Analysing x-z and y-z slices

[Graham Wright-5]

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Hello,

I have a Z-stack acquired on a Zeiss LSM 510 META confocal of a sample in 2 channels (single time point). I would like to be able to extract the x-z and y-z slices so that I can analyse the fluorescence intensity across them.

I have Imaris and ImageJ at my disposal. In Imaris I can get a view of these slices quite nicely and adjust the 'depth' and position of them using the Ortho Slicer and Oblique Slicer options. However I don't know how, if it is possible, to extract just these slices as images, which I can later analyse. Can anyone help. Or, does anyone know how to do it in ImageJ, or indeed another programme?

Alternatively is there a way to directly analyse a x-z or y-z frame across a 3D reconstruction, for fluorescence intensity, in any programme?

Thanks in advance for your help,

Graham

 

-----
Graham Wright
Microscopy & Imaging Facility

 

Temasek Life Sciences Laboratory
1 Research Link
National University of Singapore
Singapore 117604

 

P:    [phone]
M:   [phone]
E:     [hidden email]
W:   http://microscopy.tll.org.sg

[Julio Vazquez]

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Hi Graham, 

The imagej plugin "Reslice Plus" will convert an xyz stack into an xzy or yzx stack (that is, rotate the stack). you can then analyze the xz or yz sections as you normally would. I believe the Zeiss LSM Macro "Modify Images" might be able to do the same, but I cant be sure just from memory. 

--

Julio Vazquez

Fred Hutchinson Cancer Research Center

Seattle, WA 98109-1024

http://www.fhcrc.org/

=

On Jan 28, 2008, at 7:14 PM, Graham Wright wrote:

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Hello,

I have a Z-stack acquired on a Zeiss LSM 510 META confocal of a sample in 2 channels (single time point). I would like to be able to extract the x-z and y-z slices so that I can analyse the fluorescence intensity across them.

I have Imaris and ImageJ at my disposal. In Imaris I can get a view of these slices quite nicely and adjust the 'depth' and position of them using the Ortho Slicer and Oblique Slicer options. However I don't know how, if it is possible, to extract just these slices as images, which I can later analyse. Can anyone help. Or, does anyone know how to do it in ImageJ, or indeed another programme?

Alternatively is there a way to directly analyse a x-z or y-z frame across a 3D reconstruction, for fluorescence intensity, in any programme?

Thanks in advance for your help,

Graham

 

-----
Graham Wright
Microscopy & Imaging Facility

 

Temasek Life Sciences Laboratory
1 Research Link
National University of Singapore
Singapore 117604

 

P:    [phone]
M:   [phone]
E:     [hidden email]
W:   http://microscopy.tll.org.sg

[JOEL B. SHEFFIELD]

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In imageJ, you can use the Image>Stacks>Reslice command to cut a
vertical slice therough a line in any orientation across the x-y
plane.  You can decide how many slices you want in your new volume,
and what the spacing should be.

Joel


-------------- Original message ---------------
Date sent: Tue, 29 Jan 2008 11:14:16 +0800
Send reply to: Confocal Microscopy List
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From: Graham Wright <[hidden email]>
Subject: Analysing x-z and y-z slices
To: [hidden email]


Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-
bin/wa?S1=confocal Hello,
I have a Z-stack acquired on a Zeiss LSM 510 META confocal of a
sample in 2 channels (singletime point). I would like to be able to
extract the x-z and y-z slices so that I can analyse the fluorescence
intensity across them.
I have Imaris and ImageJ at my disposal. In Imaris I can get a view
of these slices quite nicely and adjust the 'depth' and position of
them using the Ortho Slicer and Oblique Slicer options. However I
don't know how, if it is possible, to extract just these slices as
images, which I can later analyse. Can anyone help. Or, does anyone
know how to do it in ImageJ, or indeed another programme?
Alternatively is there a way to directly analyse a x-z or y-zframe
across a 3D reconstruction, for fluorescence intensity, in any
programme?
Thanks in advance for your help,
Graham

-----
Graham Wright
Microscopy & Imaging Facility

Temasek Life Sciences Laboratory
1 Research Link
National University of Singapore
Singapore 117604

P: [phone]
M: [phone]
E: [hidden email]
W: http://microscopy.tll.org.sg

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

[Arvonn Tully]

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Commercial Response:

Dear Graham,

In Imaris, you can re-slice (XY, ZY, ZX,) the contents of a file by using the:
"Image Processing"-->"Rotate" command.
Then select the axis (X, Y, Z), and the direction.
The direction can be either clockwise or counter clockwise.

For example, if you have a set of XY images,  and you want the stack to now
a series of ZY slices with the "left being on top, you should rotate it
"clockwise" it along the Y axis.
Clockwise will put the the right side on the "top", Clockwise will put the
left side on the "top".

Once you have rotated the dataset, it should be re saved in the new
orientation for appropriate analysis.

Please let me know if you have any further questions or concerns.
Best Regards,

Arvonn Tully
Technical and Application Support
Western United States
Bitplane, Inc.
http://www.bitplane.com
[hidden email]