Processing a 3D image

[Martin Mendelson]

  ImageJ is a new tool for me and I'm still trying to figure it out.

  I'm up against a problem I can't find a solution to in the documentation.

  I have some cylindrical shaped tissue specimens mounted on slides under cover slips. The pressure of the cover slips has flattened the cylinder shapes so that when I view them in 3D Viewer they look like pancakes seen side on.

  Thus my question: is there a way to render the 3D image with the Z-axis expanded? It seems to me that the data are there that would allow a reasonable fidelity to the original if the Z expansion was not excessive.

  Thanks much.

  mm


Martin Mendelson, M.D., Ph.D.
Clinical Professor, Health Services
School of Public Health
University of Washington, Seattle
Visiting Fellow
School of Biological Sciences
University of Bristol, U.K.

PH: 41 22 75 85 848

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[Christine Labno-2]

Hi Martin,

You could expand your z-axis by altering the voxel depth in Image --> Properties.  Voxel depth generally = step size from image collection, but expanding it a bit will do what you want.

Best,
Christine
--------------------------------------------
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
[phone] (phone)

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Martin Mendelson [[hidden email]]
Sent: Wednesday, September 25, 2013 10:50 AM
To: [hidden email]
Subject: Processing a 3D image

  ImageJ is a new tool for me and I'm still trying to figure it out.

  I'm up against a problem I can't find a solution to in the documentation.

  I have some cylindrical shaped tissue specimens mounted on slides under cover slips. The pressure of the cover slips has flattened the cylinder shapes so that when I view them in 3D Viewer they look like pancakes seen side on.

  Thus my question: is there a way to render the 3D image with the Z-axis expanded? It seems to me that the data are there that would allow a reasonable fidelity to the original if the Z expansion was not excessive.

  Thanks much.

  mm


Martin Mendelson, M.D., Ph.D.
Clinical Professor, Health Services
School of Public Health
University of Washington, Seattle
Visiting Fellow
School of Biological Sciences
University of Bristol, U.K.

PH: 41 22 75 85 848

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[dscho]

Hi Martin,

On Wed, 25 Sep 2013, Martin Mendelson wrote:

>   I have some cylindrical shaped tissue specimens mounted on slides
>   under cover slips. The pressure of the cover slips has flattened the
>   cylinder shapes so that when I view them in 3D Viewer they look like
>   pancakes seen side on.
>
>   Thus my question: is there a way to render the 3D image with the
>   Z-axis expanded? It seems to me that the data are there that would
>   allow a reasonable fidelity to the original if the Z expansion was not
>   excessive.

The 3D Viewer heeds the pixel calibration: just click on
Image>Properties... or hit Control+Shift+P and change the "voxel depth"
(it is actually better to think about it as the distance between two
neighboring pixels with the same x,y coordinate, but the term "voxel
depth" is so common these days).

After that, you will have to re-open the image in the 3D Viewer.

Ciao,
Johannes

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