hugin used for figure in peer-reviewed publication

[Habi]

Hello all.

I'm not too much of help with coding help for hugin, but at least I
try to spread the word where possible:
I'm a PhD-Student at the University of Bern where I work with
ultrahigh resolution x-ray tomography to study the lung development in
mammals. While preparing his last paper the first author asked me to
prepare a figure to explain the machinery we use to obtain the images
[1]. I remembered that I made a panorama the first time I've been
there [2] and proposed that we use this image to illustrate the whole
process and details. Everyone agreed on this proposition, so in the
end our paper which was recently released in the Journal of Applied
Physiology [3] includes an image that was made with hugin.
I put a screenshot of the figure online [4], since I don't think that
many members of this group will be able to read the full paper online
(it will be free to read in some months, as it is with science, not my
choice...).
If you're really interested in the paper I might be able to send you a
preprint pdf, but not officially. But if you ask me, I will send it to
you...

Have a nice day
David

[1]: the TOMCAT-beamline at the Swiss Light Source, a synchrotron at
the PSI in Switzerland: http://sls.web.psi.ch/view.php/beamlines/tomcat/
[2]: see http://flickr.com/photos/habi/237003449/ for the full-sized
image
[3]: Finite Element 3D Reconstruction of the pulmonary acinus imaged
by Synchrotron X-ray tomography. http://jap.physiology.org/cgi/content/abstract/90546.2008v1
[4]: http://habi.gna.ch/wp-content/uploads/2008/07/jap-hugin.jpg

[Klaus]

Hello David,

Give my warmest regards to the EH building next door ;-)

Klaus

[Tom Sharpless]

Hi David

Impressive.

I wonder if you would mind revealing the secret of how to view a
picture full size on flickr? I never get anywhere by just clicking
around ;<.

Cheers, Tom

On Jul 24, 10:59 am, Habi <david.haberth...@gmail.com> wrote:
> Hello all.
>
> I'm not too much of help with coding help for hugin, but at least I
> try to spread the word where possible:
> I'm a PhD-Student at the University of Bern where I work with
> ultrahigh resolution x-ray tomography to study the lung development in
> mammals. While preparing his last paper the first author asked me to
> prepare a figure to explain the machinery we use to obtain the images
> [1]. I remembered that I made a panorama the first time I've been
> there [2] and proposed that we use this image to illustrate the whole
> process and details. Everyone agreed on this proposition, so in the
> end our paper which was recently released in the Journal of Applied
> Physiology [3] includes an image that was made with hugin.
> I put a screenshot of the figure online [4], since I don't think that
> many members of this group will be able to read the full paper online
> (it will be free to read in some months, as it is with science, not my
> choice...).
> If you're really interested in the paper I might be able to send you a
> preprint pdf, but not officially. But if you ask me, I will send it to
> you...
>
> Have a nice day
> David
>
> [1]: the TOMCAT-beamline at the Swiss Light Source, a synchrotron at
> the PSI in Switzerland:http://sls.web.psi.ch/view.php/beamlines/tomcat/

> [2]: seehttp://flickr.com/photos/habi/237003449/for the full-sized

[David Haberthür]

hello tom.
you should see little icons on top of the image at <http://flickr.com/photos/habi/237003449/
>, if you have turned javascrip on in your browser
one of them leads you to "all sizes" of the image at this URL: <http://flickr.com/photos/habi/237003449/sizes/l/
> where you see all versions of the file
cheers
habi

[Seb Perez-D]

On Fri, Jul 25, 2008 at 09:13, David Haberthür
<david.ha...@gmail.com> wrote:
> you should see little icons on top of the image at <http://flickr.com/photos/habi/237003449/
> >, if you have turned javascrip on in your browser
> one of them leads you to "all sizes" of the image at this URL: <http://flickr.com/photos/habi/237003449/sizes/l/
> > where you see all versions of the file

This only happens if you have an account on flickr. If you don't, here
is the link for the image:
http://farm1.static.flickr.com/82/237003449_3fd2e9380c_o.jpg

Cheers,

Seb

[David Haberthür]

Sorry, I didnt't think about that. The full-size image which I
originalyl stitched (including all the stitching errors and unsharp
parts) can also be found here: <http://habi.gna.ch/tmp/sls.jpg> (~850
KB)
cheers
David/Habi

[Tom Sharpless]

Thanks, both

Now I understand whats up with flickr -- at first I joined, and I
remember I could see full size pictures. But I was so disappointed
that they didn't serve QTVRs that I resigned, and now I can't. So I
guess I'll join again.

However "full-size" by flickr is not full-size by me.

David,

Thanks for the link to your original. I can see the details there,
which is what I like best about panos.

BTW I suppose this a coherent X-ray source, and that you are
exploiting interference to get thinner slices/higher resolution?
Could you point me at some technical details? I was an MRI engineer
in the '80s and '90s, and am still interested in advances in medical
imaging.

Regards, Tom

On Jul 25, 4:02 am, David Haberthür <david.haberth...@gmail.com>
wrote:

[David Haberthür]

Dear Tom.
The SLS [1] is a highly coherent light source, that's correct. At the
beamline we're using (TOMCAT [2]), we're not exploiting interference,
since a resolution down to 350 nm is enough for our applications.
But there are other beamlines that exploit interference, and also
diffraction or other methods, like phase-contrast, but as I don't work
with/on these beamlines I don't know much more on this...
On TOMCAT you should be able to find a lot of publications on their
site [3], I can especially recommend two publications of Marco, one of
my supervisors to read for an overview [4] and [5].
Hope that helps as refresher on imaging :)
Cheers
Habi

[1]: http://sls.web.psi.ch/
[2]: http://sls.web.psi.ch/view.php/beamlines/tomcat
[3]: http://sls.web.psi.ch/view.php/beamlines/tomcat/publications/
[4]: http://scholar.google.com/scholar.bib?hl=en&lr=&q=info:dN4hPe6kkfMJ:scholar.google.com/&output=citation&oe=ASCII&oi=citation
(I don't know if this works...)
[5]: http://scholar.google.com/scholar.bib?hl=en&lr=&q=info:aak4i2gH1X0J:scholar.google.com/&output=citation&oe=ASCII&oi=citation

PS: Don't tell anyone, but you can find a pdf of both articles here,
since it normally costs 23$ or 18$ to read them:
http://habi.gna.ch/tmp/