Hello I am trying to convert an swc file into stl, however I cannot open Vaa3D. I have a MacOS version 10.12, and downloaded the most recent Binary version which says Mac OS 10.9, but I had thought this would still work.

Thanks!

Attached is the file!

well， I have no problem to open the file! Attached is a screenshot.

Originally posted by Ary Wal:

Thanks! 

Now that I have it open, how can I save this as a stl or .obj file?
Also is there sholl analysis on Vaa3D?

Best,

Ary

Anyone know how to help?

For your two questions:

1. We do not have a direct way to convert swc file to stl or obj file at this moment. But you can first use "Plug-In" --> "neuron_utilities"-->"swc_to_maskimage_sphere_unit" to convert a swc file to a binary image. Then in 3D view, use the option "Load/Save Surf>>" under "Surf/Object" menu (attached a screenshot) to create and save surface in obj file. 

2. We do have sholl analysis in the current version.

Thanks,

Zhi

Hi Zhi,

Which version has the sholl analysis? I tried to get the newest version of the Vaa3D but it seems not compatible with my OS 10.13.4. (The older version is still working fine but doesn't have the sholl analysis function that I need)

Thanks,

HH

Dear Han-Hsuan,

Vaa3D still does not have a released plugin performing the sholl analysis.
However, if you are able to build Vaa3D from source code, we have been working on an experimental plugin that should allow you to perform it.

When you mention that you got an older version running do you refer to a specific version in github or to a binary release? Could you please specify exactly which version are you using?

In case you are interested in using our experimental version of the sholl analysis plugin we can help you getting it running step-by-step.

Best!
Linus Manubens-Gil

Hi Linus Manubens-Gil,

I have been using the Vaa3D (3.200) which works fine on my mac. (Need to use the vaa3d_script to start the program for another mac computer but not a big deal so far).

Yes, I will like to try out the experimental version of the sholl analysis and a step by step instruction will be great.

What I have been doing so far is sort he swc file>edit the "type" and "radius" column before import to Fiji for sholl analysis which take a lot of time to process my piles of images.

Thanks,

Han-Hsuan

Hi Han-Hsuan,

We are working on the cross-platform compatibility of the Sholl analysis plugin.
We hope to get back to you soon with the step-by-step instructions in the next few days.

Thanks in advance for your patience.

Best,
Linus

Dear Han-Hsuan,

At the moment we can only provide you a solution in Linux systems.

You can follow the instructions here to build vaa3d from source code:
https://github.com/Vaa3D/Vaa3D_Wiki/wiki...

To run the plugin you will also need to have R installed. This can be done in CentOs with the following commands:
sudo yum install epel-release
sudo yum install R


Some R packages also have to be installed. In a terminal, type:
R
install.packages(c("RInside", "Rcpp" , "ggplot2" ,"svglite"))

Once this is done access the directory [your vaa3d directory]/vaa3d_tools/hackathon/linus/sholl_swc_R and build the plugin using the following commands in a terminal.
qmake
make

The Sholl analysis plug-in will then be available in Vaa3D.

We will continue working on this plugin and its cross-platform compatibility in the future. I will be happy to keep posting updates on it here.

Best regards,
Linus

Thank Linus! I am new to the Linux system but will try to see how much I can get.

Please do keep me updated once your team has make any further improvements especially for cross-platform compatibility.

Best,

Han-Hsuan