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image registration

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Judy Trogadis

image registration

I am looking for a plugin for aligning serial sections. I came across a plugin - TurboReg, a collection of many CLASS files but can't find instructions for installation. It will not run by simply copying to a plugin folder. Same for StackReg (which requires TurboReg). Do other plugins exist?

In the event that I do find such a plugin, what utilities are available for further processing an aligned stack? I am hoping to manually trace outlines, fully threshold inside the traces and use VolumeJ to reconstruct objects.

I would appreciate any further suggestions.
Thank you.

Judy

Judy Trogadis
Bio-Imaging Coordinator
St. Michael's Hospital, 7Queen
30 Bond St.
Toronto, ON M5B 1W8, Canada
ph: 416-864-6060 x6337
pager: 416-685-9219
fax: 416-864-5046
[hidden email]

Joel Sheffield

Re: image registration

Hi Judy,

I have been using turbo/stackReg for some time without problems. You don't
say which operating system you are using, but in my Wondows XP, I unpack the
zip files that I download into new folders in the plugins directory. As as
a result, I now have two folders in the plugin directory --turboReg and
stackReg. What are you doing differently?

Joel

On Tue, Dec 15, 2009 at 9:26 PM, Judy Trogadis
<[hidden email]>wrote:

> I am looking for a plugin for aligning serial sections. I came across a
> plugin - TurboReg, a collection of many CLASS files but can't find
> instructions for installation. It will not run by simply copying to a plugin
> folder. Same for StackReg (which requires TurboReg). Do other plugins exist?
>
> In the event that I do find such a plugin, what utilities are available for
> further processing an aligned stack? I am hoping to manually trace outlines,
> fully threshold inside the traces and use VolumeJ to reconstruct objects.
>
> I would appreciate any further suggestions.
> Thank you.
>
> Judy
>
> Judy Trogadis
> Bio-Imaging Coordinator
> St. Michael's Hospital, 7Queen
> 30 Bond St.
> Toronto, ON M5B 1W8, Canada
> ph: 416-864-6060 x6337
> pager: 416-685-9219
> fax: 416-864-5046
> [hidden email]
>

--

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

Albert Cardona-2

Re: image registration

In reply to this post by Judy Trogadis

Hi Judie,

On Tue, Dec 15, 2009 at 9:26 PM, Judy Trogadis
<[hidden email]> wrote:
> I am looking for a plugin for aligning serial sections. I came across a plugin - TurboReg, a collection of many CLASS files but can't find instructions for installation. It will not run by simply copying to a plugin folder. Same for StackReg (which requires TurboReg). Do other plugins exist?

For Fiji, which is an ImageJ package that includes a bundle of
plugins, there's the "Virtual Stack Slice Registration", that has the
ability to register in either linear and non-linear ways:

http://pacific.mpi-cbg.de/wiki/index.php/Register_Virtual_Stack_Slices

> In the event that I do find such a plugin, what utilities are available for further processing an aligned stack? I am hoping to manually trace outlines, fully threshold inside the traces and use VolumeJ to reconstruct objects.

I suggest TrakEM2, also included in Fiji. See these video tutorials:

http://pacific.mpi-cbg.de/wiki/index.php/TrakEM2_tutorials

... and this general short introductory page:

http://pacific.mpi-cbg.de/wiki/index.php/TrakEM2

There's a documentation/manual page here:

http://t2.ini.uzh.ch/trakem2_manual.html

TrakEM2 uses the same image registration library that "Register
Virtual Stack Slices" uses, so what the latter does, the former can do
as well, even for multiple sections consisting of multi-image tile
montages.

Albert
--
http://albert.rierol.net

Judy Trogadis

Re: image registration

In reply to this post by Joel Sheffield

Hi, Joel

Using XP operating system, I did create new folders in the Plugin folder - outside ImageJ, with Windows browser, copied the files into them, however, when I opened ImageJ, I did not see the newly created folders under the Plugins. Now, I moved the files into an already existing folder and saw the TurboReg option, and will try it now.

What extra steps are required when creating a new Plugin folder?
Thanks,
Judy

>>> "JOEL B. SHEFFIELD" <[hidden email]> 12/16/2009 9:04 AM >>>
Hi Judy,

I have been using turbo/stackReg for some time without problems. You don't
say which operating system you are using, but in my Wondows XP, I unpack the
zip files that I download into new folders in the plugins directory. As as
a result, I now have two folders in the plugin directory --turboReg and
stackReg. What are you doing differently?

Joel

On Tue, Dec 15, 2009 at 9:26 PM, Judy Trogadis
<[hidden email]>wrote:

--

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

Michael Schmid

Re: image registration

Hi Judy,

it could be problem with permissions - maybe ImageJ cannot search
your first folder because the permissions do not allow it? (make also
sure that the owner is correct).
To check permissins:
Right-click on the folder and select 'Properties', then select the
'Security' tab). If you don't see a 'Security' tab, unselect the
option 'Use simple file sharing (Recommended)' in 'Advanced Settings'.

Michael
________________________________________________________________

On 16 Dec 2009, at 17:37, Judy Trogadis wrote:

> Hi, Joel
>
> Using XP operating system, I did create new folders in the Plugin
> folder - outside ImageJ, with Windows browser, copied the files
> into them, however, when I opened ImageJ, I did not see the newly
> created folders under the Plugins. Now, I moved the files into an
> already existing folder and saw the TurboReg option, and will try
> it now.
>
> What extra steps are required when creating a new Plugin folder?
> Thanks,
> Judy