Z stacks merging the image slices into one

[bluebug]

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Hello All

I would greatly appreciate if someone could suggest a method to merge the
slices from a z-stack into just one image? Is it possible to do this with
image J?


Thank you

[Tim Feinstein-2]

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Hi Caroline,

It sounds like you want to do a maximum intensity projection of your stack.  In ImageJ, you can just go to the 'Image' menu and select 'Z project…' and select maximum intensity.  If you want to get (a lot) more complicated you can see this discussion on the listserv:

http://confocal-microscopy-list.588098.n2.nabble.com/template/NamlServlet.jtp?macro=search_page&node=588098&query=smartass+projection&days=0

However, basic maximum intensity projection ought to fit your needs.  

cheers,


TF

Timothy Feinstein, PhD
Visiting Research Associate
Laboratory for GPCR Biology
Dept. of Pharmacology & Chemical Biology
University of Pittsburgh, School of Medicine
BST W1301, 200 Lothrop St.
Pittsburgh, PA  15261

On Jan 18, 2013, at 10:00 AM, bluec wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello All
>
> I would greatly appreciate if someone could suggest a method to merge the
> slices from a z-stack into just one image? Is it possible to do this with
> image J?
>
>
> Thank you

[Neil Kad]

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Use the reslice tool, and then you'll have to choose how to put them together, its fairly straighforward press '/' on the keyboard.

Cheers

Neil

> Date: Fri, 18 Jan 2013 09:00:07 -0600
> From: [hidden email]
> Subject: Z stacks merging the image slices into one
> To: [hidden email]
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello All
>
> I would greatly appreciate if someone could suggest a method to merge the
> slices from a z-stack into just one image? Is it possible to do this with
> image J?
>
>
> Thank you

     

[bluebug]

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Thanks very much everyone for the helpful comments and the links to other
threads. Reliable as always

Cheers
Caroline

[Shane van Breda]

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Hi Caroline,

Yes, you can do this. I have published an article where I used that
algorithm in ImageJ.

Here is my reference:

Van Breda, S. V., van der Merwe, C. F., Robbertse, H., & Apostolides, Z.
(2012). Immunohistochemical localization of caffeine in young Camellia
sinensis (L.) O. Kuntze (tea) leaves. Planta, 1-10.

The reference of the algorithm is:

Forster B, D van de Ville, J Berent, D Sage, M Unser (2004) Complex wavelets
for extended
depth-of-field: a new method for the fusion of multichannel microscopy
images. Microsc Res
Techniq 65:33-42

Or search for EDF (extended depth of field). Hope this helps.

Regards,

Shane

----- Original Message -----
From: "bluec" <[hidden email]>
To: <[hidden email]>
Sent: Friday, January 18, 2013 5:00 PM
Subject: Z stacks merging the image slices into one


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To join, leave or search the confocal microscopy listserv, go to:
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Hello All

I would greatly appreciate if someone could suggest a method to merge the
slices from a z-stack into just one image? Is it possible to do this with
image J?


Thank you


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