Re: 3D reconstruction (I need help)

Posted by Benjamin Schmid-2 on Jun 08, 2007; 6:22pm
URL: http://imagej.273.s1.nabble.com/3D-reconstruction-I-need-help-tp3699189p3699192.html

Hi Orkun,

can you tell me more about your system? Which computer are you using,
which operating system, and which graphics card?

It would be also helpful, if you could start it in a console, which  
would
probably provide you with more details about the reason for the crash.

If you are interested, I will tell you how to do that once you told  
me your
operating system.

Cheers, Benjamin

On Jun 8, 2007, at 12:23 PM, Orkun Ersoy wrote:

> Hi All,
> Thanks Benjamin for your reply to Emilio,
> I tried your plugin after installing Java 3D (I can see a rotating  
> cube)
> The plugin opens I used your sample stack in your web page, after
> selecting volume mode nad parameters, ImageJ crashes and is shut.
>
> Any suggestions?
> The memory of ImageJ is 1000MB in my settings...

>
> Orkun ERSOY
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Benjamin Schmid
> Sent: Friday, June 08, 2007 5:05 PM
> To: [hidden email]
> Subject: Re: 3D reconstruction (I need help)
>
> Hi Emilio,
>
> I would just like to point you to our homepage. We have worked on
> plugins regarding segmentation and
> 3D reconstruction. Our segmentation tool is mainly made for manual
> segmentation, so it may not be what
> you are looking for, but we can help you with the 3D reconstruction
> of the segmented images.
>
> Our segmentation editor can be found at
> http://132.187.25.13/bene/my/?
> category=Download&page=SegmentationEditor
>
> the 3D reconstruction and visualisation plugin at
> http://132.187.25.13/bene/my/?category=Download&page=Viewer3D
>
> We are working with flies, so all the screenshots you find there are
> made from fly brains, but nevertheless
> the software is not restricted to that.
>
> Best wishes,
>
> Benjamin
>
> On Jun 7, 2007, at 2:26 PM, Emilio Bedatou wrote:
>
>> Hello!
>>
>>   I'm new in the list and this is my first message.
>>
>>   I need help to reconstruct in 3D a burrow system that is inside
>> of a rock. Yes, its a fossil. It is a complex network of
>> interconected burrows. Burrows are not empty, they are filled with
>> rock, but slightly different to the enclosing rock. So a difference
>> of density is between rock and burrow sufficient for to be detected
>> in a tomograph.
>>   I've scanned the sample in a conventional medical scanner and
>> then, I have a lot of images of sections, spaced every 1 mm, of the
>> sample.
>>
>>   I need help for
>>                           1) In every image to select atomatically
>> the zones corresponding to burrows and then to eliminate the rest
>> of the image; and
>>                          2) with the resulting series of images of
>> "burrows sections" to make a three dimensional reconstruction of
>> the burrow system.
>>
>>   My computer skills have been exceeded when I tried to do it alone
>> using ImageJ, in fact I never use any other images software than
>> Photoshop or similar.
>>
>>   If someone can help me or at least tell me if it is, or not,
>> possible of make using ImageJ I will be very grateful.
>>
>>   Also if someone know about other software that can help me,
>> please let me know.
>>
>>   Thanks to all of you
>>
>>   Sincerely
>>
>>   Emilio Bedatou
>>   CONICET-UNLPam
>>   Av. Uruguay 151
>>   Santa Rosa-La Pampa
>>   Argentina
>>
>>  
>> ---------------------------------
>>  Preguntá. Respondé. Descubrà .
>>  Todo lo que querà as saber, y lo que ni imaginabas,
>> está en Yahoo! Respuestas (Beta).
>>  Â¡Probalo ya!