Re: Depth map and z scale

Posted by Tony Collins-4 on Jun 25, 2007; 2:33pm
URL: http://imagej.273.s1.nabble.com/Depth-map-and-z-scale-tp3699025p3699026.html

Hi Orkun,

There's the 'Z-coded stack' plugin included with MBF_ImageJ (I can email you off list with the plugin alone if required.
http://www.macbiophotonics.ca/imagej/z.htm#z_code 

You don't need to scale using this plugin.

For the labelling, this is a good example of thinking about your third dimension!
For a 3D dataset we usually we have x and y and then maybe z or t. So for example to get an intensity vs Time plot we use the Z-axis profiler function. For you to label your slices with the Z-position you could use the
"Time stamper" function specify the unit to be microns (µ = NumPad+230).
http://www.macbiophotonics.ca/imagej/annotating_images.htm#annotate_stamps
http://rsb.info.nih.gov/ij/plugins/stamper.html 

Regards,

Tony

Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Orkun Ersoy
> Sent: June 25, 2007 6:30 AM
> To: [hidden email]
> Subject: Depth map and z scale
>
> Hi All,
> I have a stack involving images taken by serial grinding and polishing
> (method in Chinga et al., 2004---Thanks Gary for this paper).
> For instance the thickness of each layer is 1 microns. I scaled the
> stack using Image/Properties and now have a z value equal to image
> number in stack.
> However, how can I create a depth map including the z value at each
> point?
> Best regards
>
> Res. Assist. Orkun ERSOY (MSc)
> Hacettepe University
> Department of Geological Engineering
> Beytepe Ankara Turkey
> [phone] / 126
>