Its flexible user interface and modular architecture make it a universal tool for processing and analysis of data from various modalities; e.g. micro-CT,[3] PET,[4] Ultrasound.

[15] This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools.

Other key Amira features are multi-planar and volume visualization, image registration,[21] filament tracing,[22] cell separation and analysis,[17] tetrahedral mesh generation,[23] fiber-tracking from diffusion tensor imaging (DTI) data,[24] skeletonization,[25] spatial graph analysis, and stereoscopic rendering[26] of 3D data over multiple displays and immersive virtual reality environments, including CAVEs.

Amira's roots go back to 1993 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB).

The new software was called "HyperPlan", highlighting its initial target application  – a planning system for hyperthermia cancer treatment.

In March 1999, the first version of the commercial Amira was exhibited at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX) booths.

Indeed – Visual Concepts GmbH selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years.

TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG).

VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences.