Amira/Avizo 3D reconstruction software

[Jennifer Clarke]

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Hi Jacqui

We have this software and I have a reasonable amount of experience with it,
although my experience is mainly limited to the tasks I have needed to do,
which is predominantly 3D colocalisation using the 3D arithmetic "exclusive
AND" operator and 3D quantification (in addition to various visualisation,
voltexes, surface displays, filtering etc).  We've also obtained centre of mass
data (bary centres, ie xzy coordinates for objects (in our case neuronal
varicosities immunolabelled for different types of neurotransmitters in spinal
cord tissue).

I too would be keen to know who else in the confocal community also uses Avizo.

Avizo is the name of the current version of what used to be Amira
http://www.vsg3d.com
My experience is with both and they are essentially different versions of the
same software

We had the Amira software with additional quantification package
We now have "Avizo Fire" which is the material sciences version of Avizo,
because the material sciences version already version includes all the
quantification modules we need.

We are using the software with "lif" files from our Leica SP5.
Originally (maybe depending on the Amira version) there was some trouble with
the lif file reader and we had to input tif series instead, but now you can
directly read the lif files - however to be able to re-open Amira/Avizo
networks (.hx files) there is a work around you need to do when you first open
your lif file.  If anyone else is trying to open lifs in Amira/Avizo and hasnt
worked this out let me know and I'll explain the workaround.

We have recently had the latest Avizo Fire version installed (6.2) and the lif
reader workaround trick doesnt work at all, looks to me to be the same errors
as the original problem in Amira.  So, I am currently doing all my work in the
earlier version (5.1).  I should contact Avizo about this to have it fixed, but
I havent yet as it takes time to send them examples of what the problem is
etc...

(I may possibly be in Auckland at the end of January 2011 for the Australian
Neuroscience Society meeting...)

Kind regards
Jen

--
Jennifer Clarke BSc (Hons) PhD
Research Associate, Anatomy and Histology
Centre for Neuroscience, School of Medicine
&
Facility Manager, Optical Microscopy Suite, Flinders Microscopy
(available for training and assistance on Mondays only)

Flinders University
GPO Box 2100, Adelaide 5001
Phone: [phone]
Email: [hidden email]

--

Quoting Jacqui Ross <[hidden email]>:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear All,
>
> I'm sorry for the off-topic enquiry. However, if anyone has a lot of
> experience with the visualisation program Amira, I would really
> appreciate hearing from you.
>
> Thanks!
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
>
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>

--
Jennifer Clarke BSc (Hons) PhD
Research Associate, Anatomy and Histology
Centre for Neuroscience, School of Medicine
&
Facility Manager, Optical Microscopy Suite, Flinders Microscopy
(available for training and assistance on Mondays only)

Flinders University
GPO Box 2100, Adelaide 5001
Phone: [phone]
Email: [hidden email]