I am having trouble creating a 3d stack with separate 2d images of the same brain in consecutive sections. I created a linker file, but am only able to see one image when I try to implement it. I know I can use neuron stitcher to do it, but am unable to find the plugin for it. Sorry, I am just learning how to do this.

As well, I was wondering what the best functions for analyzing EM images might be? I am trying to get distance between synapses and volumes and surface area of 2d and 3d images respectively. I read that you can create a curve to get the area, but am not sure how to do that. I know there is a distance function as well, but am a little confused on implementation.

To create a 3D stack, please import 2D image series by  using "File" --> "Import" --> "Import general image series to an image stack" option. At this moment, analysis functions in Vaa3D are not designed for EM images.  But you can try different functions for 3D image stacks. 

Thanks,

Zhi

Is there a way to execute "Import General Image Series to Stack" from command line?

I am trying to load a directory which contains ~400 .tif files and then run app2. When using gui for app2 my workflow is to use  Import General Image Series to Stack then select the app2 plugin. However, when using command line, I tried to use the tif directory as the input argument for app2, but it fails to open all tifs, only the first. This is Vaa3d V 3.475

Thank you