Module name
Description
Input type
Developed and maintained (as well as possible) by Erwan Plougonven. The latest release is available here.
If you have any suggestions, complaints, bug reports, you can contact me by email, eplougonven[at]uliege.be.
Last updated: November 30th, 2023.
Latest changes available here.| Module name | Description | Input type | |
| Cubical Complex | |||
|---|---|---|---|
| Cubical_Complex | Converts an image to a cubical complex | Image |
| Cubical_Complex_Check_Integrity | Checks that the image contains a properly constructed cubical complex | Image |
| Cubical_Complex_Collapse | Collapses a cubical complex (similar to skeletonising) | Image | | Cubical_Complex_Decompose | Decomposes a cubical complex into surfaces, surface intersections, etc. | Image |
| Cubical_Complex_Extract_Faces | Creates a point set, line set, surface set, et hexahedron set for each type of face | Image |
| Cubical_Complex_Post_Crop | Post-processing to recreate a cubical complex structure after a cropping | Image |
| Draw_Cubical_Complex | Draws a cubical complex, as cubes, square faces, edges, and points | Image |
| Geometry | |||
| Count_Pixels | Counts pixels having certain intensity values | Image |
| Create_Sphere_Pack_Image | Generates an image of a sphere packing from the set of sphere centres | Points |
| Create_Trackers | Generates a time series of trackers in a flow field | Vector field / Image |
| Displace_Vertices | Randomly moves vertices of a graph, in the edge directions | Graph |
| Distance Map | Computes the distance map of the object | Image |
| Draw_Cubes | Draws cubes where the pixels should be. | Image |
| Draw_Differences | Draws cubes where the differences between images are. | Image / Image |
| Draw_Element | Draws the pixels having a given non-zero integral value as cubes. | Image |
| Draw_Elements | Draws certain pixels having a given non-zero integral value as cubes. | Image |
| Draw_Separations | Draws faces shared between pixels of different elements. | Image |
| Draws_Vectors | Draws vectors of a vector field. | Vector field |
| Extract_Plane | Extracts a plane of centred vertical pixels. | Complex scalar field |
| Extract_Elements | Extracts elements using a mask. | Image / Image |
| Keep_Tube | Extracts pixels contained in centred vertical tube | Image |
| Linear_Regression | Performs a linear regression on a set of points | Points |
| Measure_Elements | Performs measures on elements in a label field. | Image |
| Merge_Close_Points | Merges points that are closer than a given distance. | Points |
| Partition to graph | Generates a graph from a decomposition | Image |
| Pixels_In_Closed_Surface | Finds pixels inside closed surfaces | Surface / Image |
| Pixels_Of_Triangles | Finds pixels containing a given set of triangles | Surface / Image |
| Point_List | Creates a list of points from an image and a threshold | Image |
| Points_In_Pairs | Pairs up two sets of points | Points / Points |
| Points_To_Image | Creates an image where foreground pixels contain an input point | Points / Image |
| Smooth_Camera_Path | Smoothes a camera path with Hermite splines | Camera path |
| Proximity_Field | Creates a scalar field quantifying how much of a given phase is nearby | Image |
| Register | Registers two sets of points, already matched up | Points / Points |
| Relabel_Elements | Relabels elements of a partitioned object to best match a reference partitioning | Image / Image |
| Rose_Diagram | Computes the rose diagram of an autocorrelation. | Image |
| Slice_Image | Slices an image given a plane of arbitrary orientation. | Plane / Image |
| Thickness_Map | Computes the thickness map. | Image |
| Morphology | |||
| Bottlenecks | Finds the least constricting paths from source to target. | Image / Image / Image |
| Classify points | Topological pixel classification | Image |
| Connected components | Extracts connected components according to size and number | Image |
| Dilate_Erode | Morphological dilation or erosion | Image |
| Discrete Lambda Medial Axis | Computes the discrete lambda medial axis the squared Eulidean distance map | Image |
| Envelope | Creates a binary mask of the envelope of the object | Image |
| Extrema | Extracts either minima or maxima from an image | Image |
| Fill holes | Fills holes or cavities | Image |
| Find sides | Labels the six sides of an axis-aligned 3D object | Image |
| Geodesic_Distance | Computes the geodesic distance in an object, from marked pixels | Image / Image |
| Geodesic_Dilation | Performs elementary geodesic dilations | Image / Image |
| Grayscale_Topology | Computes topological stuff (kernel, levelling) on grayscale images | Image |
| Hysteresis Thresholding | Performs a hysteresis thresholding of the image | Image |
| Invade | Priority-driven region invasion | Image |
| Label_Connected_Components | Labels connected components according to points | Image / Points |
| Medial Axis | Computes the medial axis | Image |
| Open_Close | Morphological opening or closing | Image |
| Outer_Edge | Extracts the outer edge of an object | Image |
| Partition | Decomposes an object into elements | Image |
| Plug Holes | Plugs tunnels going through the object. | Image |
| Pore_Merge | Merges pores if they have a big enough connecting surface. | Image |
| Pore_Statistics | Computes statistics on pores in a pore (or particle) decomposition | Image |
| Topological image repair | Preprocessing for a skeletonisation | Image |
| Topological Numbers | Computes Minkowsky functionals or Betti numbers | Image |
| Watershed | Computes the watershed in an image, provided seeds | Image / Image - Skeleton |
| Watershed Segmentation | Binarises an image using the watershed on the gradient. | Image |
| Signal | |||
| Align | Finds the translation for an optimal alignment of two images | Image / Image |
| Autocorrelation | Performs a centred autocorrelation | Image |
| Block_Save | Saves an image block by block | Image |
| Conditional_Diffusion | Performs a (locally) anisotropic diffusion | Image |
| Continuous_Maximal_Flow | Computes the globally minimal surface, for segmentation | Image / Image |
| Convert_To_Byte | Converts to 8-bit datatype | Image / Image |
| Deriche_Filter | Performs a convolution with a Gaussian (or its derivative) | Image |
| Distance_Histogram | Computes greylevels in an image given a map of values to group them | Image / Image |
| Edge_Response | Calculates the edge response of the image | Image |
| Gauss_Transform | Computes in-between values, supposing a convolution with a Gaussian on the input sample | Spreadsheet |
| Gradient | Calculates the gradient of the image | Image |
| Gradient_Metrify | Transforms an image gradient into a metric for minimal surface computations | Image |
| FFT | Computes the Fourier transform of the image | Image |
| Histogram_ | Creates a histrogram on the image greylevels | Image |
| Invert | Creates a negative of the image | Image |
| Isometry | Swaps or flips coordinates | Image - Surface - Points |
| K-Means Clustering | Clustering algorithm | Image |
| Kuwahara | 3D Euclidean adaptive Kuwahara filter | Image |
| Local thresholding - Niblack | Thresholding method based on local mean and variance | Image |
| Mean | Averages the image in a 3x3x3 neighbourhood | Image |
| Median | Sets pixel value to the median of the set of neighbouring values | Image |
| Pixel_Statistics | Compiles statistics on the pixels (number of pixels, mean) according to a given mask | Image / Image |
| Relabel_Pixels | Relabels pixels such that all labels are consecutive. | Image |
| Set_Border | Sets border pixels of a 1, 2 or 3D image to a specified value | Image |
| Snakes | Active surfaces algorithm | Image / Points |
| Subsample | Subsamples large images | Image |
| Threshold_Global | Makes image "black and white" | Image |
| Skeleton | |||
| Channel Network Extract | Extracts channels contained in a mask. | Channel Network / Image |
| Channel Network Filter | Filters channels as a function of their length, aspect ratio, etc. | Channel Network |
| Channel Network Measure | Extracts various channel-level geometric quantities | Channel Network |
| Channel Network process | Merges channels when identified as the same. | Channel Network |
| Channel Network to Lines | Converts a channel network to a lineset. | Channel Network |
| Contact orientations | In a skeleton graph, compiles edge orientations in a spreadsheet | Skeleton |
| Draw skeleton | Draws a skeleton (type HxSkeleton) as a graph | Skeleton |
| Skeletonise | Skeletonises the image | Image |
| Skeletonise2 | Skeletonises the image using a parallel asymmetric scheme | Image |
| Skeletonise surface | Modifies surfacic skeleton topology to obtain curvilinear skeleton | Image |
| Skeleton Graph to Channel Network | Converts an HxSkeleton structure to a HxChannelNetwork structure. | Skeleton |
| Skeleton_Graph_To_Points | Converts a skeleton graph to a point set. | Skeleton |
| Skeleton_Image_To_Graph | Converts a curvilinear skeleton to a graph structure HxSkeleton | Image |
| Skeleton_Process | Post-processing skeleton graph to define element positions | Skeleton |
| Tomography | |||
| Append Circles | Appends circles to a set | Circles |
| Back_Project | Performs a back projection of projections | Image |
| Create_Projections | Generates projections in parallel beam geometry. | Image |
| Draw Circles | Creates a set of lines representings the circles from their definition, i.e. (centre,radius) | Circles |
| Draw Cylinder | Creates a surface representing a tube from its definition, i.e. (axis extremities, radius) | Cylinder |
| Encircle | Finds the smallest circle around points from cross-sections of the image | Image |
| Fit Cylinder | Fits a cylinder on a set of circles | Circles |
| Project on Cylinder | Creates a distance map of the points from the cylinder | Points / Cylinder |
| Miscellaneous | |||
| In Create->Others | |||
| Convert_Scene_To_PovRay | Generates a POV-Ray file of the scene displayed in viewer 0 | |
| Create_Colormap | Creates a colormap of random colors for each integer value | |
| Create_Sphere_Packing | Creates different types of sphere packing. | |
| Load_Reconstructions | Creates a 3D raw file that stacks reconstructed slices. | |
| In Display | |||
| Clipped_Orthos | Shows a set of cross-sections cutting a corner of the image | Image |