Re: 3D Reconstruction from tissue sections

[morphmet]

-------- Original Message --------
Subject: Re: 3D Reconstruction from tissue sections
Date: Thu, 12 Nov 2009 07:44:47 -0800 (PST)
From: Murat Maga <m...@u.washington.edu>
To: morphmet@morphometrics.org
References: <4afc1eba.6010...@morphometrics.org>

Did you try 3D slicer? http://www.slicer.org/

It is free and works with volume data. You may have an issue if your
sections are a bit off in their orientation, or does not have exactly
same dimensions. In any event, Slicer would take any bitmap data format
(jpg, png, tiff etc...) and you can render, segment or measure. It works
on Mac, Windows, or Linux.

Hope this helps,
M

A. Murat Maga, PhD
Senior Fellow
University of Washington
Dept. Pediatrics, Division of Craniofacial Medicine
1959 NE Pacific St. HSB RR234
Seattle, WA 98195
(206) 616-9703



morphmet wrote:

-------- Original Message --------
Subject: 3D Reconstruction from tissue sections
Date: Tue, 10 Nov 2009 15:32:26 -0800 (PST)
From: Adams, Dany <dany.ad...@tufts.edu>
To: <morphmet@morphometrics.org>

I am having trouble finding/choosing software that I can use to turn my
serial histological sections into 3D images.  I found a great list on

Morphmet in a letter from 2008, but it covers so much (or, the four sites it lists cover so much) I'm still overwhelmed by trying to figure out which program does what I need. It may just be a vocabulary problem, but I seem to be finding a lot of programs to analyze 3D reconstructions once they already exist.

I found something called BioVis 3D that does what I need although it is PC based and it would be a strain on my budget. Paraview looks promising, but I can't get it to open any of my image files (?!). Does anyone out there do 3D reconstructions of tissue sections ? Is there a way to do this in ImageJ, and, if so, where can I find instructions ? Can anyone suggest the right keywords to use in a search ? Mac is best, but I can use PC if necessary, and truly ideal would be something I could use to generate data for import into MorphoJ.

Many thanks,

Dany

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