aligning slices in a stack

[Glen MacDonald]

Is there a plugin for image stacks that will allow nudging a range of slices in x and y?

My confocal has an odd problem where the stack shifts a few pixels at about 400 µm into the volume,
then shifts again about every 30 to 120 µm after that.   Until this gets tracked down a fixed, I need to  
realign some datasets.  

thanks,
Glen

[Joel Sheffield]

Try the Turboreg plugin.

Joel

---- Original message ----
>Date: Tue, 27 Mar 2007 10:53:53 -0800
>From: Glen MacDonald <[hidden email]>  
>Subject: aligning slices in a stack  
>To: [hidden email]
>
>Is there a plugin for image stacks that will allow nudging a
range of slices in x and y?
>
>My confocal has an odd problem where the stack shifts a few
pixels at about 400 µm into the volume,
>then shifts again about every 30 to 120 µm after that.  
Until this gets tracked down a fixed, I need to  
>realign some datasets.  
>
>thanks,
>Glen

Joel B. Sheffield
Professor, Department of Biology
Temple University
Philadelphia, PA 19122
[hidden email]
http://astro.temple.edu/~jbs

[NeLaS]

Glen,

You can also try with stackreg
<http://bigwww.epfl.ch/thevenaz/stackreg/>plugin which does recursive
alignment, and it is very practical to use. It
is necessary to have turboreg
<http://bigwww.epfl.ch/thevenaz/turboreg/>installed, so you may try
both :-)

bruno


--
Bruno C. Vellutini
organelas.com

Centro de Biologia Marinha (CEBIMar)
Universidade de São Paulo
Av. Manoel H. do Rego km 131,5
11600-000 São Sebastião, SP, Brasil
http://www.usp.br/cbm/

[Jim Murray]

Can you help me fix a problem I am having with ImageJ on a Mac?  When  
I draw a scale bar and try to set the scale by typing the Known  
Distance into the dialog box, the box won't change.  The numbers in  
them are frozen and can't be edited.

I've tried deleting the prefs.

Using v. 1.3.1, but also tried 1.3.7.  Running MacOS 10.4.8.

I am running v 1.3.2 on a different computer running OS 10.4.9 and it  
works fine.

thanks


James A. Murray
Assoc. Prof., Department of Biology
156 Lewis Science Center
University of Central Arkansas
Conway, AR  72035
PH: 501-450-5923
FAX: [phone]
mailto:[hidden email]
http://www.uca.edu/biology/faculty_details_comp.php?user_id=28

[Wayne Rasband]

ImageJ 1.38, available at <http://rsb.info.nih.gov/ij/notes.html>,
fixes a bug on Intel Macs that sometimes prevents numeric fields in
dialog boxes from being edited. Here is the note about this problem
from the News page.

     1.38j, 12 February 2007
         Thanks to Robert Dougherty, worked around a bug that
         sometimes  caused the first numeric field in a dialog box
         to not be editable on Intel Macs.

-wayne

On Mar 27, 2007, at 11:28 PM, Jim Murray wrote:

> Can you help me fix a problem I am having with ImageJ on a Mac?  When
> I draw a scale bar and try to set the scale by typing the Known
> Distance into the dialog box, the box won't change.  The numbers in
> them are frozen and can't be edited.
>
> I've tried deleting the prefs.
>
> Using v. 1.3.1, but also tried 1.3.7.  Running MacOS 10.4.8.
>
> I am running v 1.3.2 on a different computer running OS 10.4.9 and it
> works fine.
>
> thanks
>
>
> James A. Murray
> Assoc. Prof., Department of Biology
> 156 Lewis Science Center
> University of Central Arkansas
> Conway, AR  72035
> PH: 501-450-5923
> FAX: [phone]
> mailto:[hidden email]
> http://www.uca.edu/biology/faculty_details_comp.php?user_id=28
>

[Frederic V. Hessman]

For those who haven't downloaded the latest version, you can get  
around it by simply tabbing through once and trying again.

Rick

On 29 Mar 2007, at 6:56 pm, Wayne Rasband wrote:

> ImageJ 1.38, available at <http://rsb.info.nih.gov/ij/notes.html>,  
> fixes a bug on Intel Macs that sometimes prevents numeric fields in  
> dialog boxes from being edited. Here is the note about this problem  
> from the News page.
>
>     1.38j, 12 February 2007
>         Thanks to Robert Dougherty, worked around a bug that
>         sometimes  caused the first numeric field in a dialog box
>         to not be editable on Intel Macs.
>
> -wayne
>
> On Mar 27, 2007, at 11:28 PM, Jim Murray wrote:
>
>> Can you help me fix a problem I am having with ImageJ on a Mac?  
>> When I draw a scale bar and try to set the scale by typing the  
>> Known Distance into the dialog box, the box won't change.  The  
>> numbers in them are frozen and can't be edited.
>>
>> I've tried deleting the prefs.
>>
>> Using v. 1.3.1, but also tried 1.3.7.  Running MacOS 10.4.8.
>>
>> I am running v 1.3.2 on a different computer running OS 10.4.9 and  
>> it works fine.
>>
>> thanks
>>
>>
>> James A. Murray
>> Assoc. Prof., Department of Biology
>> 156 Lewis Science Center
>> University of Central Arkansas
>> Conway, AR  72035
>> PH: 501-450-5923
>> FAX: [phone]
>> mailto:[hidden email]
>> http://www.uca.edu/biology/faculty_details_comp.php?user_id=28
>>

------------------------------------------------------------------------
------------------------
Dr. Frederic V. Hessman     [hidden email]
Institut für Astrophysik          Tel.  [phone]
Friedrich-Hund-Platz 1         Fax [phone]
37077 Goettingen                 Room F04-133
http://www.Astro.physik.Uni-Goettingen.de/~hessman
------------------------------------------------------------------------
-------------------------
MONET: a MOnitoring NEtwork of Telescopes
http://monet.Uni-Goettingen.de
------------------------------------------------------------------------
-------------------------