While Amira can be used to visualize and operate on arbitrarily complex sets of data, the general sequence of steps is similar for most uses.  First data is loaded into the system and displayed in one or more representations.  Then interactions or computations may be done.  Finally, new or transformed data may be saved, or the network of modules may be saved.

At the top of the module pool window select the file menu and pick 'LOAD'.  This presents a file browser window that allows you to move to the directory where your data is located.  The filenames are listed in the file browser as well as the file format type for each file that Amira recognizes.  Unrecognizable files are assumed to be 'raw' image files and Amira will present a window in which raw image parameters may be entered.

In the module pool window below the green boxes are data modules, the yellow boxes represent display modules and the reddish box is a computation module.  In this example wing.iv (Inventor data format) was loaded.  A second data set, wing.am (Amira mesh format - CFD data) was also loaded.  The data object wing.mag was computed from wing.am using the 'Magnitude' computational module.  Valid computational or display methods can be found by clicking on the data modules (in the label area) with the right mouse button.  When a method is chosen its icon is displayed the dependency connection is automatically made.  Computation or display modules may have their own associated methods as well and are accessed in the same way (right mouse button).

The orange square on the module icon indicates that the data or method associated with that module is active in the current display.  In this example all three data modules' data are available and the IvDisplay and DisplayISL display methods are contributing to the viewer.  GridView is not displaying any output.  These orange button may be toggled either in the module pool or in the work area.

The lower part of this window is the module work area.  Here details of a module and its parameters or 'Port' are displayed.  In this example the user has access to the Draw Style port for the IvDisplay method.  The 'Shaded' option is selected.  Other typical draw style options include Lines, Points, Transparent and others that might appropriate for the specific data type.

Here we also see a second module's ports displayed in the work area.  GridView is currently not contributing to the viewer, though its data and dependencies are all still in tact.

Most display, computational and measurement methods display a direct link to their documentation on the module icons.  Clicking the '?' on any icon will produce a window with the Amira documentation browser and the section of the User Guide for that module.  The 'Help' menu at the top of the module pool window provides access to the top level of the on-line User Guide.

The View menu option provides access to a variety of viewer options including layout (multiple viewer windows), background options, transparency options, lighting options, fog options, global axes display, measuring options and 'Easy Fade' (be sure to give this a try!).

Finally, data may be saved.  The module network, which is really a script that tell Amira which modules to load, how to connect them and records various state information, may be saved so that the entire visualization may be restored at a later time or may be sent to another user.  Also, data objects may be stored in a variety of formats.  Input data objects may be stored in a different file format or as a different data type.  And computed data objects may be stored in various formats.  Not all data types or formats can be saved in all formats; this is not a anything-to-anything conversion tool.  Amira will present only the formats that are appropriate or that are implemented in Amira.  There are, however, various intermediate computations and conversion that can be done to provide more flexibility.