3d reconstruction

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3d reconstruction

Janine Prange-Kiel
Dear All,

I am new at the list, therefore, you may appologize if the question is way to stupid:

I want to reconstruct GFP labelled neurons in the brain. Specially I am interested in long projections (from the hypothalamus into the hippocampus) and thought I could use serial sections of defined thickness. Is there any ImageJ plugin that would faciliate this task? And/or does anybody from the list is experienced with this task and could provide information.
Thanks!

Janine


PD Dr. J. Prange-Kiel
Institut für Anatomie I: Zelluläre Neurobiologie
Universitätsklinikum Hamburg-Eppendorf

Martinistr. 52

D-20246 Hamburg

Tel.:++49-40-42803-3578
Fax:++49-40-42803-4966
e-mail: [hidden email]


--
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):

Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg

Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Ricarda Klein
Prof. Dr. Dr. Uwe Koch-Gromus
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Re: 3d reconstruction

PR Muston, Physiology
Not quite what you asked, but you might find this useful.
It is a link to some s/ware which I have been using for a year or so.

There is an active and helpful usergroup and the s/ware is under continuous
development.

From you point of view it has the added bonus of being developed by
neuroscientists.

<http://synapses.bu.edu/tools/index.htm>

Robert


--On 09 May 2007 20:43 +0200 Janine Prange-Kiel
<[hidden email]> wrote:

> Dear All,
>
> I am new at the list, therefore, you may appologize if the question is
> way to stupid:
>
> I want to reconstruct GFP labelled neurons in the brain. Specially I am
> interested in long projections (from the hypothalamus into the
> hippocampus) and thought I could use serial sections of defined
> thickness. Is there any ImageJ plugin that would faciliate this task?
> And/or does anybody from the list is experienced with this task and could
> provide information. Thanks!
>
> Janine
>
>
> PD Dr. J. Prange-Kiel
> Institut für Anatomie I: Zelluläre Neurobiologie
> Universitätsklinikum Hamburg-Eppendorf
>
> Martinistr. 52
>
> D-20246 Hamburg
>
> Tel.:++49-40-42803-3578
> Fax:++49-40-42803-4966
> e-mail: [hidden email]
>
>
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und
> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>
> Universitätsklinikum Hamburg-Eppendorf
> Körperschaft des öffentlichen Rechts
> Gerichtsstand: Hamburg
>
> Vorstandsmitglieder:
> Prof. Dr. Jörg F. Debatin (Vorsitzender)
> Dr. Alexander Kirstein
> Ricarda Klein
> Prof. Dr. Dr. Uwe Koch-Gromus



----------------------
PR Muston
[hidden email]
Microvascular Research Laboratories
Bristol Heart Institute
Department of Physiology
University of Bristol
Bristol, BS2 8EJ
www.mvrl.org
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Re: 3d reconstruction

Albert Cardona
In reply to this post by Janine Prange-Kiel
Hi Janine,

If by 'reconstruct' you mean to create 3D meshes, I am writing a program to do
just that.

    http://www.ini.uzh.ch/~acardona/trakem2.html

Besides exact meshes generated from painted areas or from outlines, one can also
quickly sketch tubes and spheres (ideal for neurites at confocal resolution).
Tubes are drawn as lines across multiple sections, and spheres as single points
with a radius. See for example this image of a 3D scene generated with TrakEM2:

    http://www.ini.uzh.ch/~acardona/img/unfinished.jpg


We are very close to release a proper 3D viewer for ImageJ itself. Perhaps one
or two more weeks.


Albert

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Re: 3d reconstruction

Dianne Patterson
Are these tools only meant for the microscopic level?  I have MRIs of the
hippocampus...I'd like to get volume measurements of the hippocampus.  Any
suggestions?  (I have played with ITK_snap and intend to give it another
try...it seemed a bit unstable on windows at the time (several months ago)..

Thankyou,

Dianne

On 5/9/07, Albert Cardona <[hidden email]> wrote:

>
> Hi Janine,
>
> If by 'reconstruct' you mean to create 3D meshes, I am writing a program
> to do
> just that.
>
>     http://www.ini.uzh.ch/~acardona/trakem2.html
>
> Besides exact meshes generated from painted areas or from outlines, one
> can also
> quickly sketch tubes and spheres (ideal for neurites at confocal
> resolution).
> Tubes are drawn as lines across multiple sections, and spheres as single
> points
> with a radius. See for example this image of a 3D scene generated with
> TrakEM2:
>
>     http://www.ini.uzh.ch/~acardona/img/unfinished.jpg
>
>
> We are very close to release a proper 3D viewer for ImageJ itself. Perhaps
> one
> or two more weeks.
>
>
> Albert
>
> --------------------------------------------------------------------
> This message was sent using Webmail@INI: https://webmail.ini.ethz.ch
>



--
Dianne Patterson, Ph.D.
[hidden email]
ERP Lab
University of Arizona
621-3256 (Office)
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Re: 3d reconstruction

Albert Cardona
For those of you who'd like to test TrakEM2 for modeling:
I have just released a new version fixing lots of little bugs, and introducing
cross-correlation options for optimal automatic stitching of montages.

If anyone has access to Windows and MacOSX machines, I'd appreciate some
comments on whether the program runs as expected.


> Are these tools only meant for the microscopic level?


A segmentation editor like TrakEM2 is scale-free: you can create 3D models from
a bacteria' flagellum to a blue whale and beyond.

Please let me know if you run into issues. The current beta version still
contains lots of little details to smooth out.

The 3D visualization, fully integrated into ImageJ, will come in less than two
weeks.

TrakEM2 changes very quickly, almost every other week there is a new beta
release. See:

http://www.ini.uzh.ch/~acardona/news.html


Albert

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Re: 3d reconstruction

Benjamin Schmid-2
In reply to this post by Janine Prange-Kiel
Hi Janine,

we developed a segmentation editor as an ImageJ plugin some time ago.  
It allows you to go to a
stack of images and label each slice, i.e. assign a certain material  
to a selected region. It's very easy
to use. If you have previously worked with Amira, it is even easier,  
since it's similar to the
segmentation editor there.

You find it, together with a description how to use it, at

http://132.187.25.13/bene/my/?category=Download&page=SegmentationEditor

If you want to visualize your result, you might also want to have a  
look at our 3D viewer, which is
available as ImageJ plugin:

http://132.187.25.13/bene/my/?category=Download&page=Viewer3D

The 3D viewer uses Java3D, so if you want to use it, you have to  
install Java3D on your machine.
If you are interested, but have problems with the installation, you  
can use the Java3D installer plugin:

http://132.187.25.13/bene/my/?category=Download&page=InstallJava3D

Cheers,
Benjamin Schmid


On May 9, 2007, at 8:43 PM, Janine Prange-Kiel wrote:

> Dear All,
>
> I am new at the list, therefore, you may appologize if the question  
> is way to stupid:
>
> I want to reconstruct GFP labelled neurons in the brain. Specially  
> I am interested in long projections (from the hypothalamus into the  
> hippocampus) and thought I could use serial sections of defined  
> thickness. Is there any ImageJ plugin that would faciliate this  
> task? And/or does anybody from the list is experienced with this  
> task and could provide information.
> Thanks!
>
> Janine
>
>
> PD Dr. J. Prange-Kiel
> Institut für Anatomie I: Zelluläre Neurobiologie
> Universitätsklinikum Hamburg-Eppendorf
>
> Martinistr. 52
>
> D-20246 Hamburg
>
> Tel.:++49-40-42803-3578
> Fax:++49-40-42803-4966
> e-mail: [hidden email]
>
>
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und  
> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>
> Universitätsklinikum Hamburg-Eppendorf
> Körperschaft des öffentlichen Rechts
> Gerichtsstand: Hamburg
>
> Vorstandsmitglieder:
> Prof. Dr. Jörg F. Debatin (Vorsitzender)
> Dr. Alexander Kirstein
> Ricarda Klein
> Prof. Dr. Dr. Uwe Koch-Gromus
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Re: 3d reconstruction

Albert Cardona
In reply to this post by Dianne Patterson
 From popular demand, I've prepared a PDF version of the TrakEM2 manual:

    http://www.ini.uzh.ch/~acardona/trakem2_manual.pdf


which will always be updated and available from the online manual page:

    http://www.ini.uzh.ch/~acardona/trakem2_manual.html


Albert
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Re: 3d reconstruction

Francesco Lassandro
In reply to this post by Dianne Patterson
Hi Dianne,
we are working about volume meaurements on CT scans, in particular on
lymphomas, at the moment we have produced a plugin that allows area
measurement with a single click (a sort of magic wand) based on edge
detection. this ImageJ plugin (YAWI 2D) is available at
http://yawi3d.sourceforge.net/

ciao
Francesco


----- Original Message -----
From: "Dianne Patterson" <[hidden email]>
To: <[hidden email]>
Sent: Thursday, May 10, 2007 1:11 AM
Subject: Re: 3d reconstruction


> Are these tools only meant for the microscopic level?  I have MRIs of the
> hippocampus...I'd like to get volume measurements of the hippocampus.  Any
> suggestions?  (I have played with ITK_snap and intend to give it another
> try...it seemed a bit unstable on windows at the time (several months
ago)..

>
> Thankyou,
>
> Dianne
>
> On 5/9/07, Albert Cardona <[hidden email]> wrote:
> >
> > Hi Janine,
> >
> > If by 'reconstruct' you mean to create 3D meshes, I am writing a program
> > to do
> > just that.
> >
> >     http://www.ini.uzh.ch/~acardona/trakem2.html
> >
> > Besides exact meshes generated from painted areas or from outlines, one
> > can also
> > quickly sketch tubes and spheres (ideal for neurites at confocal
> > resolution).
> > Tubes are drawn as lines across multiple sections, and spheres as single
> > points
> > with a radius. See for example this image of a 3D scene generated with
> > TrakEM2:
> >
> >     http://www.ini.uzh.ch/~acardona/img/unfinished.jpg
> >
> >
> > We are very close to release a proper 3D viewer for ImageJ itself.
Perhaps

> > one
> > or two more weeks.
> >
> >
> > Albert
> >
> > --------------------------------------------------------------------
> > This message was sent using Webmail@INI: https://webmail.ini.ethz.ch
> >
>
>
>
> --
> Dianne Patterson, Ph.D.
> [hidden email]
> ERP Lab
> University of Arizona
> 621-3256 (Office)