Analyze 4.0 Enhancements
New features and enhancements that were previously built into Analyze version 4.0.
Major New Modules/Functionality
Module-Specific Enhancements
Major New Modules/Functionality
BIRPacs Add-On
New DICOM communications for Analyze - BIRPacs provides the communications necessary for Analyze to receive, query, retrieve, and send images to other DICOM entities, eliminating the need to separately store DICOM image files and sort them into volumes for loading into Analyze. The features of BIRPacs include:
- Volume image selection using Patient/Study/Series hierarchy.
- Direct loading of series into Analyze as 3D volume images.
- Rapid access to DICOM header information to review specific scan details.
- BIRPacs database and DICOM receiver process running independent of Analyze.
- Custom database queries from BIRPacs database (sortable on any information).
- DICOM server administration for configurable DICOM entity name and port number.
Virtual Endoscopy
New Virtual Endoscopy module with interactive endoscopic navigation interface and intuitive localization images, including 3D endoscopic object recognition and visualization. Includes improved sequencing ability for endoscopic fly-through sequence generation.
Surface Extractor
Integration of former Tiler and Contours functionality into new, enhanced Surface Extractor module, with completely new and improved interface and additional output options to support connectivity to finite element analysis programs (via PATRAN format) and rapid prototyping systems (via binary STL output and using real-world scaled coordinates).
Application Critical 2D and 3D Registration
New, application-critical algorithms added to 2D and 3D Registration methods, including:
- Non-rigid 2D and 3D registration using multiresolution, piecewise-linear algorithm;
- Nine degree of freedom NMI registration (scale space search);
- 3D 'point cloud' to surface registration (non-image based point coordinates);
- Isocoordinate registration for anisotropic volume images (automatically resampled base).
Coronary Artery Calcium Scoring
New application-specific module for Coronary Artery Calcium Scoring from EBCT image data, including output of Agatston score, total calcific area, and total calcific volume on a per-lesion, per-artery segment, and total heart basis.
Tree Analysis
Important enhancements to Tree Analysis functionality to allow interactive editing of extracted tree information using rendered images from multiple viewpoints, and a new diagramatic tree map display to elucidate complex branching relationships.
Brain Atlas
Implementation of Talairach-Tournoux Brain Atlas for registration to other volume images using an interactive Analyze tool and output as an Analyze image file or Analyze object map for further atlas-based interactions.
General Improvements
Based on improved AVW 4.0 software library.
Support for new Windows ME and XP operating systems.
New, interactive method for establishing and managing user-specific default settings for module parameters, including:
- 'One-click' default setting to copy current parameter value as default.
- 'Defaults' editor for assignment of option-specific default settings.
- Control of global window defaults, including size and position.
Image canvas print ability added to all Analyze modules for direct printing of the contents of any display canvas and tools windows.
Module-Specific Enhancements
Load / Load As:
Multiple image file loading via selection of multiple files in the file selection box (Load As - PC version only) and subsequent loading of all the volumes selected.
Default colormap control in Intensities panel (Load Colormap option) for loading all data with specific default colormap.
Per-slice Shear Factor correction for shifting slices during loading (see gantry tilt info in Import/Export).
New shape-based interpolation option for resizing of volume images during loading of binary volume images or object maps as volumes.
Support added to manage 64-bit float (double float) numeric value representation.
Import/Export:
Continued enhancement to DICOM image format support, including:
- Enhanced JPEG-compressed DICOM image management.
- Support for eFilm DICOM images added.
- Support for multiframe X-ray Angiographic (XA) cine loops added.
Automatic recognition and correction for CT gantry tilt FOV shearing effect, restoring slice-based registration along the acquisition axis. This is keyed by the presence of a value in DICOM Acquisition Gantry/Detector Tilt field (0018|1120).
For DICOM CT volumes, Image Rescale Intercept (0028|1052) and Image Rescale Slope (0028|1053) are now used to rescale the CT values, usually for the purpose of automatic rescaling to Hounsfield units. NOTE: This will occur for all CT data that is imported from DICOM data, so CT value ranges will be significantly different that with previous versions of Analyze (actually handled correctly now as Hounsfield units).
Improved Raw Data import tool, including examination of actual data values for exploration of image data format.
Volume Render:
Direct rendering of difference volumes (created by subtracting loaded volume and related volume).
'Change View' rotation interaction improved by adding the ability to regenerate the rotated image upon mouse button release (previously only when cursor moved outside of the window).
Movie:
Ability to output multipanel movie frames for 4-D data to an image sequence stored in the Analyze Workspace added to the Movie module. This allows saving of multipanel sequences for conversion to other format types (such as Quicktime) for use with other movie players outside of Analyze.
Image Calculator:
Improved support of keyboard use for entry of numbers, operators, and actions ('Enter' same as '=', Backspace for deleting entries).
Spatial Filter:
Added 'sticks' filter to provide an improved method for noise reduction. This filter uses circularly-symmetric rotational line segments as multiple filter kernels, outputing numeric combinations of the properties of voxel sets processed by these kernels (maximum, minimum, average max, average min, etc.). This directionally-dependent filter has been used successfully in noise reduction for ultrasound images.
Added low pass filter support for 24-bit RGB images.
Image Edit:
Added ability to restrict the Autotrace region growing process by an enclosing object from a loaded object map, providing regional growth control based on specific objects for improved Autotrace functionality.
Morphology:
A new watershed operator has been added, providing an algorithm which will segment connected structures in a binary volume using ultimate erosion and regrowth to determine dividing lines between the objects.
Surface Extractor:
Completely new interface design for surface extraction algorithms and contour extraction, with improved management of controling parameters for each algorithm and easy output file format selection and saving of surfaces.
New Marching Cubes implementation includes the ability to use volume image-based gradients for normal computation for surface polygons (produces much smoother- appearing surfaces).
New output surface format support added for:
- PATRAN - to support connectivity to Finite Element Analysis (FEA) applications.
- Binary STL - to improve connectivity to rapid prototyping (model building) systems (note that both binary STL and ASCII STL are now supported).
The output of surface coordinate information can now be done in either the discrete voxel coordinates in the volume image, or the coordinates can be scaled using the voxel size information into coordinates in the original measurement space of the image acquisition.
2D Registration:
A mutual information-based, piecewise-linear non-rigid registration algorithm has been implemented for improved 2D slice-to-slice registration capabilities. The algorithm is based on hierarchical subdivision of the image space, with beginning and ending grid sizes as determined by the user, where within each grid section the subregions are registered using standard normalized mutual information techniques. The image is transformed at each hierarchical subdivision level by combining the transformations determined for each grid section as a weighted, linear combination of the transformations in the neighborhood of the point being transformed. The implementation also includes manual control capabilities for the transformation in each grid section, allowing interactive correction or initial condition setting with visual feedback.
3D Registration:
Several improvements have been implemented in the 3-D volume-to-volume normalized mutual information registration capability in Analyze, including:
Isocoordinate base volume registration - the base volume is now automatically interpolated to be anisotropically sampled (cubic) to provide a more stable basis for the resampling of the match volume during the registration process. The Cursor Link tool can also show this base volume in the cubic resampled space.
The fundamental search algorithm for normalized mutual information now permits searching the scale dimensions of the volume, implementing a full nine degree of freedom registration algorithm. Controls for these additional three degrees of freedom can be found in the MatchLab interface.
A new feature has been added to allow the registration of a 3D 'point cloud' to a 3D binary surface using the chamfer distance transform algorithm in Surface Matching. The 'point cloud' can consist of coordinates derived from any source, such as mechanical tracking and coordinate sampling devices, or from landmark positions as sampled directly from other volume images using modules within Analyze.
As with 2D registration, a mutual information-based, piecewise-linear non-rigid registration algorithm has been added to the 3D volume-to-volume registration capabilities of Analyze. This algorithm is based on the hierarchical subdivision of the 3D volume space into successively smaller subvolumes, where the beginning and ending subvolume size are under user control. Each subvolume is registered based on standard normalized mutual information registration techniques. At each hierarchical level, the independent subvolume registration transformations are combined on a specific voxel basis to provide the non-rigid transform for each voxel. These transformations are combined through a weighted, linear combination of the transforms for subvolumes in the neighborhood of the voxel being transformed. The non-rigid registration can be preconditioned by a standard, rigid-body normalized mutual information registration.
Region Of Interest:
A 'Linked Cursor' feature has been added to ROI (left button panel) when both an input volume and a related volume are loaded. This permits simultaneous investigation of both volumes by linked cursor selection of a common point and output of the coordinates of that point and the values from both the input and related volumes.
Added ability to restrict the Autotrace region growing process by an enclosing object from a loaded object map, providing regional growth control based on specific objects for improved Autotrace functionality.
Tree Analysis:
Many important improvements have been made to the Tree Analysis module, most all in response to requests and suggestions by users of this module:
- Multiple viewpoints have been added for viewing the extracted tree(s).
- Renderings from the original volume image can be combined with tree display.
- Using multiple viewpoints, editing tools now allow the interactive manipulation and editing of the tree branching patterns and connectivity associations between trees.
- Tree labeling has improved to manage trees of greatly increased complexity.
- An extracted, diagramatic representation of the tree branching relationships has been implemented to provide an unambiguous reference for the entire tree.
- An image volume can be regenerated by application of the BAP values at each tree node to build up a representation of the tree based on these measured values.
Publish:
Many improvements have been implemented in the Publish module, most with a focus on creation of images for publication (rather than for direct printing). These enhancements include:
- Object grouping / ungrouping.
- Multiple object alignment tools
- Interactive color setting for all objects.
- Improved intensity control for embedded images, including independent controls for each image and the ability to copy settings to other images.
- Added support for multivolume images, with volume selection for embedded images.
Fonts and graphics now handled internal to Publish (rather than via the external Ghostscript application), providing greatly improved font characters and graphic object representation.
Simplified operation of the Page Setup window, including optimal setup for constructing of output images (rather than printer pages).
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