two user questions about TrakEM2

[Ignacio Arganda-Carreras]

Hello Albert,

Some TrakEM2 users made me a couple of questions that you can probably
answer fast:

1) Is there a non-programmatic way of importing new images into a TrakEM2
project into existing layers and apply to them the same transforms that the
images in those layers have? The idea is to align one channel of the
dataset and then import the other channels on top.

2) Is it possible to make objects like "balls" visible from other layers
than the one where they were added?

Thanks a lot!

ignacio

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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

[Albert Cardona-2]

2013/3/22 Ignacio Arganda-Carreras <[hidden email]>

> Hello Albert,
>
> Some TrakEM2 users made me a couple of questions that you can probably
> answer fast:
>
> 1) Is there a non-programmatic way of importing new images into a TrakEM2
> project into existing layers and apply to them the same transforms that the
> images in those layers have? The idea is to align one channel of the
> dataset and then import the other channels on top.
>

I would do it with a script: there are plenty of details on applying
transforms to images here:
http://fiji.sc/wiki/index.php/TrakEM2_Scripting

See as well the API for the Patch class, which has methods for copying and
setting the affine and coordinate transforms (non-linear transforms are
expressed with coordinate transforms):
http://repo.or.cz/w/trakem2.git/blob/HEAD:/TrakEM2_/src/main/java/ini/trakem2/display/Patch.java



>
> 2) Is it possible to make objects like "balls" visible from other layers
> than the one where they were added?
>

Yes: if the ball radius is large enough, it will show into adjacent
sections in red and blue (before and after). To enable this, right-click
and choose "Display - Properties", and increase the "layers to color cue"
from the default of 0 to any number, like e.g. 1 to see only in the next
and previous.


>
> Thanks a lot!
>


You are welcome.

Albert


--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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

[Ignacio Arganda-Carreras]

That was very helpful!

Thanks again!

ignacio

On Fri, Mar 22, 2013 at 2:57 PM, Albert Cardona <[hidden email]> wrote:

> 2013/3/22 Ignacio Arganda-Carreras <[hidden email]>
>
>> Hello Albert,
>>
>> Some TrakEM2 users made me a couple of questions that you can probably
>> answer fast:
>>
>> 1) Is there a non-programmatic way of importing new images into a TrakEM2
>> project into existing layers and apply to them the same transforms that the
>> images in those layers have? The idea is to align one channel of the
>> dataset and then import the other channels on top.
>>
>
>
>
> I would do it with a script: there are plenty of details on applying
> transforms to images here:
> http://fiji.sc/wiki/index.php/TrakEM2_Scripting
>
> See as well the API for the Patch class, which has methods for copying and
> setting the affine and coordinate transforms (non-linear transforms are
> expressed with coordinate transforms):
>
> http://repo.or.cz/w/trakem2.git/blob/HEAD:/TrakEM2_/src/main/java/ini/trakem2/display/Patch.java
>
>
>
>>
>> 2) Is it possible to make objects like "balls" visible from other layers
>> than the one where they were added?
>>
>
> Yes: if the ball radius is large enough, it will show into adjacent
> sections in red and blue (before and after). To enable this, right-click
> and choose "Display - Properties", and increase the "layers to color cue"
> from the default of 0 to any number, like e.g. 1 to see only in the next
> and previous.
>
>
>>
>> Thanks a lot!
>>
>
>
> You are welcome.
>
> Albert
>
>
> --
> http://albert.rierol.net
> http://www.ini.uzh.ch/~acardona/

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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