3D Volume Processing¶
3D Load Z-Stack¶
Load a multi-page TIFF file as a 3D volume.
Details
Each page in the TIFF becomes one Z-slice. Mode "Grayscale" outputs VolumeData (Z, H, W). Mode "Color (RGB)" outputs VolumeColorData (Z, H, W, 3).
| Direction | Port | Type |
|---|---|---|
| Output | volume |
volume |
| Output | volume_color |
volume_color |
Properties: Z Spacing, XY Spacing
3D Slice Viewer¶
Interactive Z-slice browser for 3D volumes.
Details
Accepts volume, volume_mask, or volume_label input. Use the slider to scrub through slices and the axis selector to view XY/XZ/YZ planes.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Input | volume_mask |
volume_mask |
| Input | volume_label |
volume_label |
3D Volume Viewer¶
Interactive 3D isosurface viewer for volume masks and label volumes.
Details
Extracts meshes via marching cubes and renders them with Three.js. For label volumes, each label gets a distinct colour.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Input | volume_label |
volume_label |
Properties: Opacity, ``
3D Split RGB¶
Split a 3D color volume (Z, H, W, 3) into R, G, B channel volumes.
| Direction | Port | Type |
|---|---|---|
| Input | volume_color |
volume_color |
| Output | volume |
volume |
| Output | volume |
volume |
| Output | volume |
volume |
| Output | red |
red |
| Output | green |
green |
| Output | blue |
blue |
3D Merge RGB¶
Merge R, G, B grayscale volumes into a single 3D color volume.
Details
Unconnected channels default to zero.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Input | volume |
volume |
| Input | volume |
volume |
| Input | red |
red |
| Input | green |
green |
| Input | blue |
blue |
| Output | volume_color |
volume_color |
3D RGB to Gray¶
Convert a 3D color volume to grayscale.
Details
Methods: Luminosity (Rec.709), Average, or extract a single channel.
| Direction | Port | Type |
|---|---|---|
| Input | volume_color |
volume_color |
| Output | volume |
volume |
Properties: Method
3D Gaussian Blur¶
Apply 3D Gaussian blur to a volume.
Details
Sigma can be set independently for Z and XY axes to account for anisotropic voxel spacing.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Output | volume |
volume |
Properties: Sigma XY, Sigma Z
3D Invert¶
Invert a 3D volume (for uint8: 255 − value; for bool: logical NOT).
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Output | volume |
volume |
3D Invert Mask¶
Invert a 3D binary mask (logical NOT).
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
3D Max Projection¶
Maximum Intensity Projection (MIP) along an axis.
Details
Collapses a 3D volume to a 2D image by taking the max value per pixel. Commonly used in fluorescence microscopy to visualize Z-stacks.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Output | image |
image |
Properties: Axis
3D Min Projection¶
Minimum Intensity Projection along an axis.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Output | image |
image |
Properties: Axis
3D Mean Projection¶
Mean Intensity Projection along an axis.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Output | image |
image |
Properties: Axis
3D Apply Mask¶
Apply a 3D mask to a volume — zero out voxels outside the mask.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Input | volume_mask |
volume_mask |
| Output | volume |
volume |
3D Threshold¶
Threshold a 3D volume to produce a binary volume mask.
Details
Methods: manual value, Otsu auto-threshold, Li auto-threshold.
| Direction | Port | Type |
|---|---|---|
| Input | volume |
volume |
| Output | volume_mask |
volume_mask |
Properties: Method, Threshold
3D Distance Ring Mask¶
Expand a 3D mask outward by a given distance (ring / shell mask).
Details
Uses the Euclidean distance transform. The spacing-aware option accounts for anisotropic voxel dimensions (e.g. Z ≠ XY).
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
Properties: Distance (px), ,
3D Remove Small Obj¶
Remove small 3D connected components from a volume mask.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
Properties: Min Size (voxels), Connectivity
3D Fill Holes¶
Fill small holes / voids inside a 3D volume mask.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
Properties: Max Hole Size (voxels)
3D Erode¶
3D morphological erosion with ball / cube / octahedron kernel.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
Properties: Radius (voxels), Kernel
3D Dilate¶
3D morphological dilation with ball / cube / octahedron kernel.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
Properties: Radius (voxels), Kernel
3D Open¶
3D morphological opening (erosion → dilation). Removes small protrusions.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
Properties: Radius (voxels), Kernel
3D Close¶
3D morphological closing (dilation → erosion). Fills small gaps.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_mask |
volume_mask |
Properties: Radius (voxels), Kernel
3D Label¶
Label connected components in a 3D binary volume.
Details
Outputs a label volume (integer per region) and a properties table with volume, centroid, bounding box, and equivalent diameter.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_label |
volume_label |
| Output | table |
table |
Properties: Connectivity
3D Watershed¶
3D marker-based watershed to separate touching objects.
Details
Pipeline: distance transform → peak detection → watershed.
| Direction | Port | Type |
|---|---|---|
| Input | volume_mask |
volume_mask |
| Output | volume_label |
volume_label |
| Output | table |
table |
Properties: Min Object Sep. (px)