Hi Kevin,

Thanks for interesting in our alignment tool. You may refer to Dr. Hanchuan Peng's paper https://www.nature.com/nmeth/journal/v8/... to download the software or compile from the source by your own from https://github.com/Vaa3D/v3d_external/tr... Basically it is a landmark-based alignment method, you need a template image and a landmark set of it (you can create it using vaa3d manually or detect it automatically with your own methods), then try running it with command line: 

jba -t "template_image.tif" -s "subject_image.tif"  -L "template.marker" -w 10 -o "output_image.tif" 

The JBA aligner is developed for aligning general 2D/3D image alignment. Sometime we might need pre/post process images to let the alignment work as we expected. It is highly depending on your studying cases. Hope this will help. Feel free to contact us if you still have any questions.

Best,
Yang 

Originally posted by Kevin Leo: