11/ How do I format my data so that I can see it with JAtlasViewer?

There are 3 aspects to formatting your data:

1. Converting image files to Woolz format
2. Generating a VTK surface for 3D feedback
3. Structuring the data directories

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Converting 3D image files to Woolz format

The program WlzExtFFConvert will convert the following 3D image formats:

• Amira Lattice
• Stanford Density
• ICS (International Cytometry Standard)
• BioRad Confocal
• SLC (Single Look Complex, from Synthetic Aperture Radar)
• Sunvision VFF
• VTK (Visualisation Toolkit)
• stacks of 2D Microsoft .bmp (Greyscale 8-bit)*
• stacks of 2D .pgm (raw 8-bit)*
• stacks of 2D .tiff (8-bit or 16-bit)*

* These require a simple control file as well.

For more information about WlzExtFFConvert see the FAQ

The 3D feedback image used by JAtlasViewer is in VTK format. Instructions for generating a VTK file from a 3D Woolz file can be found here.

The directories need to be structured according to a particular convention so that JAtlasViewer can build an anatomy tree for each 3D grey-level object.

In the following diagrams ...

• a name with .wlz extension represents a file in the Woolz image format.
• a name with .vtk extension represents a file in the VTK image format.
• a name followed by / represents a folder (or directory)

Here:

• name.wlz represents the 3D grey-level reconstruction of an embryo.
• name.vtk represents the corresponding 3D surface.
• anatomy/ is a folder which may contain .wlz and .vtk files representing anatomy components of this embryo. It must be called 'anatomy' (all lower case).

A more detailed example using the ts10 embryo stage is shown below.