Voxel depth 3D viewer

[Adam Buttress]

Hi,

I have created a 3D image in 3D viewer from a stack and set the spacing along the z-axis using the voxel depth.

How do I 'fill-in' the voxels so that fractures in my specimen image are solid, rather than the 3d image looking like a set of 2d images layered on top of each other with a particular spacing??

Many thanks Adam.

Adam Buttress
Postgraduate Researcher
Nottingham Transportation Engineering Centre (NTEC)
The University of Nottingham
University Park
Nottingham
NG7 2RD
Mob: [phone]
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[samjlord]

You can interpolate data between z-planes to fill in between slices. One option is to use the Image->Stacks->Reslice command and insert the correct voxel dimensions. This will effectively rotate the stack and interpolate the data so the voxels are square. Then you can render the image using the 3D viewer.

Another option is the plugin Interactive Stack Rotation:
http://fiji.sc/wiki/index.php/Interactive_Stack_Rotation

After you select the plugin from the menu, simply hit the return key and the data is automatically interpolated.

I don't really know the algorithms that either of these commands use to interpolate the data, so be wary if you are performing quantitative measurements.

Maybe a future version of the 3D Viewer will have a checkbox and have the ability to interpolate the data itself.

-Sam

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[Stephan Saalfeld]

Hi,

[...]

> I don't really know the algorithms that either of these commands use
> to interpolate the data, so be wary if you are performing quantitative
> measurements.
>

Interactive Stack Rotation uses tri-linear interpolation.  So in case
that the stack is not rotated, slices are linearly interpolated.

Best,
Stephan

> Maybe a future version of the 3D Viewer will have a checkbox and have the ability to interpolate the data itself.
>
> -Sam
>
> _______________________________________________________
>
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Adam Buttress]

Hi Sam,

Many thanks. The first option seems to work well.

Adam.

Adam Buttress
Postgraduate Researcher
Nottingham Transportation Engineering Centre (NTEC)
The University of Nottingham
University Park
Nottingham
NG7 2RD
Mob: [phone]
________________________________________
From: Sam Lord [[hidden email]]
Sent: Sunday, June 03, 2012 6:45 AM
To: [hidden email]; Adam Buttress
Subject: Re: Voxel depth 3D viewer

You can interpolate data between z-planes to fill in between slices. One option is to use the Image->Stacks->Reslice command and insert the correct voxel dimensions. This will effectively rotate the stack and interpolate the data so the voxels are square. Then you can render the image using the 3D viewer.

Another option is the plugin Interactive Stack Rotation:
http://fiji.sc/wiki/index.php/Interactive_Stack_Rotation

After you select the plugin from the menu, simply hit the return key and the data is automatically interpolated.

I don't really know the algorithms that either of these commands use to interpolate the data, so be wary if you are performing quantitative measurements.

Maybe a future version of the 3D Viewer will have a checkbox and have the ability to interpolate the data itself.

-SamThis message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it.   Please do not use, copy or disclose the information contained in this message or in any attachment.  Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.
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