Amira (Software)

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What is Amira and What does it do?

Amira is a diverse, powerful visualization software with a very friendly Graphic User Interface (wait till you see Slicer). It is capable of visualizing and analyzing industrial standard data. At this lab, we mainly use it to achieve the goal of segmentation and stereoscopic 3D visualization of anatomical structures. Here are some other known but not well used functions of Amira

  • Microscopic image processing, color field support
  • 4D data display
  • Multi-modality image registration


Why do I care?

If you are reading this, either you are following the steps of master students (or PhD) or developer like me providing IT support to the lab. In the first case, you need to know the very basics about how to use Amira properly for your project. In the second case, you need to know how to provide support to the students to the best of your ability and update this Wiki while you are at it.

What are the alternatives?

I hate not having choices so you will have TWO other means to achieve the same goal of 3D visualization: 3D Slicer and OsiriX. I personally find Amira is easier to use when it comes to Segmentation while OsiriX has the best GUI and ease of use. Slicer3 has a very weird GUI design that takes a while to understand but is very well rounded in terms of both visualization and segmentation and adaptability to clinical applications.



Future Improvment of Amira

  • Group select multiple surf and hit attach SurfaceView and attach a surface view to every single one of them...
  • Easire ways to grouply toggle visibility (the grouping module for SurfaceView is REALLY slow somehow... it's faster for me to hardcode hotkey for them than that way. A special module that controls the visibility of other modules maybe just by toggling this module on/off?
  • A surf gen module that generate the labels into MANY individual .surf file.
  • Do not ask when save. Just autosave everything.