[vtkusers] MRI Tiff stacks

[Harris Scott R CIV AFRL/SNJM]

NIH Image can read TIFF stacks and has a scripting language, so you can use it to read a stack and spit out
individual TIFF files for each slice. I'm not sure if NIH Image can read compressed TIFFs.  It's a great
program, however.

Scott Harris, Ph.D.
AFRL/SNJM
3109 P Street Bldg 622
WPAFB OH 45433-7700

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-----Original Message-----
From: Maneesh Yadav [mailto:97yadavm at utsc.utoronto.ca]
Sent: Thursday, August 02, 2001 2:40 PM
To: Lisa Sobierajski Avila
Cc: vtkusers at public.kitware.com
Subject: Re: [vtkusers] MRI Tiff stacks


Hi Lisa,
I'm not sure if you can be of much help, but the 'tiff stack' is
a single file (?).  The data is from mouseatlas.caltech.edu, (you can
click an embryo and get the tiff stack from the bottom of the page, here
is an example:

http://mouseatlas.caltech.edu/Stacks_and_movies/13.5dpc-Stacks_and_movies/13.5dpc_NIH_stacks/Stack,Cor1750_50,256*256_NoZF

I've never heard of these stacks before, but apparently NIH Image can view
them...if anyone can suggest as to how to get this data into VTK that'd be
great...(it don't think it is quite as simple as a concatenated set of
TIFF's but it shouldn't be much more complicated than that)...

On Wed, 1 Aug 2001, Lisa Sobierajski Avila wrote:

> Hello Maneesh,
>
> If you haven't tried it already, you might want to download VolView
> (http://www.kitware.com/products/volview.html). If your tiff stack is a set
> of 2D tiff images (is there such as thing as a 3D tiff image?) then you
> should be able to read it in and visualize it. This will give you a quick
> idea of what VTK is capable of doing with such data.
>
> Let me know if you have any questions.
>
> Lisa
>
>
> At 05:58 PM 7/31/2001, you wrote:
> >Hi all,
> >Many moons ago I was trying to write some molecular viz stuff in vtk but
> >it never turned out (not so much vtk's fault as it was sort of underlying
> >molecular semantics that frusturated me)
> >
> >Anyhoo I'm back to vtk as I have some mouse embryo MRI data that I'd like
> >to visualize and
> >I've been  given a tiff stack, which I really not sure how to process (is
> >it just a  concatenated set of tiff files?). I think Sebastien Barre's
> >tutorial provides me with most of the other help I'll need.
> >
> >Any other advice from people who have done this sort of thing would be
> >appreciated.
> >
> >Many Thanks,
> >Maneesh Yadav
> >
> >
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>



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