Posted by
Robert Kirmse-2 on
Jul 24, 2013; 9:03am
URL: http://imagej.273.s1.nabble.com/newbie-needs-to-know-about-3D-tp5004118p5004122.html
Hi John,
I don't know if I understood the imaging process of your sample correctly
but here are my thought for your process.
If you haven't already, download the Fiji package
it is essentially ImageJ with a bunch of pre-installed Plugins,
including a lot that deal with stack registration i.e. alignment
and segmentation. Of course you can also download the plugins
for ImageJ seperately
Without having seen your images
I would already start in ImageJ/Fiji,
and import the whole series into a stack
1. Fiji > File > Import > Image Sequence (your files need to be numbered)
2. Fiji > Plugins > Registration > Stackreg (this should already help you with a decent alignment, but also try other methods from the registration plugins to see what is best for you data.
This should give you a nicely aligned stack that you can movie through.
Crop the stack to your needs in ImageJ/Fiji
3. Segmentation,
You need a good Segmentation editor that can handle different objects that are traced
either manually or automatically. In these editors you won't have the problem you described
because the program takes care of the outlines you draw and to which object they belong.
Afterwards you can render the outlines that belong to each object.
My experience with Segmentation editors in ImageJ is limited so I can't give a good recommendation
I normally used the imod package (developed for electron microscopy) for manual segmentation.
However even with good tools manual segmentation is quite time intensive.
Also if you "just" want to generate a 3D rendering try Fiji > Plugins > Volume Viewer
Here you have to experiment with the display option and the transfer curves to bring out
the feature you want and surpress the unwanted features. I guess for what you want
the option "Volume" under Mode is probably what you want.
You could also have a look at the Ilastik package in addition to the Segmentation plugins in
Fiji which is a good trainable segmentation tool that also offers 3D rendering options.
Anyway, Segmentation will require some learning time, so be prepared to spent some time
researching and trying different tools.
Cheers
Robert
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html