help > Scripting Vaa3D for Batch Analysis OR Writing a Plugin
Feb 21, 2021  03:02 PM | snowpalm
Scripting Vaa3D for Batch Analysis OR Writing a Plugin
Hi all,

I am looking for a way to batch-process multiple images with Vaa3D on Windows.
As of now, the features that I would like to use is loading a Landmark file and executing an automatic tracing.

How should I go about achieving this?
From searching "scripting" in Vaa3D, I have only found that it confirms that it is possible to script, but I am not sure how this is made possible.

If I were to use a command line execution of Vaa3D, I will have to write a plugin that loads an appropriate landmark file and executes an automatic tracing, won't I?
Or is there a way for me to load marker files from the Terminal?
I tried 
vaa3d.exe /i ~\c3_B6_20x_4.tif /i ~\c3_B6_20x_4.marker
but the error message was
Directly loading a marker or csv file into Vaa3D's main window is ambiguous.
You can either open it directly in a 3D viewer window of an image, or literally associate
it with an existing image, or literally convert it to a Point Cloud .APO file and then open.

So, I am thinking that I can do
  • Command-Line execution
  • Load image and marker file
  • load Vaa3D_Neuron2/vn2.dll for automatic tracing.
But I am not sure how to load the marker files in command line execution or associate the marker files with the images directly.

Any advice would be greatly appreciated!


Okay, so I realized that executing the plugin from the terminal has an option to load a "marker" file (at least for this plugin)
This my command line:
vaa3d.exe /x vn2 /f app2 /i ~\image.tif /p ~\marker_file.csv 0 1 1 1 1 ....

Now the issue is that I keep getting an error when loading the marker file.
1 markers loaded
The first marker is invalid
Fail to call plugin function.

How should the file be structured?
I have it as:

#x, y, z
10, 10, 1,
20, 20, 1,

This is how Vaa3D GUI saves the landmarks (ignoring shape and radius and comment columns).
I have also tried with .txt and .marker file formats, but none of them works.

Please let me know!
Thank you.

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Scripting Vaa3D for Batch Analysis OR Writing a Plugin
snowpalm Feb 21, 2021
snowpalm Feb 22, 2021