1. Use "TeraConverter" (under Advanced --> Big-Image-Data) to convert your file to TeraFly format.
2. Open your converted TeraFly format image using "TeraFly" (under Advanced --> Big-Image-Data).
3. In TeraFly mode, use the menu in the left bar to define a soma marker location and save the annotation including three files (xx.ano, aa,ano.apo, and xx.ano.swc).
4. Open "ultratracer" plugin, keep "va3draw/raw image or tc file" empty. select the saved "xx.ano.apo" as the "marker file", the highest resolution folder as the "terafly format file".
5. Run the plugin.

All TeraConverter and TeraFly related questions, please check our paper (http://www.nature.com/nmeth/journal/v13/...)

Thanks,

Zhi