VFX: A System for Constructing Automatic 3D Image-Analysis Processes Allen Austin, Janice Turlington, Greg Simon, and William E. Higgins Departments of Electrical Engineering, Computer Science and Engineering, and Bioengineering Penn State University University Park, PA 16802 Manual Contents Introduction Categories of Functions Filter ``Sigma'' - sigma filter ``maximum homogeneity'' - the maximum-homogeneity filter ``Symmetric_Nearest_Neighbor'' - symmetric nearest-neighbor mean filter ``Salt_and_Pepper_Removal'' - remove salt and pepper (spike) noise ``Anisotropic_Diffusion'' - anisotropic diffusion filter ``4D_Filtering'' - 4D mean filter and grayscale inversion ``Median'' - a median filter ``Average_Maximum'' - average/maximum filter ``Average_Minimum'' - average/minimum filter ``Lowpass'' - lowpass filter ``watershed_maxh'' - the watershed-based maximum-homogeneity filter   Morphology ``Binary_Erosion'' - binary erosion ``Binary_Dilation'' - binary dilation ``Binary_Opening'' - morphological binary opening ``Binary_Closing'' - morphological binary closing ``Minimum'' - local minimum ``Maximum'' - local maximum ``Grayscale_Erosion'' - grayscale erosion ``Grayscale_Dilation'' - gray-scale dilation ``Grayscale_Opening'' - morphological grayscale opening ``Grayscale_Closing'' - morphological grayscale closing ``Conditional_Dilation'' - conditional dilation ``4D_Morphology'' - 4D mathematical morphology functions ``tophat transform'' - detect peaks ``Ultimate_Erosion'' - ultimate erosion   Topology ``3D_conn_comp'' - three-dim. connected components analysis ``2D_conn_comp'' - two-dim. connected components analysis ``Cavity_Deletion'' - delete interior cavities ``Homotopic_Thinning'' - thin an input volume ``Homotopic_Thickening'' - conditional homotopic thickening   Segmentation ``Hysteresis_Thresholding'' - thresholding using hysteresis ``Cue-based_Hyst_Threshold''--Hysteresis Thresholding using a biopsy image ``Bright_region_grow'' - segment a volume using region growing ``Cue-based_region_grow'' - segment a volume using user defined cues ``Seeded_region_grow''--segment an image using thresholded region growing ``Cue-based_relaxation''-- segment an image using relaxation labeling ``Relaxation_labeling''--Relaxation labeling using manually-set statistics of image regions ``Cue-based_watershed'' - segment an image using watershed analysis using cues ``Cue-based_WS_relax'' - segment an image using watershed relaxation using cues ``Marker-based_WS_relax'' - segment an image using watershed relaxation using markers ``morphological_gradient'' - morphological gradient ``Sobel edge operator'' - Sobel edge operator ``Kirsch edge operator'' - Kirsch edge operator ``border of binary vol'' - find borders in a binary volume ``nonmax suppression'' - non-maximum suppression ``3D_Adaptive_thresholding'' - automatically threshold a 3-D volume   Manipulation ``copy vol1 to vol2'' - copy one volume into another ``two-volume ops'' - pointwise functions combining 2 volumes ``threshold'' - intensity thresholding ``Gray-scale inversion'' - Gray-scale inversion ``zero hi voxels'' - zero out bright voxels ``zero lo voxels'' - zero out dim voxels ``complement'' - complement a volume ``3D_Expand'' - generate an expanded (zoomed) version of an image ``3D_Shrink'' - generate a shrunken (subsampled) version of an image ``save largest region'' - extract largest region from segmentation volume ``Flip'' - Flip a 3D Image ``Resize'' - Save a resized 2D/3D Image ``Range Labelling'' - Set a range of gray values to one value ``Level Slicing'' - pull out a range of gray values ``add Gaussian noise'' - add Gaussian noise to a volume ``Linear_Interpolation'' - Linearly interpolates a non-isotropic 8-bit image. ``umbra'' - compute the umbra of a volume ``Zero_Padding'' - pads an image with zeroes. ``Image_Masking'' - masks out of given region. ``Embed_Image'' - Embed a smaller image into a given location in a larger image. ``Assign'' - Assign a specified gray level to a selected voxel.   Measurement ``Region properties'' - find properties of a segmented volume ``volume properties'' - Compute various properties of a volume ``histogram'' - compute a histogram of a volume ``3-D histogram'' - compute a 3-D histogram ``min.-bounding cuboid'' - finding object bounds   Turnkey ``LV Extract'' - extract left ventricular chambers ``solid-blob extract'' - extract bright solid blobs ``object separation'' - separate connected objects ``region isolation'' - extract a large bright region ``fill concave gaps'' - fill concave gaps in objects Input/Output ``Display'' - Display an image files in D4 or mdisplay ``Load'' - load a volume into vfx memory ``Save'' - write a volume to disk ``Create_Image'' - generate an arbitrarily-sized image of zeros Bibliography About this document This work was supported in part by research grants CA53607 from the National Cancer Institute of the National Institutes of Health, a Whitaker Bioengineering Foundation Grant, a Penn State Research Initiation Grant, and an NSF Research Equipment Grant. to report any bugs found in this manual or for more information on IMPROMPTU.

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