Depth map and z scale

[Orkun Ersoy]

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
 

[Tony Collins-4]

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
>

[karo03]

... possibly you are looking for the macro blanket.txt from Gabriel  
Landini ?

//--------------8<-----------------
// Blanket Transform
// Implements K. Rodenacker's blanquet tranform
// where each pixel in the result represents the
// maximum slice number in which the pixel is set.
// Assumes a binary stack where image=255 and
// the background is 0.
// G. Landini 17/1/2007

run("Divide...", "stack value=255");
s=nSlices();

// run("32-bit");
for (i=2;i<=s;i++) {
  setSlice(i);
  run("Multiply...", "slice value="+i);
}
run("Z Project...", "start=1 stop=" + s + " projection=[Max  
Intensity]");
rename("blanket");
// setMinAndMax(0, s);
run("Fire");
run("Enhance Contrast", "saturated=0");
//--------------8<-----------------

Regards
Karsten

Am 25.06.2007 um 12:30 schrieb Orkun Ersoy:

> 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
>

[Christopher Coulon-2]

Hi,

I have been using Eclipse as an IDE for ImageJ and recently switched to
using Netbeans, but I have run across a problem: I am getting an out of
memory error stating that all available memory (63mb) has been used.  I used
to get this error in Eclipse with ImageJ until Volker Bäcker kindly showed
me how to increase the memory of ImageJ in Eclipse by opening the ImageJ run
configuration dialog and typing -Xms256m ­Xmx512m into the VM arguments.
Can anyone show me how to do that in Netbeans?  Thanks in advance,

Chris Coulon