unrolling a z-stack

[Elizabeth Crowell]

Dear ImageJ experts,

I am taking images of fibers that occur on the periphery of cells, and acquiring
z-stacks of the entire cell.  The cells are roughly cylindrical.
For visualization purposes, it would be useful to virtually slice open these
cells and unroll them so that I can see the fibers on every face of the
cylinder in the same plane.
Is there a means of doing this?  Has anyone encountered this issue before?

Segmentation of the cells should not be a problem, since I can simply delete the
signal outside of the cells in each slice.  (This does not need to be a
high-through-put procedure.)

Thank you in advance for your ideas...

Sincerely,

Elizabeth Crowell
Laboratoire de Biologie Cellulaire
INRA / Institut Jean-Pierre Bourgin
Route de Saint-Cyr
78026 Versailles cedex
FRANCE

Tel: [phone]
Fax: [phone]

[Bill Mohler]

I would suggest rotating projections around the y-axis
(Image>Stack>3dProject), followed by cropping to a small central region
for each projection image, and then use of some sort of stitching
software to build the whole "panorama".

There is a whole field of panoramic photographic rendering that also has
listservs that might help with the stitching details.  There may also be
ImageJ plugins to do the work.

Elizabeth Crowell wrote:

> Dear ImageJ experts,
>
> I am taking images of fibers that occur on the periphery of cells, and acquiring
> z-stacks of the entire cell.  The cells are roughly cylindrical.
> For visualization purposes, it would be useful to virtually slice open these
> cells and unroll them so that I can see the fibers on every face of the
> cylinder in the same plane.
> Is there a means of doing this?  Has anyone encountered this issue before?
>
> Segmentation of the cells should not be a problem, since I can simply delete the
> signal outside of the cells in each slice.  (This does not need to be a
> high-through-put procedure.)
>
> Thank you in advance for your ideas...
>
> Sincerely,
>
> Elizabeth Crowell
> Laboratoire de Biologie Cellulaire
> INRA / Institut Jean-Pierre Bourgin
> Route de Saint-Cyr
> 78026 Versailles cedex
> FRANCE
>
> Tel: [phone]
> Fax: [phone]
>
>  

--
William A. Mohler
Associate Professor
Dept. of Genetics and Developmental Biology
University of Connecticut Health Center
MC-3301
263 Farmington Ave.
Farmington, CT   06030-3301

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*Mobile: [phone]*
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skype: wmohler

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P Think before you print

[Julian Cooper]

Hi Elizabeth,

If I understand your problem correctly you can achieve this with the Radial
Reslice plugin:

http://rsb.info.nih.gov/ij/plugins/radial-reslice/index.html

Start with a line selection with the initial end on the centre of the cell
and use the plugin to rotate 360° about that end. This will give you a stack
of slices of the cell rotated about the centre. If you reslice
(Image>Stacks>Reslice or press '/') this resulting stack from the right or
left the peripheral fibres should be displayed in the stack as you require.
I use this technique to "unroll" cylindrical bones to visualise the pattern
of a fracture or non-union.

I hope this helps.

Kind regards,

Julian

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On
> Behalf Of Elizabeth Crowell
> Sent: 15 October 2009 16:26
> To: [hidden email]
> Subject: unrolling a z-stack
>
>
> Dear ImageJ experts,
>
> I am taking images of fibers that occur on the periphery of
> cells, and acquiring
> z-stacks of the entire cell.  The cells are roughly cylindrical.
> For visualization purposes, it would be useful to virtually
> slice open these
> cells and unroll them so that I can see the fibers on every
> face of the
> cylinder in the same plane.
> Is there a means of doing this?  Has anyone encountered this
> issue before?
>
> Segmentation of the cells should not be a problem, since I
> can simply delete the
> signal outside of the cells in each slice.  (This does not
> need to be a
> high-through-put procedure.)
>
> Thank you in advance for your ideas...
>
> Sincerely,
>
> Elizabeth Crowell
> Laboratoire de Biologie Cellulaire
> INRA / Institut Jean-Pierre Bourgin
> Route de Saint-Cyr
> 78026 Versailles cedex
> FRANCE
>
> Tel: [phone]
> Fax: [phone]
>