draw or delete pixels of images in a stack

[aget]

Hi, could anyone give advice about editing images, like deleting some areas, or draw something, in an image 3D stack? i want to manually clean some unrelated noise in it and make a better 3D. Thanks.

[Thomas Boudier]

Hi,

A nice way for doing that is to use 3Dviewer :

select your stack in the 3dviewer
get the right orientation
select the freehand selection tool
draw the part you want to remove
use "fill selection" in 3dviewer

Thomas


Le 18/10/2012 10:49, aget a écrit :

> Hi, could anyone give advice about editing images, like deleting some areas,
> or draw something, in an image 3D stack? i want to manually clean some
> unrelated noise in it and make a better 3D. Thanks.
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/draw-or-delete-pixels-of-images-in-a-stack-tp5000436.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan-2]

I need to manually align (no - auto alignment won't work) THREE images (A,B,C).  Aligning B to A, and then aligning C to A,
will work just fine (in version 2 I might want to align both B and C to A at the same time…but, one step at a time).

My plan is to display A and B and provide controls to: a) move/rotate B and b) use a slider to cross fade between A and B to check the alignment.

When done, all I want (for now) is to write out a 3x3 matrix representing the transformation to apply to B to align it with A.

[I may eventually want to deal with non-rigid-body transformations…but later, much later]

So - who has a plugin that does this, or something like it, or something else that uses the same basic tools (move an image around wrt a second image, crossfade slider).

I'll be in Mondorf Wednesday-Sunday.  I hereby offer a beer to the best response!

I'm on the road (mostly in the air) starting tomorrow (Friday) - but I'll be reading e-mail and here.  

--
Kenneth Sloan
[hidden email]
 
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stephan Saalfeld]

Hi Ken,

have you tried TrakEM2?  It's in Fiji and here is a nice screencast for
how to do manual alignment:

http://www.youtube.com/watch?v=ImiMTkfKlno&feature=youtu.be

You can get the affine matrix through Fiji's Beanshell interpreter.
Select the aligned image and execute:

Display.getFront().getActive().getAffineTransform();

Best,
Stephan




On Thu, 2012-10-18 at 19:22 -0500, Kenneth Sloan wrote:

> I need to manually align (no - auto alignment won't work) THREE images (A,B,C).  Aligning B to A, and then aligning C to A,
> will work just fine (in version 2 I might want to align both B and C to A at the same time…but, one step at a time).
>
> My plan is to display A and B and provide controls to: a) move/rotate B and b) use a slider to cross fade between A and B to check the alignment.
>
> When done, all I want (for now) is to write out a 3x3 matrix representing the transformation to apply to B to align it with A.
>
> [I may eventually want to deal with non-rigid-body transformations…but later, much later]
>
> So - who has a plugin that does this, or something like it, or something else that uses the same basic tools (move an image around wrt a second image, crossfade slider).
>
> I'll be in Mondorf Wednesday-Sunday.  I hereby offer a beer to the best response!
>
> I'm on the road (mostly in the air) starting tomorrow (Friday) - but I'll be reading e-mail and here.  
>
> --
> Kenneth Sloan
> [hidden email]
>  
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kenneth Sloan-2]

I'll check it out - thanks.

--
Kenneth Sloan
[hidden email]



On Oct 19, 2012, at 1:50 , Stephan Saalfeld wrote:

> Hi Ken,
>
> have you tried TrakEM2?  It's in Fiji and here is a nice screencast for
> how to do manual alignment:
>
> http://www.youtube.com/watch?v=ImiMTkfKlno&feature=youtu.be
>
> You can get the affine matrix through Fiji's Beanshell interpreter.
> Select the aligned image and execute:
>
> Display.getFront().getActive().getAffineTransform();
>
> Best,
> Stephan
>
>
>
>
> On Thu, 2012-10-18 at 19:22 -0500, Kenneth Sloan wrote:
>> I need to manually align (no - auto alignment won't work) THREE images (A,B,C).  Aligning B to A, and then aligning C to A,
>> will work just fine (in version 2 I might want to align both B and C to A at the same time…but, one step at a time).
>>
>> My plan is to display A and B and provide controls to: a) move/rotate B and b) use a slider to cross fade between A and B to check the alignment.
>>
>> When done, all I want (for now) is to write out a 3x3 matrix representing the transformation to apply to B to align it with A.
>>
>> [I may eventually want to deal with non-rigid-body transformations…but later, much later]
>>
>> So - who has a plugin that does this, or something like it, or something else that uses the same basic tools (move an image around wrt a second image, crossfade slider).
>>
>> I'll be in Mondorf Wednesday-Sunday.  I hereby offer a beer to the best response!
>>
>> I'm on the road (mostly in the air) starting tomorrow (Friday) - but I'll be reading e-mail and here.  
>>
>> --
>> Kenneth Sloan
>> [hidden email]
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html