new bUnwarpJ release (consistent elastic image registration)

[Ignacio Arganda Carreras]

Dear all,

I just uploaded a new version of bUnwarpJ on the site:

http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/

It comes with a new set of options,  you can now
- load masks from files.
- evaluate the initial similarity between images.
- load affine transformations as starting point for the algorihtm.
- use the result of automatic landmark detections such as MOPS and SIFT
(see
http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/#SIFT_and_MOPS_plugin_support_)

bUnwarpJ and SplineDeformationGenerator are now integrated in Fiji:

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

Hope you'll enjoy it! All feedback will be appreciated!

cheers!

ignacio

PS: SplineDeformationGenerator has also a new version so it can run on
Fiji, but there is no important changes in the code:
http://biocomp.cnb.csic.es/%7Eiarganda/SplineDeformationGenerator/


--
Ignacio Arganda-Carreras
Escuela Politécnica Superior
Laboratorio B-408     Phone: [phone]
Universidad Autónoma de Madrid
Ctra. de Colmenar Viejo, Km. 15
Madrid 28049,  Spain

E-mail: [hidden email]
Website: http://www.ii.uam.es/~iarganda

[lechristophe]

By the way, does this mean that Fiji is public now ? I did not see any
announcement on this list, and I was waiting since Albert Cardona
teased us one month ago.
I'll download it and try it right away.

Christophe

On Fri, Jun 13, 2008 at 16:36, Ignacio Arganda Carreras
<[hidden email]> wrote:

> Dear all,
>
> I just uploaded a new version of bUnwarpJ on the site:
>
> http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/
>
> It comes with a new set of options,  you can now
> - load masks from files.
> - evaluate the initial similarity between images.
> - load affine transformations as starting point for the algorihtm.
> - use the result of automatic landmark detections such as MOPS and SIFT (see
> http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/#SIFT_and_MOPS_plugin_support_)
>
> bUnwarpJ and SplineDeformationGenerator are now integrated in Fiji:
>
> http://pacific.mpi-cbg.de/wiki/index.php/Main_Page
>
> Hope you'll enjoy it! All feedback will be appreciated!
>
> cheers!
>
> ignacio
>
> PS: SplineDeformationGenerator has also a new version so it can run on Fiji,
> but there is no important changes in the code:
> http://biocomp.cnb.csic.es/%7Eiarganda/SplineDeformationGenerator/
>
>
> --
> Ignacio Arganda-Carreras
> Escuela Politécnica Superior
> Laboratorio B-408     Phone: [phone]
> Universidad Autónoma de Madrid
> Ctra. de Colmenar Viejo, Km. 15
> Madrid 28049,  Spain
>
> E-mail: [hidden email]
> Website: http://www.ii.uam.es/~iarganda
>

[Ignacio Arganda Carreras]

Hehehe, Fiji has to be a little bit more in the darkness :D You can use
it though by "git-pulling" but don't download the packages yet.

ignacio

Christophe Leterrier wrote:

> By the way, does this mean that Fiji is public now ? I did not see any
> announcement on this list, and I was waiting since Albert Cardona
> teased us one month ago.
> I'll download it and try it right away.
>
> Christophe
>
> On Fri, Jun 13, 2008 at 16:36, Ignacio Arganda Carreras
> <[hidden email]> wrote:
>  
>> Dear all,
>>
>> I just uploaded a new version of bUnwarpJ on the site:
>>
>> http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/
>>
>> It comes with a new set of options,  you can now
>> - load masks from files.
>> - evaluate the initial similarity between images.
>> - load affine transformations as starting point for the algorihtm.
>> - use the result of automatic landmark detections such as MOPS and SIFT (see
>> http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/#SIFT_and_MOPS_plugin_support_)
>>
>> bUnwarpJ and SplineDeformationGenerator are now integrated in Fiji:
>>
>> http://pacific.mpi-cbg.de/wiki/index.php/Main_Page
>>
>> Hope you'll enjoy it! All feedback will be appreciated!
>>
>> cheers!
>>
>> ignacio
>>
>> PS: SplineDeformationGenerator has also a new version so it can run on Fiji,
>> but there is no important changes in the code:
>> http://biocomp.cnb.csic.es/%7Eiarganda/SplineDeformationGenerator/
>>
>>
>> --
>> Ignacio Arganda-Carreras
>> Escuela Politécnica Superior
>> Laboratorio B-408     Phone: [phone]
>> Universidad Autónoma de Madrid
>> Ctra. de Colmenar Viejo, Km. 15
>> Madrid 28049,  Spain
>>
>> E-mail: [hidden email]
>> Website: http://www.ii.uam.es/~iarganda
>>
>>    
>
>
>
>  

--
Ignacio Arganda-Carreras
Escuela Politécnica Superior
Laboratorio B-408     Phone: [phone]
Universidad Autónoma de Madrid
Ctra. de Colmenar Viejo, Km. 15
Madrid 28049,  Spain

E-mail: [hidden email]
Website: http://www.ii.uam.es/~iarganda

[Gabriel Landini]

> >> I just uploaded a new version of bUnwarpJ on the site:
> >>
> >> http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/

That is great, thank you. Unfortunately it gives an error of "wrong version"
if run under Java 1.5.0. linux. I guess that this was compiled under 1.6.0?

Java 1.6.0 linux has a bug that delays anything that requires showing a dialog
(unless one is running gnome, I think).
This problem is also happening in the latest fiji. :-(

Regards

Gabriel

[dscho]

Hi,

On Fri, 13 Jun 2008, Christophe Leterrier wrote:

> By the way, does this mean that Fiji is public now ? I did not see any
> announcement on this list, and I was waiting since Albert Cardona teased
> us one month ago.

Heh.

> I'll download it and try it right away.

Please be aware that this is a pre-release as of now... I know, we lag
behind a month and 12 days, but we really do not want to give users a bad
experience on their first try.  And the goal _is_ high: make installation
painless.

Ciao,
Dscho

[Ignacio Arganda Carreras]

OK, now you should be able to run it under Java 1.5. Thanks for the
feedback!

Fiji is all compiled with 1.5.0 though...

Cheers!

ignacio

Gabriel Landini wrote:

>>>> I just uploaded a new version of bUnwarpJ on the site:
>>>>
>>>> http://biocomp.cnb.csic.es/~iarganda/bUnwarpJ/
>>>>        
>
> That is great, thank you. Unfortunately it gives an error of "wrong version"
> if run under Java 1.5.0. linux. I guess that this was compiled under 1.6.0?
>
> Java 1.6.0 linux has a bug that delays anything that requires showing a dialog
> (unless one is running gnome, I think).
> This problem is also happening in the latest fiji. :-(
>
> Regards
>
> Gabriel
>
>
>
>  

--
Ignacio Arganda-Carreras
Escuela Politécnica Superior
Laboratorio B-408     Phone: [phone]
Universidad Autónoma de Madrid
Ctra. de Colmenar Viejo, Km. 15
Madrid 28049,  Spain

E-mail: [hidden email]
Website: http://www.ii.uam.es/~iarganda