Re: Versatile Wand for Multispectral Image Stacks?

Posted by Christian Liebig-3 on Mar 10, 2016; 11:16am
URL: http://imagej.273.s1.nabble.com/Versatile-Wand-for-Multispectral-Image-Stacks-tp5015825p5015841.html

Hi Bill,

maybe spectral similarity mapping would do the trick. You give a
reference spectrum and then each pixel in the hyperspectral image is
assigned a similarity value. If you then threshiold it should give you
the desired output.

I have a macroset doing this. It is functional but still under
development and has no documentation. But if you think it is what you
need I can help you setting it up.
You can download the set here
<https://owncloud.tuebingen.mpg.de/public.php?service=files&t=fe31e6513aeb00a8c3070cf5f60cdd83>.
What you need is the zNormaliser and SpectralSimilarity.

Best,
Christian


On 09.03.2016 02:34, Bill Beggs wrote:

> Hi everyone.
>
> I use ImageJ for segmentation of 8-big grayscale multispectral images produced from energy dispersive x-ray analysis of heterogeneous inorganic powders.   So for example, I collect a set of images of the same scene, but each individual image is produced from characteristic xrays for Ca, Si, Al, Fe, Mg etc.
>
> The individual particles that compose these powders have variable chemical composition and I classify the particles into families of similar composition for quantification and other analyses.
>
> I'm familiar with the various segmentation plugins and I find Weka
> Segmentation cumbersome unfortunately.
>
> What I would really like to see is a tool similar to Versatile Wand, but
> that operates on a stack of images.  Essentially, from a selection, it
> would calculate something like a z-axis profile and select all other
> locations that exibited a similar profile within adjustable tolerances.
>
> Does anyone know if something like this exists?
>
> Many thanks.
>
> -Bill.
>
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--
Christian Liebig, PhD

Light Microscopy Facility
Max-Planck-Institute for Developmental Biology
Spemannstrasse 35
D-72076 Tuebingen
Germany

Phone:  [phone]
e-mail: [hidden email]


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