Re: Versatile Wand for Multispectral Image Stacks?

Posted by Bill Beggs on Mar 10, 2016; 4:01pm
URL: http://imagej.273.s1.nabble.com/Versatile-Wand-for-Multispectral-Image-Stacks-tp5015825p5015843.html

Thanks Christian.  That sounds promising.

I'll check it out.

-Bill

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christian Liebig
Sent: Thursday, March 10, 2016 5:19 AM
To: [hidden email]
Subject: Re: Versatile Wand for Multispectral Image Stacks?

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

--
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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