Visualizing Scanbox stacks with Vaa3D

Some scanbox functions allow you to export *.sbx files to *.tif files that can be then visualized using other software like Vaa3d or ImageJ.  For example, after collecting a z-stack you can use sbxtifstack() to generate a tif file that can be read directly using Vaa3d.  If your stack has the hypothetical file name abc_010_nnn.sbx (where nnn represent the different slices of the stack), all you have to do is to type

sbxtifstack('abc_010')

This will align all the images for each of the individual slices and generate a tif file named abc_010_stack.tif. Opening this file in Vaa3D and visualizing the volume will give you something like this:

v3a

You can easily rotate and visualize your data and Vaa3D provides a number of plug-ins for further analysis. A similar process can be followed if you are more familiar with ImageJ.

 

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