These plug-ins provide 3D image filters. Unless otherwise noted, they take a gray scale image of abitrary pixel type as input, process it and hand it to the next filter in the pipeline.
bandpass binarize close convert crop dilate downscale erode gauss gradnorm growmask invert kmeans label mask median mlv open reorient resize sandp scale selectbig sepconv sws tee ws
intensity bandpass filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| max | float | 3.40282e+38 | maximum of the band |
| min | float | 0 | minimum of the band |
image binarize filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| max | float | 3.40282e+38 | maximum of accepted range |
| min | float | 0 | minimum of accepted range |
morphological close. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| hint | string | black | a hint at the main image content (black|white) |
| shape | factory | [sphere;r=2] | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
image pixel format conversion filter. Supported parameters are:
| Name | Type | Default | Description | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a | float | 1 | linear conversion parameter a | ||||||||||||||||||||||||
| b | float | 0 | linear conversion parameter b | ||||||||||||||||||||||||
| map | dict | opt |
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| repn | dict | ubyte |
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Crop a region of an image, the region is always clamped to the original image size in the sense that the given range is kept.. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| begin | streamable | [<0,0,0>] | begin of cropping range |
| end | streamable | [<4294967295,4294967295,4294967295>] | end of cropping range, maximum = (-1,-1,-1) |
3d image stack dilate filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| hint | string | black | a hint at the main image content (black|white) |
| shape | factory | [sphere;r=2] | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
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 | 3dbounds | [<1,1,1>] | blocksize |
| bx | uint | 1 | blocksize in x direction |
| by | uint | 1 | blocksize in y direction |
| bz | uint | 1 | blocksize in z direction |
| kernel | string | gauss | smoothing filter kernel to be applied (filter width is determined based on the scaling factor) |
3d image stack erode filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| hint | string | black | a hint at the main image content (black|white) |
| shape | factory | [sphere;r=2] | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
isotropic 3D gauss filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| w | int | 1 | filter width parameter |
Use an input binary mask and a reference gray scale image to do region growing by adding the neighborhood pixels of an already added pixel if the have a lower intensity that is above the given threshold.. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| min | float | 1 | lower threshold for mask growing |
| ref | io | (required) | reference image for mask region growing. For supported file types see Plugin type: 3dimage/io |
| shape | factory | 6n | neighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape |
3D 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 |
A filter to label the connected components of a binary image.. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| n | factory | 6n | neighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape |
Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary.. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| input | io | (required) | second input image file name. For supported file types see Plugin type: 3dimage/io |
median 3d filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| w | int | 1 | filter width parameter |
Mean of Least Variance 3D image filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| w | int | 1 | filter width parameter |
morphological open. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| hint | string | black | a hint at the main image content (black|white) |
| shape | factory | [sphere;r=2] | structuring element. For supported plug-ins see Plugin type: 3dimage/shape |
3D image reorientation filter. Supported parameters are:
| Name | Type | Default | Description | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| map | dict | xyz |
| ||||||||||||
Resize an image. The original data is centered within the new sized image.. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| size | streamable | [<0,0,0>] | new size of the image a size 0 indicates to keep the size for the corresponding dimension. |
salt and pepper 3d filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| thresh | float | 100 | thresh value |
| w | int | 1 | filter width parameter |
3D image scale filter. Supported parameters are:
| Name | Type | Default | Description |
|---|---|---|---|
| interp | string | [bspline:d=3] | interpolation method to be used |
| s | 3dbounds | [<0,0,0>] | target size (component 0:use input image size) |
| sx | uint | 0 | target size in x direction (0:use input image size) |
| sy | uint | 0 | target size in y direction (0:use input image size) |
| sz | uint | 0 | target size in y direction (0:use input image size) |
A filter that creats a binary mask representing the intensity with the highest pixel count.The pixel value 0 will be ignored, and if two intensities have the same pixel count, then the result is undefined. The input pixel must have an integral pixel type.. (This plug-in doesn't take parameters)
3D 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 |
| kz | factory | [gauss:w=1] | filter kernel in z-direction. For supported plug-ins see Plugin type: 1d/spacialkernel |
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: 3dimage/shape |
| seed | string | (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 | (required) | name of the output file to save the image too.. For supported file types see Plugin type: 3dimage/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: 3dimage/shape |
| thresh | float | 0 | Relative gradient norm threshold. The actual value threshhold value is thresh * (max_grad - min_grad) + min_grad. Bassins seperated by gradients with a lower norm will be joined |