TrakEM: When are mipmaps necessary?

[tmacrina]

Hey guys,
 
I'm working through implementing this pipeline in TrakEM (right now, using Jython and building from Albert's script on the project website):
1. Import images
2. Apply CLAHE filter to patches
3. Elastically align layers
4. Export transformed layers as images
 
When should I generate/regenerate mipmaps? Is is possible to get through that process without generating mipmaps at all?
 
Thanks for the help!
 
Tommy

[Saalfeld, Stephan]

If you mean elastic montage then you would need no mipmaps, just for
final rendering (generating the scale levels costs almost nothing).  If
you mean elastic alignment across layers then you will need the mipmaps
before because it will use them to save time loading images.

Do you know this project?

https://github.com/saalfeldlab/parallel-elastic-alignment

It's pretty messy but may have a lot of code that you could reuse.

Best,
Stephan



On Sat, 2015-05-02 at 19:16 -0700, tmacrina wrote:

> Hey guys,
>  
> I'm working through implementing this pipeline in TrakEM (right now, using
> Jython and building from  Albert's script
> <http://fiji.sc/TrakEM2_Scripting#Create_a_TrakEM2_project_for_fast_visualization.2C_without_mipmaps>  
> on the project website):
> 1. Import images
> 2. Apply CLAHE filter to patches
> 3. Elastically align layers
> 4. Export transformed layers as images
>  
> When should I generate/regenerate mipmaps? Is is possible to get through
> that process without generating mipmaps at all?
>  
> Thanks for the help!
>  
> Tommy
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/TrakEM-When-are-mipmaps-necessary-tp5012681.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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Albert Cardona-2]

Hi Tommy,

You'll need mipmaps to elastically align layers.
For exporting, you don't need to if you use the 16-bit exporter that reads
directly from the original images, transforming them on the fly.

Albert

2015-05-02 22:16 GMT-04:00 tmacrina <[hidden email]>:

> Hey guys,
>
> I'm working through implementing this pipeline in TrakEM (right now, using
> Jython and building from  Albert's script
> <
> http://fiji.sc/TrakEM2_Scripting#Create_a_TrakEM2_project_for_fast_visualization.2C_without_mipmaps
> >
> on the project website):
> 1. Import images
> 2. Apply CLAHE filter to patches
> 3. Elastically align layers
> 4. Export transformed layers as images
>
> When should I generate/regenerate mipmaps? Is is possible to get through
> that process without generating mipmaps at all?
>
> Thanks for the help!
>
> Tommy
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/TrakEM-When-are-mipmaps-necessary-tp5012681.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
http://albert.rierol.net
http://www.janelia.org/lab/cardona-lab
http://www.ini.uzh.ch/~acardona/

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

[tmacrina]

Thanks guys. And thanks for the project link, Stephan!