How to activate AmiraWhat's New in Amira 5.3?
Changes and new features for basic Amira
DemoDirector
This new feature has been created as the graphical front-end for the familiar DemoMaker module. It facilitates creating animations and demos by providing a timeline window that allows placing and manipulating events in an intuitive manner. The timeline window can be launched from the Console window title bar whenever a DemoMaker module has been created. New events are now more easily created from a dialog where all Pool modules are listed in a tree list. The available ports of each module will be shown when the list of module entries is expanded.
with all Pool modules listed in a tree list.
Spreadsheet redesign and enhancements
Amira’s SpreadSheet object has been largely reworked. It includes the following new features and more:
The viewer (button Show in the Properties of the SpreadSheet object) now shows up as a convenient table widget supporting copy and paste as well as sorting rows according to columns.
Spreadsheet objects may contain more than one table.
Spreadsheets can now be saved in MS Open XML format, which supports direct exchange with MS Excel and other compatible spreadsheet calculator applications.
A new functionality in SpreadSheet objects can be used to highlight items marked in the spreadsheet. SpatialGraphStatistics is one of the modules that use this new functionality. When module SpatialGraphView is connected to SpatialGraphStatistics, highlighted rows in the spreadsheet will be highlighted in the SpatialGraphView.
New Modules
PlotSpreadSheet Plots spreadsheet contents in a curve.
SpreadSheetFilter Exports rows according to a user-defined range of column values.
SpreadSheetToCluster Converts a spreadsheet with x, y, and z coordinate columns into a cluster object.
SurfacePaths/SurfacePath Editor With SurfacePaths a new type of data object storing lines defined on triangulated surface meshes is introduced. The data objects and their dedicated editor, the SurfacePath Editor, can be used to measure distances on surfaces. The editor automatically computes shortest paths on a continuous surface but can also be restricted to existing edges of the triangulated surface.
ComputeDistanceToPoint For SpatialGraph objects, this module computes the shortest distance from a user-specified point to all other points on the graph and stores it as a point attribute.
LabelSpatialGraph Labels a SpatialGraph object at points or nodes according to a spatially coincident LabelField.
SplitVolume converts a mosaic image into an image stack. For example, a mosaic DICOM image as created by certain DICOM scanners. The module can also be used to split a time series contained in a single volume into its time steps.
ConnectedComponents has been improved to support short (16-bit signed or unsigned numbers) and integer (32-bit signed) fields. Also, a dedicated mode for analyzing connected regions in label fields has been added. If a label image is requested for output, the user can specify the output type as a regular LabelField, unsigned short (16 bit) or unsigned integer (32 bit), depending on the number of unique labels.
SurfaceThickness This module is useful for computing the thickness of flat regions from surface objects. To do so, at each vertex, the module computes the distance along the vertex normal to the normal's intersection with the closest triangle of the same material. To get a reasonably reliable thickness estimate the surface should be smooth and opposing triangles should be approximately parallel.
AverageVolumes A module that allows computing the average and/or standard deviation of several uniform scalar fields or label fields with optional transformation set for each field. The calculation is performed out-of-core so that the input data need not reside in memory during processing.
CannyEdgeDetector A new compute module that implements an image filter for edge detection. This filter produces a binary image where edges are represented as foreground voxels.
Updated Modules
ClusterView has a new option to scale size of the spheres based on the data values attached to the cluster vertices (check option plates and scale plates).
BoundingBox has new ports to specify the color and width of the lines drawn and to enable additional lines indicating the center of the bounding box.
New Neuro Option
A new option dedicated to users in brain research has been created. The option features a comprehensive set of modules to analyze and display diffusion weighted MR imaging results. Another set of modules is dedicated to the analysis of perfusion weighted CT and MR images.
A separate license (AmiraNeuro) is required. Please contact This e-mail address is being protected from spambots. You need JavaScript enabled to view it for pricing information.
Modules
ComputeTensor Computes a second-order tensor from diffusion weighted images.
ComputeTensorOutOfCore Computes a tensor from diffusion weighted images residing on hard disk.
CreateGradientImage Creates a gradient image from a given tensor field.
EigenvectorToColor Generates a directionally encoded color (DEC) image from the eigenvectors of a tensor field.
FiberTracking Generates fiber lines from seed regions inside the tensor field to detect potential fiber tracts from diffusion weighted MR images.
ComputePerfusion Computes the perfusion related measures mean transit time (MTT), blood flow (CBF), and blood volume (CBV) from a perfusion weighted image series (MR or CT).
ExtractEigenvalues Compute the eigenvalue decomposition of a connected tensor field.
Changes and new features in Amira Developer Option
ITK integration Users of the Developer Option can now use the ITK (Insight Tool Kit) library to integrate existing ITK code or to create new code that uses the ITK library. For getting started with the ITK engine the Development Wizard now offers an example ITK filter project.
On 64-bit Windows Amira now supports Visual Studio 2008 (Visual C++ 9.0)
A class reference has been added. It can be accessed by opening <Amira-Install-Dir>/share/devref/Amira/index.html in a web browser.
Changes and new features in the Mesh Option
RemeshSurface The new RemeshSurface module may be used to improve triangle quality of triangulated surface meshes. The module takes a surface object as input and re-meshes it by moving the vertices to meet certain regularity criteria. Besides number of triangles, re-meshing objectives are either high regularity or isotropic vertex placement.
New File Format
Abaqus (.inp format) Tetrahedral grids can now be exported for SIMULIA’s Abaqus program (www.simulia.com). Along with the tetrahedra, optional scalar values defined on the tetras can be exported.
Changes and new features in the Microscopy Option
Filament Editor
The Filament Editor has been significantly improved by adding new tracing options and editing tools. The most important changes are listed below:
View options tab SpatialGraphView group has a slider to control line width in the 3D viewer.
Node size and line width can now be controlled in the tracing window.
Tools options tab Graph Info now generates tables with label group statistics. For each label group a tabbed table is inserted listing all segments associated with a particular label. Note that buttons Export to XML and Graph summary have been removed in order to unify the window layout with the new spreadsheet design. Exporting to XML can be performed using the regular Save data as… dialog. A graph summary can be achieved with appropriate labeling. Also, Rank is now considered a regular segment attribute and will have a column in the table only if the attribute exists.
New tool Remove isolated points removes points or nodes with no adjacent segments.
A new tracing method Linear lets the user trace straight lines.
In port Filament type the user can now specify whether the filaments are represented as bright against a dark background or as dark against a bright background (applies to interactive tracing only).
New option Snap to Graph: When commencing a new tracing line with one of the interactive tools previously there was a tolerance of 5 pixels within which the generation of a new branching node on an existing segment was enforced. Now this snap mechanism can be disabled.
Editing tools New tool Select sub-graph selects the sub-graph downstream from a selected node or segment. Clicking with the Shift key pressed selects the upstream sub-graph (in direction of root segment). This tool is available only if a root segment/node has been set with Set Root button.
New tool Select shortest path which calculates the shortest path between an arbitrary pair of nodes or segments.
New tool Move selected node lets you move a node in the tracing window.
All graph editing tools are now equipped with modifier keys to make working more efficient. A table of all modifier keys and their function is given in the User’s Guide.
Viewer The 3D slice now draws a yellow frame of exactly the size of the field of view currently visible in the tracing window
Label Editor The sequence of labels can be changed by dragging labels up and down in the label list. Complete label sub-trees can be moved into other label groups.
New Modules
ShapeAnalysis Analyzes regions in a label field with respect to their shape by approximating an ellipsoid to each label. The parameters of the ellipsoids as well as position and volume are output in a SpreadSheet object.
MorphologicSeparation This module attempts to separate similarly sized objects that touch each other. The input to the module is a label field. Objects are identified by their connectivity and their label number. The objects are separated based on their morphology.
LocalThreshold Is a module to perform threshold segmentation according to local criteria. The module is useful whenever low frequency gradients prohibit the use of global thresholds. Four different approaches cited in the literature have been implemented.
Further improvements and changes
Modules
CreateSphere was available in the Molecular Option only. This has been changed so that all Amira customers may use it.
TridelityView The module to drive Tridelity’s MultiView Autostereo displays is now also available on 64-bit Linux and Mac OS X.
CalculusMatlab The connection to the Matlab server has been improved. The module can now transfer surfaces, surface fields, and line sets from Amira to Matlab. Also, CalculusMatlab can now be accessed directly from the Create menu and therefore does not need to be connected to a field anymore.
Port interconnection
This new feature links two ports so that port settings are synchronized across modules. The new connect Tcl command is available for all ports and enables ports to be connected to corresponding ports of another module of the same type. Example of usage (from the console command line):
OrthoSlice sliceNumber connect OrthoSlice2
connects port sliceNumber of OrthoSlice to the port sliceNumber of OrthoSlice2. To disable connection enter
OrthoSlice sliceNumber disconnect OrthoSlice2
A new render mode, none, in the MPR Viewer removes the 3D rendering from the 3D viewer component. Only 2D slice updates are displayed. This can be used to improve the interactivity of the tool.
Segmentation Editor
A 3D crosshair option has been added to the 3D MPR tool. The tool is now controlled by a 3-state button and allows cycling through the list of states 3D MPR -> Crosshair -> None.
Selection tools like the Add/Subtract buttons in the Segmentation Editor are now drawn in red if their action would change the assignment of voxels not currently visible.
Two new navigation arrow buttons will change the currently active viewer to display the slice with the next or previous selection.
Display and masking has a new toggle show which hides/shows the blue mask on the slice views.
The Grow / Shrink buttons used to do an all-slices operation when All slices option is checked. This has been changed. Now these button trigger the corresponding 3D operation. The all-slices version can still be selected from the Selection/Grow(Shrink) menu.
Surface Editor
Tcl commands checkHoles and closeHoles has been added to the Surface Editor.
GUI
Sub-applications Sub-applications now have a Help button.
Text field editing Text fields now accept new values when the user presses Return or clicks somewhere into the GUI. Previously, moving the mouse pointer out of the field triggered a focus change.
Preferences
In the General tab it is now possible to specify the maximum number of documents (files and networks) displayed in the Recent Files menu.
Preferences can be saved to disk and reloaded later, or reset to the default values.
Pickable button
A new button [] in the Properties area of each display module allows the user to disable/enable picking of its geometry in the 3D viewer. This can be used to prevent accidental changes when working with several modules that interact with the mouse, e.g. OrthoSlice, SelectROI, etc.
The Pool menu now has two new entries to enable or disable this option globally.
A new help menu option Examples opens a help page with links to demo scripts provided with the Amira software.
Download the complete Release Notes.
