Posted by
Albert Cardona-2 on
Nov 27, 2015; 9:44pm
URL: http://imagej.273.s1.nabble.com/Standalone-ImgLib2-usage-tp5005746p5015039.html
Hi Avital,
For custom registration, I'd use the mpicbg library, which has most if not
all functionality that you'll need, like e.g. ability to define a 3D
transform by a bunch of point correspondences and then map a 3D image
through it. Fiji has it included. The source code is here:
https://github.com/axtimwalde/mpicbgFor automated 3D segmentation there aren't any great options within Fiji. I
suggest using the ilastik software:
http://ilastik.org/As for scripting ImgLib2: if you know java, I'd use it directly. It's quite
straightforward really; cursors abstract it all for you. Read this paper,
particularly the supplemental code examples:
http://bioinformatics.oxfordjournals.org/content/28/22/3009.longBest,
Albert
2015-11-27 14:36 GMT-05:00 Avital Steinberg <
[hidden email]>:
> Hi Albert,
> I just noticed your post from October. I can use ImageJ's Java API,
> ImageJ's
> macro language and Fiji's Javascript language. I will need to do 3D
> segmentation and some custom 3D alignments of 3D images, and imgLib2 seems
> to have some useful methods. However, it looks complicated to use.
>
> Is there a user friendly way of accessing methods from imgLib2? (a user
> friendly scripting wrapper would be awesome!) Or any other tool with built
> in segmentation and registration methods that would be possible to learn
> for
> someone who can program in Java?
>
> Thanks and happy Thanksgiving,
> Avital
>
>
>
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