Analyze Modules

The following summarizes the advanced algorithms and major features of the Analyze software system

Analyze Main Control Panel

Analyze

• Launching pad for all Analyze programs, either from menus or power bar icons.
• Configurable, multiple power bar(s) for iconic representations of programs.
• Control canvas for loaded volume images with iconic representation of images.
• Configurable loaded volume location for multiple, independent sessions.
• System resource monitor (disk, memory, time, etc.)
• Powerbar editor and icon layout facility
• Support for multiple user preferences (interface options, etc.)

Image Data Retrieval and Management

Import Export

• Import/export of standard image file formats and many commercial scanner formats.
• Conversion to/from over 30 standard image formats, including the DICOM standard.
• Template for specification of image information for unknown formats.
• Automated construction of volume image files from groups of individual image files.
• High fidelity, rapid image compression/decompression using wavelets.
• Access to tape devices for I/O of image data in many formats.

File Manager

• Graphical file manager with iconic representation of images and other file types.
• Direct drag and drop to/from the Analyze file manager and other Analyze programs.

Image Data Loading and Storing

Load/Load As - Save/Save As

• Support for native image file formats without need for conversion.
• Volume image resizing based on automated isotropic sampling (noncubic resizing).
• Interactive subregioning, flipping, and padding of volume image.
• Data type conversion with intensity windowing or thresholding.
• Direct output to any supported file format.

2-D Image Generation and Display

Multiplanar Sections

• Interactive reformatting and display of multiplanar images.
• Interactive intensity windowing.
• Interactive dissection and intersection through 3-D volumes.

Oblique Sections

• Interactive oblique images through 3-D volumes.
• Image volume reformatting along any arbitrary oblique axis.
• Interactive generation of "curved" images and radial images.

Movie

• Cine movie displays with multiple panels, variable size, and speed control.

3-D Image Generation and Display

Volume Render

• Fully interactive volume rendering of 3-D images.
• Both transmission and reflection raycasting models.
• Depth, gradient, composited and phong shaded surfaces.
• Voxel and object compositing with transparency.
• Divergent perspective ray casting/rendering.
• Interactive colorizing and voxel texture mapping.
• Interactive, graphical control of all divergent viewing specifications.
• Control of multiple viewing positions (cameras).
• Sequence generation between camera positions for cine fly-throughs (e.g., virtual endoscopy).
• Variable illumination and angle-of-view.
• Variable render masks and dynamic preview modes.
• Radial cylindrical and stereo-pair rendering.
• Maximum intensity, integrated and surface projections.
• Numerical projection rendering.
• Multiplanar dissection and subregioning.
• Interactive orthogonal and oblique sectioning.
• Manual editing and automatic definition of objects.
• Rendering of combined or individual segmented objects.
• Interactive rendered object manipulation.
• Mirror image rendering for independent objects.
• Linear and curvilinear surface measurements.
• Direct surface area and volumetric measurements.
• Powerful, flexible movie generator with control of frame-to-frame updates of volume rendering parameters (e.g., rotations, dissections, dissolutions, etc.).

3-D Model Generation and Display

Contours

• Automatic extraction of contours from isosurfaces or objects.
• Output to common contour file formats (IGES, SLC, ASCII list).

Tiler

• Surface extraction from voxel-based structures using advanced algorithms:
  • Deformable model with adaptive surface fitting for surface extraction.
  • Kohonen net-based surface 'shrink wrapping' extraction.
  • Fritzke 'cell growth' extraction.
  • Marching cubes surface extraction.
• Based on user-specification of a given number of desired polygons (polygonal budget)
• Output to common surface file formats (IGES, DXF, OBJ, IV, STL, VRIO, VRML, POLY).

Viewer

• Model viewer for viewing multiple extracted surfaces (wireframe and shaded).

Image Processing

Image Calculator

• Metaphor of hand-held calculator for powerful algebraic and boolean operations on images.
• Formula design and execution for customized 2-D and 3-D image processing.
• Image algebra for combining images from formulas.
• Mathematical, logical, and transcendental operations.
• 3-D matrix operations and geometric transformations.

Histogram Operations

• Linear and adaptive histogram operations.

Spatial Filter

• Spatial and frequency domain image processing.
• User-defined convolution kernels.
• Inhomogeneity correction based on statistical means filtering.

Filter Designer

• Interactive, graphic-based design of custom filters.

3D FFT

• 2-D and 3-D FFT and deconvolution routines.
• Image transformation and compression using wavelets.

Image Segmentation

Image Edit

• Interactive manual object segmentation.
• 2-D and 3-D region growing for object segmentation.

Morphology

• 2-D and 3-D math morphology for object segmentation.
• Automatic edge contour extraction.

Object Extractor

• Automated segmentation based on 3-D morphological processing.
• User definition of bounded region on selected image(s) within volume to condition segmentation.
• Output of binary or masked grayscale segmented volume to other Analyze programs.

Image Registration and Fusion

2D and 3D Registration

• Fusion (registration and integration) of multimodal images.
• Intra- and inter-modality registration.
• Registration using advanced normalized mutual information maximization.
  • Permits registration without need for prior segmentation.
• Registration using surface matching of common surfaces.
• Efficient section-to-section registration for 3-D volumes of serial images.

Image Mensuration and Quantitative Analysis

Line Profile

• Interactive plotting and measurement of line and trace profiles.

Region Of Interest (ROI)

• Interactive definition of multiple regions of interest.
• Selection and automatic sampling of regions of interest.
• Measurement of dimensions and densities.
• Measurement of regional shape and texture.
• ASCII data file format for exporting to standard analysis programs.

Tree Analysis

• Analysis of tree structures (lengths, branching angles, cross-sectional areas).

Stereology

• Surface area and volume measurement by stereology.

Ancillary Programs

Publish

• Interactive screen editor with text, labels and graphics.
• Hardcopy printing of text and images, including full color postscript.
• Extensive interactive color definition and manipulation.

Help

• On-line, context sensitive help documentation and tutorials.
• Documentation in HTML format, use with web browsers.