help > Access voxels code!
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Dec 3, 2018 08:12 PM | Marouane Benmoussa - Burgundy university
Access voxels code!
i have a stack of 2d slices we make at a laboratory of mouse
brain, and we chose your software to do the 3d reconstruction, then
after this step we have to calculate volume of some neurons and
stuff like this, which will require from us to access the
voxels of our 3D reconstruction.
The question is which class i can use to access the voxels of my 3d reconstruction, or in a simpler way which classes you use to do the reconstruction from 2d slices?
The question is which class i can use to access the voxels of my 3d reconstruction, or in a simpler way which classes you use to do the reconstruction from 2d slices?
Dec 3, 2018 09:12 PM | Zhi Zhou
RE: Access voxels code!
You can use "Plug-In" -->
"neuron_utilities" --> "global_neuron_feature" to calculate
features based on the reconstruction you generated. You
can also directly save the reconstruction as SWC format. The
information about SWC format can be found in
here: http://research.mssm.edu/cnic/swc.html
Originally posted by Marouane Benmoussa:
Originally posted by Marouane Benmoussa:
i have a stack of 2d slices we make at a
laboratory of mouse brain, and we chose your software to do the 3d
reconstruction, then after this step we have to calculate volume of
some neurons and stuff like this, which will require from us
to access the voxels of our 3D reconstruction.
The question is which class i can use to access the voxels of my 3d reconstruction, or in a simpler way which classes you use to do the reconstruction from 2d slices?
The question is which class i can use to access the voxels of my 3d reconstruction, or in a simpler way which classes you use to do the reconstruction from 2d slices?
Dec 3, 2018 11:12 PM | Marouane Benmoussa - Burgundy university
RE: Access voxels code!
ok , now in your Code wich class that can allow me to access the
voxels of my 3d reconstructions...?
Dec 4, 2018 01:12 AM | Zhi Zhou
RE: Access voxels code!
In our plugin interface, you can use NeuronTree
getSWC(v3dhandle image_window) to get the information of your
reconstruction, which is a NeuronTree struct. And you can
use Image4DSimple * getImage(v3dhandle image_window) to get
the information of your image. which is a Image4DSimple class.
Plugin API: https://github.com/Vaa3D/Vaa3D_Wiki/wiki/PluginAPI.wiki
/Users/zhiz/Documents/work/v3d/v3d_external/v3d_main/basic_c_fun/basic_surf_objs.cpp
Originally posted by Marouane Benmoussa:
Plugin API: https://github.com/Vaa3D/Vaa3D_Wiki/wiki/PluginAPI.wiki
/Users/zhiz/Documents/work/v3d/v3d_external/v3d_main/basic_c_fun/basic_surf_objs.cpp
Originally posted by Marouane Benmoussa:
ok , now in your Code wich class that can allow
me to access the voxels of my 3d reconstructions...?
Dec 4, 2018 03:12 PM | Marouane Benmoussa - Burgundy university
RE: Access voxels code!
hey ,
the plug in list i have is empty i dont know why ..even though i did exactly everything written in how to bbuild on linux section ! what can i do to get plugins
the plug in list i have is empty i dont know why ..even though i did exactly everything written in how to bbuild on linux section ! what can i do to get plugins
Dec 5, 2018 06:12 PM | Zhi Zhou
RE: Access voxels code!
You can check a number
of examples
in vaa3d_tools/released_plugins/v3d_plugins folder.
Originally posted by Marouane Benmoussa:
Originally posted by Marouane Benmoussa:
hey ,
the plug in list i have is empty i dont know why ..even though i did exactly everything written in how to bbuild on linux section ! what can i do to get plugins
the plug in list i have is empty i dont know why ..even though i did exactly everything written in how to bbuild on linux section ! what can i do to get plugins