TrakEM2 registration of new images

[Ashwin]

Hi All,

 I have a trakEM2 project that has is registered (stitched tiles in xy and aligned in Z) to which I want to add new images. Would I have to start from scratch and re-import all images to a new project and proceed with registration or could I integrate it with the existing project. To make things hard, I have some treeline object that have been traced in the older registered version, would I have to re-trace these treeline objects as well?

I am not sure how to approach this issue, any help would be great.

Thanks,
Ashwin

[Albert Cardona-2]

2013/12/2 Ashwin <[hidden email]>

> Hi All,
>
>  I have a trakEM2 project that has is registered (stitched tiles in xy and
> aligned in Z) to which I want to add new images. Would I have to start from
> scratch and re-import all images to a new project and proceed with
> registration or could I integrate it with the existing project. To make
> things hard, I have some treeline object that have been traced in the older
> registered version, would I have to re-trace these treeline objects as
> well?
>
> I am not sure how to approach this issue, any help would be great.
>
> Thanks,
> Ashwin
>

Hi Ashwin,

here's what I would do:

A) If you will add images in new layers rather than in existing layers:

1. Lock all existing images.
2. Add the new images, which will be in new layers at the end.
3. Register from the last (locked) layer to the end.

While not "perfect", this will give you a reasonable volume to work with.


B) If you will add images into exiting layers, or want a "perfect"
registration:

1. "Save As" to a different XML file
2. Open the new one and remove the treelines and other annotations
3. Add the new images
4. Re-register all.
5. Open the old XML
6. Right-click on the Object Tree of the old and choose "Send to - Sibling
project...", which will transfer the treelines from the old to the new,
following the appropriate transformations of the underlying images.

The "sibling project" approach works because the old layers and images have
the same IDs in the new volume, having the latter been created with "Save
As".

Albert

>
>
>
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[Ashwin]

Hi Albert,

Thanks for the suggestions. For my purposes approach A may not work as the new images are a few additional tiles that are part of existing layers. Having them at the end of the volume may not work. Approach B is more promising, I had a few questions about this.

- Do I keep the older images locked in the new Save As project?
- If not,  after re-registering all tiles does the "send to -sibling.." send the treelines to the coordinates with old transformations?  I guess, I don't understand how having the same IDs ensures that the treelines get updated with the new transformations?

Thanks,
Ashwin

[Albert Cardona-2]

> On Dec 2, 2013, at 5:25 PM, Ashwin <[hidden email]> wrote:
>
> Hi Albert,
>
> Thanks for the suggestions. For my purposes approach A may not work as the
> new images are a few additional tiles that are part of existing layers.
> Having them at the end of the volume may not work. Approach B is more
> promising, I had a few questions about this.
>
> - Do I keep the older images locked in the new Save As project?
> - If not,  after re-registering all tiles does the "send to -sibling.." send
> the treelines to the coordinates with old transformations?  I guess, I don't
> understand how having the same IDs ensures that the treelines get updated
> with the new transformations?

Don't lock the images if you want the best possible tranformations, and the transfer of the treeline is done by concatenating first the inverse of the tranform under the image in the old with the tranform under the same image (by id) in the new Trakem2 project.

Albert

>
> Thanks,
> Ashwin
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/TrakEM2-registration-of-new-images-tp5005767p5005784.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Ashwin]

Hi Albert,

I had another question regarding the same;

The old project with the treelines was created from another project with much larger images. This was done to make scrolling faster. I fear when I add new images to this project and re-register the images the new transformations will leave many gaping spaces between the images as the sibling project does not have any overlaps between the images.

I also realizes that I cant transfer treelines between a sibling project (with smaller images for easy scrolling) and its parent project with larger images as the image ids do not match.

How do we tackle this problem? Any ideas would be great.

Thanks,
Ashwin

[Albert Cardona-2]

2013/12/4 Ashwin <[hidden email]>

> Hi Albert,
>
> I had another question regarding the same;
>
> The old project with the treelines was created from another project with
> much larger images. This was done to make scrolling faster. I fear when I
> add new images to this project and re-register the images the new
> transformations will leave many gaping spaces between the images as the
> sibling project does not have any overlaps between the images.
>
> I also realizes that I cant transfer treelines between a sibling project
> (with smaller images for easy scrolling) and its parent project with larger
> images as the image ids do not match.
>
> How do we tackle this problem? Any ideas would be great.
>

If only a scaling factor separates the large vs the small version of the
projects, then write a script to copy the Treeline objects from one to the
other, with a multiplication in the x,y by the scale. Using jython and the
TrakEM2 API, the script will be rather short. Notice that the clone method
of the Treeline has a Project argument, i.e. when cloning you can assign
the object to a different Project. If the IDs of the layers are the same,
that will help lots. Otherwise you'll have to write a few more lines in
your script to transfer the layer IDs.

Get the open Project instances with the static call Project.getProjects(),
and then call getRootLayerSet on them to get the LayerSet that contains the
e.g. Treelines.

http://fiji.sc/wiki/index.php/TrakEM2_Scripting
http://www.ini.uzh.ch/~acardona/api/ini/trakem2/display/LayerSet.html
http://www.ini.uzh.ch/~acardona/api/ini/trakem2/display/Treeline.html

Albert

>
> Thanks,
> Ashwin
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/TrakEM2-registration-of-new-images-tp5005767p5005812.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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http://www.ini.uzh.ch/~acardona/

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