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Release Notes 2.3

Introduction

This document describes changes and improvements in version 2.3 of the Visualization and 3D Reconstruction system amira and of the expandable version amiraDev 2.3.

Supported Platforms

Microsoft Windows 95/98/ME/NT4/2000 (Recommended: Windows 2000)
HP-UX 11.0 with OpenGL support
SGI Irix 6.5.x (all SGI graphics cards))
SUN Solaris 2.7 (Creator, Elite, Expert 3D graphics, or better)
Linux with OpenGL support (RedHat 7.1)

Details about Software and Hardware configuration are listed in the section "System Requirements" of the User's Guide included in this distribution and also available at http://www.amiravis.com.

In order to add custom extensions to amira also a C++ compiler is also required. Details about the supported compilers and compiler versions can be found in the section "System Requirements" of the Programmer's Guide included in the amira developer version.

Changes Since amira 2.2

Slice aligner: new tool for manual and automatic alignment of 2D slices in a 3D image stack (facilitates reconstruction of geometric models from mechanical/histological cross sections, tutorial and demo included).
New features for interactive image segmentation, e.g., a wrapper tool, allowing to interpolate 3D shapes from just a few segmented slices, or smoothing by means of morphological operations.
Option to view the current selection and segmented regions in the image segmentation editor in 3D. The selection can also be edited, e.g., cropped away, in 3D.
New interactive tool for surface editing (move points, flip edges, collapse edges, refines triangles, delete triangles, define new triangles, specify boundary condition IDs and more).
Better support for multi-channel images (individual channels can be grouped into one object, editors and modules can work directly on the multi-channel object, this includes OrthoSlice, ObliqueSlice, ProjectionView, Resample, CropEditor, and Voltex).
Better support for time-dependent data using a time step controller (caches and replaces individual time steps on request, can be invoked via "Load Time Series..." option of the file menu).
Improvements and new tools for measurement (lengths and angles).
New options for resampling: specify voxel size of output data set, take dimensions and/or resolution of output from reference object.
New module ApplyTransform (resamples transformed 3D image onto new grid with identity transformation, resamples 3D image onto a new grid oriented as defined by a slicing module).
Improved quality of reconstructed surfaces (compactify option and option for edge contraction in the GMC module).
"Virtual slider" in text fields (shift-click into a text field displaying a numeric value and move the mouse while keeping the
mouse button pressed in order to change the value, mouse wheel works as well).
Volume rendering: support for palette textures and SGI/HP color table extension (less memory consumption, improved performance), real-time selection of subvolumes via a tabbox dragger (can be activated using the command "Voltex showBox 1"), much less flicker when rotating objects in 2D texture mode.
New file formats: BioRad confocal images, Metamorph STK format, Fidap neutral file format, I-DEAS file format, Analyze 3D images.
Improvements for many existing file formats: ZEISS LSM (16-bit, multi-channel), Leica 3D (memory handling), Fluent (boundary ids).
Instead of the bounding box now on default the voxel size can be entered in the crop editor, the read raw dialog, and the channel conversion dialog. The bounding box option is still available, too.
Improved console behavior (TAB auto completion, less flicker).
Redesigned DICOM import dialog: DICOM files are listed in a table and can be sorted according to different criteria such as series id, file name, z position, date.
ProjectionView: new option for combinded pseudo-color display of both the projected values and the depth information (max + depth), support for projection of subvolumes (restrict option).
New module ProjectionViewCursor (can be attached to a ProjectionView, shows location of the voxel containing the maximum value).
New module VertexMorph for interpolating between two vertex set objects (e.g. surfaces) with the same number of vertices.
New module Histogram for computing histograms for any scalar field regardless of the coordinate type.
New module CorrelationPlot for plotting the correlation matrix of two regular 3D input images of the same dimension. Possibility to segment the images by manually drawing contours into the correlation matrix.
New module SurfaceArea to compute the surface and/or the volume of the different patches or regions of a surface.
Enhanced version of the DistanceMap module.
New option "pack & go" option for exporting network scripts. New preference dialog for further customizing the save network behaviour.
Viewer toggles are shown on the icons in the object pool (objects don't need to be selected any more in order to change the viewer mask).
New modules selected from a parent's popup menu are automatically selected now (behaviour can be turned off in the preferences dialog).
Performance improvements for illuminated field lines (DisplayISL module) on several platforms like Windows/NVidia.
Better support for transparencies in slicing modules such as OrthoSlice and ObliqueSlice by use of OpenGL's alpha test function.
Surfaces may now have more than 32767 patches.
Snapshots are always written as 3 channel RGB images, not RGBA. Improved compatibility of exported TIFF files with Windows applications.
Support for a user-defined material database.
Specification of colors in the parameter dialog via a color chooser.
Data in plot window can be saved in Excel csv format.
amira 2.3 is based on the newest releases of Open Inventor (version 2.6.2), Qt (version 2.3.1), and Tcl (version 8.3.2).
All patches released since amira 2.2 are incorporated in the new version for all platforms. This includes bug fixes as well as functionality enhancements.
Many small bug fixes, performance and quality enhancements.

Changes Specific to amiraDev 2.3

New data type HxTime and associated port/interface HxPortTime.
New API for defining time-out methods/functions for animation tasks.
Two new example modules in the demo package illustrating the new concepts (MyDynamicColormap, MyAnimateColormap).
Support for multiple result objects in compute modules (HxCompModule).
Parent objects are now being notified if down-stream modules connect or disconnect (HxObject).
New evaluator interface allowing the user to define higher-order interpolation methods for 3D data fields.

New Options

Starting with amira 2.3 a separate option called amiraMOL is available for the visualization of moleculs (see ReleaseNotes for amiraMOL).
Starting in Q3/2001 a separate option for resolution enhancement by computational deconvolution will be available