Context
The PLY format is used for storing nominally flat polygons and their properties. If you have a CT scan, it is typically a single file or sequence of files that are a reconstructed tomogram. These will be grayscale data. To generate a PLY file, you must first extract a surface from this grayscale information.
Process
- The simplest method in Amira-Avizo is to use the Isosurface module followed by an Extract Surface module.
A demonstration is available in this tutorial video: Calculate Surface Area from Grayscale Data. - Alternatively, if the Isosurface method does not accurately capture the desired interface, you can approach this with segmentation. Once you have segmentation data in Amira-Avizo as label data, you can use the Generate Surface module to turn it into a surface.
A detailed tutorial can be found here: Amira-Avizo Software | Surface reconstruction from 3D images. - In both cases, once you have an Amira-Avizo-formatted surface, you can export it to PLY or STL with the File>Export Data As… dialogue and select the desired data type from the list of possible options (note: different from the Save As… dialogue).