General information


Amira is a modular software package for the visualization and analysis of scientific data. The user can assemble his application from individual software modules in a graphical user interface or via script, which is used to display, analyze and process his data. The focus is on applications from the life sciences and medicine, but the software can also be used in other fields, as Amira contains a broad repertoire of basic visualization techniques.

Here is a selection of the features that Amira offers:

  • Reading of single images and image stacks
  • Support for image registration and image processing in 2D and 3D
  • Aids for model reconstruction from 3D image data (serial section reconstruction) with generation of triangular surfaces or tetrahedral grids
  • Surface reconstruction from measuring points
  • Volume visualization
  • Segmentation Editor
  • Filament Editor
  • Skeletonization
  • General visualization techniques for polygons, volume data, flows etc.
  • Coupling with Matlab for calculations
  • Virtual Reality - representation of models
  • Control of applications through a scripting language
  • Extensibility through C++ programming

Access to Amira


The LRZ has one floating license from Amira. In addition, the XScreen option in V2C of the LRZ can be used to display Amira applications in a virtual reality environment. The Virtual-Reality feature is restricted to an older version of Amira.
Amira is only useful on a system with a graphics card, so it should be called on the remote visualization systems of the LRZ. For more information about remote visualization at the LRZ please visit https://doku.lrz.de/display/PUBLIC/Remote+Visualisation

Using Amira

Successful working with Amira urgently requires an initial training. The chapter "Getting Started" and the following tutorials in the Amira Users' Guide (see section "Documentation") can be a good source of information. You will also find information on how to import data.
You can find videos about the training from the manufacturer here:  Thermo Fisher Scientific Learning Center

Documentation

The Amira documentation can be accessed in a session via the Help menu. The manuals and further information can also be downloaded from the manufacturer's website (Amira page of Thermo Fisher Scientific). Unfortunately, there is no direct link to the extensive (50 MB!) User's Guide on this page, but you can search for it by using the keyword "Amira" (choose "All Documents & Support" first) on top of the page. This will result in a list of manuals for different versions, here the list from 12.10.2021: List of Amira manuals). If you only want to read the manual, you won't block the license this way.

Support

If you have questions or problems regarding Amira, please contact Jutta Dreer (Dreer_AT_lrz_PUNKT_en) or describe your problem via the service desk of the LRZ at https://servicedesk.lrz.de/de.

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