Hi,
I am installing the s2 plugin in Vaa3D 3.2.After the compilation operation, the s2 folder containing libs2.so is automatically generatedWhen I click on the submenu s2 under the menu plugins in vaa3d, it will pop up an interface.All the buttons in the interface could response to me.Does this mean that the s2 plugin has been installed successfully?When I click the "select data to trace" button,the system tells me that only the .marker file is allowed to open.I don't know where to find the.marker file.To run the s2 plug-in, must it combine with the microscope or just find the .marker file?

Are you using simulator? Only Simulator is for large image stack tracing purpose. To use this feature, you will need prepare 2 file inputs.

1. the image stack you wish to trace.
2. a marker file that stores the starting point for tracing.

Therefore, you are supposed to generate such marker file by yourself.

Hsienchi

The "gold166" folder has been downloaded in my computer from the Bigneuron github website.
According to your suggestion, I have converted a .v3dpbd file in the "gold166" folder to .marker file.
When I open the .marker file in simulator feature under the S2 plug-in, the s2 plug-in didn't respond.
Could you give me some advice?

v3dpbd is a image stack format, i.e., the .v3dpbd file you mentioned is supposed to be your image stack to trace on. It has nothing to do with marker file. However, currently S2 simulator only supports terafly image file system, particularly in .tif for each tile unit. Thus you will need 1 more step to have your image data prepared: Go to 'Advanced' tab on Vaa3D main window, under 'Big-Image-Data', click 'TeraConverter'. There you can convert your original image stack into terafly image arrangement. Remember to choose TIFF (tiled, 3D) for your destination.

Another thing I would like mention: Marker file is a document that only stores the information of the location you MARKED. You cannot convert a image stack into a marker file. What you need to do is to open the image stack in Vaa3D, then in 3D view window right click on the image stack to call out a menu. From that menu, select '1-right-click to define a marker', then mark your marker at the place where you wish the tracing process to start with.

Back in S2 simulator, you will need to specify the paths of your terafly images and marker file in order to have it run correctly.

Let me know if you have a problem converting the data to terafly.