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


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:


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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