | filter width parameter in [0, 2147483647] |
2D image noise filter: add additive or modulated noise to an image. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
g | factory | [gauss:mu=0,sigma=10] | noise generator. For supported plug-ins see Plugin type: generator/noise |
mod | bool | 0 | additive or modulated noise |
morphological open. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
hint | set | black | a hint at the main image content Supported values are:(black, white, ) |
shape | factory | [sphere:r=2] | structuring element. For supported plug-ins see Plugin type: 2dimage/shape |
Morphological pruning. Pruning until convergence will erase all pixels but closed loops.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
iter | int | 0 | Number of iterations to run, 0=until convergence in [1, 1000000] |
Region growing startin from a seed until only along increasing gradients. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
n | factory | 8n | Neighborhood shape. For supported plug-ins see Plugin type: 2dimage/shape |
seed | io | (input,required) | seed image (bit valued). For supported file types see Plugin type: 2dimage/io |
salt and pepper 3d filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
thresh | float | 100 | thresh value in [0, 3.40282e+38] |
w | int | 1 | filter width parameter in [0, 2147483647] |
2D image downscale filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
interp | factory | [bspline:d=3] | interpolation method to be used . For supported plug-ins see Plugin type: 1d/splinekernel |
s | 2dbounds | [[0,0]] | target size as 2D vector |
sx | uint | 0 | target size in x direction, 0: use input size in [0, 4294967295] |
sy | uint | 0 | target size in y direction, 0: use input size in [0, 4294967295] |
2D image intensity separaple convolution filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
kx | factory | [gauss:w=1] | filter kernel in x-direction. For supported plug-ins see Plugin type: 1d/spacialkernel |
ky | factory | [gauss:w=1] | filter kernel in y-direction. For supported plug-ins see Plugin type: 1d/spacialkernel |
2D image filter that evaluates the mean over a given neighborhood shape. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
shape | factory | 8n | neighborhood shape to evaluate the mean. For supported plug-ins see Plugin type: 2dimage/shape |
This plug-in sorts the labels of a gray-scale image so that the lowest label value corresponts to the lable with themost pixels. The background (0) is not touched. (This plug-in doesn't take parameters)
seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
grad | bool | 0 | Interpret the input image as gradient. |
mark | bool | 0 | Mark the segmented watersheds with a special gray scale value |
n | factory | [sphere:r=1] | Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape |
seed | string | (input,required) | seed input image containing the lables for the initial regions |
Save the input image to a file and also pass it through to the next filter. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
file | io | (output,required) | name of the output file to save the image too.. For supported file types see Plugin type: 2dimage/io |
Morphological thinning. Thinning until convergence will result in a 8-connected skeleton. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
iter | int | 0 | Number of iterations to run, 0=until convergence in [1, 1000000] |
This filter sets all pixels of an image to zero that fall below a certain threshhold and whose neighbours in a given neighborhood shape also fall below a this threshhold. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
shape | factory | 4n | neighborhood shape to take into account. For supported plug-ins see Plugin type: 2dimage/shape |
thresh | double | 5 | The threshhold value in [-1.79769e+308, 1.79769e+308] |
Transform the input image with the given transformation.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
file | io | (input,required) | Name of the file containing the transformation.. For supported file types see Plugin type: 2dtransform/io |
basic watershead segmentation.. Supported parameters are:
Name | Type | Default | Description |
---|---|---|---|
evalgrad | bool | 0 | Set to 1 if the input image does not represent a gradient norm image |
mark | bool | 0 | Mark the segmented watersheds with a special gray scale value |
n | factory | [sphere:r=1] | Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape |
thresh | float | 0 | Relative gradient norm threshold. The actual value threshhold value is thresh * (max_grad - min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined in [0, 1] |
mia-2dimagefilter mia-2dimagefilterstack mia-2dsegment-fuzzyw mia-2dseries2dordermedian mia-2dseriesgradMAD mia-2dseriessmoothgradMAD mia-2dstackfilter byslice:2dstack/filter