morphmet
Fri, 13 Nov 2009 06:56:54 -0800
-------- Original Message -------- Subject: RE: 3D Reconstruction from tissue sections Date: Thu, 12 Nov 2009 12:18:53 -0800 (PST) From: Dominique Adriaens <dominique.adria...@ugent.be> To: <morphmet@morphometrics.org> References: <4afc4a10.9080...@morphometrics.org> Hi, We are using Amira for a while now, which works perfect when using histological sections. Bummer with most of the biomedical software is that it relies on MRI or CT data, which implies that sections are nicely aligned. However, that is not the case when using histological data. So far, I know only of Amira that has the option to align (both manually and automatically) histological sections, before you can do segmenting. Best Dominique Prof. Dr. Dominique Adriaens Ghent University Evolutionary Morphology of Vertebrates & Zoology Museum K.L. Ledeganckstraat 35, B-9000 Gent BELGIUM tel: +32 9 264.52.19, fax: +32 9 264.53.44 E-mail: dominique.adria...@ugent.be URL: http://www.fun-morph.ugent.be/ http://www.zoologymuseum.ugent.be/ -----Original Message----- From: morphmet [mailto:morphmet_modera...@morphometrics.org] Sent: donderdag 12 november 2009 18:47 To: morphmet Subject: Re: 3D Reconstruction from tissue sections -------- Original Message -------- Subject: Re: 3D Reconstruction from tissue sections Date: Thu, 12 Nov 2009 08:25:53 -0800 (PST) From: Goodwin Lawlor <goodwin.law...@ucd.ie> To: morphmet@morphometrics.org References: <4afc1eba.6010...@morphometrics.org> Hi, Have a look at these applications: http://www.bioimagexd.net http://www.slicer.org They are fee, cross platform, applications based on the same library as Paraview. Regards, Goodwin 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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