Determining the profile of an uneven surface in an XYZ data stack

[oojeyboojey]

Hi,

I've seen a couple of old posts that ask similar questions to this, but there weren't any solutions posted. I hope you can help!

I have obtained three-dimensional (xyz) image stacks of a piece of tissue. The brightest signal is detected at the tissue surface. Above the tissue is air, which yields a very low signal. The surface of the tissue is uneven.

How can I determine the z-coordinate of the tissue surface for each xy position?

Thanks for your help!

[Pariksheet Nanda]

On Thu, Sep 6, 2012 at 7:09 AM, oojeyboojey <[hidden email]> wrote:
> I have obtained three-dimensional (xyz) image stacks of a piece of tissue.
> The brightest signal is detected at the tissue surface. Above the tissue is
> air, which yields a very low signal. The surface of the tissue is uneven.
>
> How can I determine the z-coordinate of the tissue surface for each xy
> position?

If I understand correctly, the problem you're having is you open your
dataset in ImageJ and it appears as a stack with the image leaves
ordered by Time only (which ImageJ does by default), and what you'd
like to do is open your image as a Hyperstack so that you can navigate
independently over Z and Time.

Try import your data using the Bio-formats plugin.
If you are using FIJI, this plugin is included

If you have ImagJ, here are download and usage instructions:
http://loci.wisc.edu/bio-formats/imagej
Usage in section 8.2:
http://www.openmicroscopy.org/site/support/training/training-documents/imagej

Pariksheet

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[oojeyboojey]

Hi Pariksheet,

Thanks for your reply. Actually, time is not a variable in my data set. I have a data stack (each slice of which was taken at effectively the same time) that is three dimensional in the x, y and z spatial axes. It's a chunk of wrinkled biological tissue that I want to find the surface of. So, for each x,y coordinate I want to return a z value (i.e. slice number) for the maximum intensity.

I will take a look at the links you've provided and see if there's anything there that can help.

[David Hovis]

You might look at TopoJ, which is included in FIJI these days.  It is under the Analyze menu.  

http://fiji.sc/wiki/index.php/TopoJ


On Sep 12, 2012, at 9:39 AM, oojeyboojey wrote:

> Hi Pariksheet,
>
> Thanks for your reply. Actually, time is not a variable in my data set. I
> have a data stack (each slice of which was taken at effectively the same
> time) that is three dimensional in the x, y and z spatial axes. It's a chunk
> of wrinkled biological tissue that I want to find the surface of. So, for
> each x,y coordinate I want to return a z value (i.e. slice number) for the
> maximum intensity.
>
> I will take a look at the links you've provided and see if there's anything
> there that can help.
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Determining-the-profile-of-an-uneven-surface-in-an-XYZ-data-stack-tp4999960p5000031.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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