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VSG's Avizo visualization software

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Knecht, David

VSG's Avizo visualization software

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Does anyone have experience with Avizo software for visualization and measurement? We are having a presentation by them tomorrow but I have never heard of the package before. Thanks- Dave

Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

Christian Götze

Re: VSG's Avizo visualization software

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Hi David,

but perhaps you have heard of amira? It's the same base. Don't know
exactly why and how but in the meantime there seem to be two companies
selling it - Visage Imaging calls it amira (the "original" name) and VSG
calls it Avizo.

It's an excellent visualization tool and used by a large number of
groups around the world. The user interface is, let's say, something you
need to get used to because it's quite different from everything else
but you can have quite good visualizations out of it.

Hope that helps
Christian

Am 10.02.2011 16:48, schrieb David Knecht:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Does anyone have experience with Avizo software for visualization and measurement? We are having a presentation by them tomorrow but I have never heard of the package before. Thanks- Dave
>
> Dr. David Knecht
> Department of Molecular and Cell Biology
> Co-head Flow Cytometry and Confocal Microscopy Facility
> U-3125
> 91 N. Eagleville Rd.
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
> 860-486-4331 (fax)

--
Christian Götze

arivis - Multiple Image Tools GmbH
Kröpeliner Straße 54, D-18055 Rostock

http://www.arivis.com

Jennifer Clarke

Re: VSG's Avizo visualization software

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To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear David and list

Our facility has had Amira/Avizo/AvizoFire software for 3D reconstruction etc for many years
Whilst available for our whole facility, it is only a few users, predominantly myself and a few people in my lab, who use it.
Its fantastic for 3D image math and visualisation, I do a considerable amount of 3D colocalisation work on z-stacks with it, in particular doing neurochemical analysis of nerve terminals in spinal cord slices.

There is a small bug regarding uploading of lif (Leica image format files) when you come to re-opening saved Amira/Avizo networks, we reported this ages ago, its still a problem but we have worked out a simple workaround so contact me off list if you need. The workaround works in most but not all versions, hence I currently use AvizoFire v6.1 where it works and not AvizoFire v6.2 where it doesnt. (v6.3 now available, havent tried it yet). (You can of course always just load tif stacks). I havent worked with data sets from other formats.

It struggles abit with large data sets, eg z-stacks 1024x1024x50 (frequent errors saying cant allocate sufficient bytes to perform image arithmetic - can usually work around by repeated re-loading of network, restarting of software and having all channel displays off for the calculation, and would definately struggle with isosurfaces on such size data sets), but works super smooth on eg 512x512x50 stacks

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
(training and assistance available on Mondays only)

Flinders University
GPO Box 2100, Adelaide 5001
Phone: 61 8 8204 6454/ 61 8 8204 6637
Email: [hidden email]
________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Christian Götze [[hidden email]]
Sent: Friday, 11 February 2011 3:39 AM
To: [hidden email]
Subject: Re: VSG's Avizo visualization software

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi David,

but perhaps you have heard of amira? It's the same base. Don't know
exactly why and how but in the meantime there seem to be two companies
selling it - Visage Imaging calls it amira (the "original" name) and VSG
calls it Avizo.

It's an excellent visualization tool and used by a large number of
groups around the world. The user interface is, let's say, something you
need to get used to because it's quite different from everything else
but you can have quite good visualizations out of it.

Hope that helps
Christian

Am 10.02.2011 16:48, schrieb David Knecht:

--
Christian Götze

arivis - Multiple Image Tools GmbH
Kröpeliner Straße 54, D-18055 Rostock

http://www.arivis.com

Tao Tong

Re: VSG's Avizo visualization software

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

I have the same issue of the Leica format files.

I discovered that the safest way for re-opening Amira/Avizio network is to
save the data in Amira Mesh format. Although this increase the storage
requirement, it ensures the network can be opened normally in the future.

For very large data set, Amira has a large data set option, I believe it
downsample the dataset first, then re-load needed parts on the fly.

It is interesting to note there is another Amira variant, ZIBAmira:

http://amira.zib.de/

<http://amira.zib.de/>Best,

Tao

On Thu, Feb 10, 2011 at 6:28 PM, Jen Clarke <[hidden email]
> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear David and list
>
> Our facility has had Amira/Avizo/AvizoFire software for 3D reconstruction
> etc for many years
> Whilst available for our whole facility, it is only a few users,
> predominantly myself and a few people in my lab, who use it.
> Its fantastic for 3D image math and visualisation, I do a considerable
> amount of 3D colocalisation work on z-stacks with it, in particular doing
> neurochemical analysis of nerve terminals in spinal cord slices.
>
> There is a small bug regarding uploading of lif (Leica image format files)
> when you come to re-opening saved Amira/Avizo networks, we reported this
> ages ago, its still a problem but we have worked out a simple workaround so
> contact me off list if you need. The workaround works in most but not all
> versions, hence I currently use AvizoFire v6.1 where it works and not
> AvizoFire v6.2 where it doesnt. (v6.3 now available, havent tried it yet).
> (You can of course always just load tif stacks). I havent worked with data
> sets from other formats.
>
> It struggles abit with large data sets, eg z-stacks 1024x1024x50 (frequent
> errors saying cant allocate sufficient bytes to perform image arithmetic -
> can usually work around by repeated re-loading of network, restarting of
> software and having all channel displays off for the calculation, and would
> definately struggle with isosurfaces on such size data sets), but works
> super smooth on eg 512x512x50 stacks
>
> 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
> (training and assistance available on Mondays only)
>
> Flinders University
> GPO Box 2100, Adelaide 5001
> Phone: 61 8 8204 6454/ 61 8 8204 6637
> Email: [hidden email]
> ________________________________________
> From: Confocal Microscopy List [[hidden email]] On
> Behalf Of Christian Götze [[hidden email]]
> Sent: Friday, 11 February 2011 3:39 AM
> To: [hidden email]
> Subject: Re: VSG's Avizo visualization software
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi David,
>
> but perhaps you have heard of amira? It's the same base. Don't know
> exactly why and how but in the meantime there seem to be two companies
> selling it - Visage Imaging calls it amira (the "original" name) and VSG
> calls it Avizo.
>
> It's an excellent visualization tool and used by a large number of
> groups around the world. The user interface is, let's say, something you
> need to get used to because it's quite different from everything else
> but you can have quite good visualizations out of it.
>
> Hope that helps
> Christian
>
> Am 10.02.2011 16:48, schrieb David Knecht:
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Does anyone have experience with Avizo software for visualization and
> measurement? We are having a presentation by them tomorrow but I have never
> heard of the package before. Thanks- Dave
> >
> > Dr. David Knecht
> > Department of Molecular and Cell Biology
> > Co-head Flow Cytometry and Confocal Microscopy Facility
> > U-3125
> > 91 N. Eagleville Rd.
> > University of Connecticut
> > Storrs, CT 06269
> > 860-486-2200
> > 860-486-4331 (fax)
>
> --
> Christian Götze
>
> arivis - Multiple Image Tools GmbH
> Kröpeliner Straße 54, D-18055 Rostock
>
> http://www.arivis.com
>

--
http://tongtao.com

George McNamara

Re: VSG's Avizo visualization software

In reply to this post by Knecht, David

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Dave,

As noted in the other replies, excellent 3D rendering and impressive
volume and related measurements (confocal Z-series of a Dictyostelium
aggregate expressing plasma membrane fluorescent protein, nuclear
excluded cytoplasmic GFP and a nuclear DNA counterstain might be fun to
give them ... or find a blood vessel volume dataset). However, the
anti-user interface was a huge negative for me, and my guess is they
have not changed it.

I was pleased by my first experience with Leica MATRIX (for SP5 confocal
and STED), which saves in OME TIFF file format either to an OMERO (or
presumably any other OME compliant server), but can save to the local
hard drive. Regardless of whether you have Leica confocal(s), being able
to save (or export later) to OME TIFF folder/file structure and
efficiently open in analysis software is becoming important (avoiding
LIF file issue of another reply).

Enjoy,

George

On 2/10/2011 10:48 AM, David Knecht wrote:

--

George McNamara, PhD
Analytical Imaging Core Facility
University of Miami

Christian Götze

Re: VSG's Avizo visualization software

In reply to this post by Jennifer Clarke

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Commercial remark!

Hi Jen,

if you have problems visualizing large data sets you should have a look
on our arivis Browser software. It is specialized in handling,
visualizing and analyzing even very large data sets which don't fit into
memory. Feel free to contact me directly for questions.

More on http://www.arivis.com/en/features

Best,
Christian

Am 11.02.2011 00:28, schrieb Jen Clarke:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear David and list
>
> Our facility has had Amira/Avizo/AvizoFire software for 3D reconstruction etc for many years
> Whilst available for our whole facility, it is only a few users, predominantly myself and a few people in my lab, who use it.
> Its fantastic for 3D image math and visualisation, I do a considerable amount of 3D colocalisation work on z-stacks with it, in particular doing neurochemical analysis of nerve terminals in spinal cord slices.
>
> There is a small bug regarding uploading of lif (Leica image format files) when you come to re-opening saved Amira/Avizo networks, we reported this ages ago, its still a problem but we have worked out a simple workaround so contact me off list if you need. The workaround works in most but not all versions, hence I currently use AvizoFire v6.1 where it works and not AvizoFire v6.2 where it doesnt. (v6.3 now available, havent tried it yet). (You can of course always just load tif stacks). I havent worked with data sets from other formats.
>
> It struggles abit with large data sets, eg z-stacks 1024x1024x50 (frequent errors saying cant allocate sufficient bytes to perform image arithmetic - can usually work around by repeated re-loading of network, restarting of software and having all channel displays off for the calculation, and would definately struggle with isosurfaces on such size data sets), but works super smooth on eg 512x512x50 stacks
>
> 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
> (training and assistance available on Mondays only)
>
> Flinders University
> GPO Box 2100, Adelaide 5001
> Phone: 61 8 8204 6454/ 61 8 8204 6637
> Email: [hidden email]
> ________________________________________
> From: Confocal Microscopy List [[hidden email]] On Behalf Of Christian Götze [[hidden email]]
> Sent: Friday, 11 February 2011 3:39 AM
> To: [hidden email]
> Subject: Re: VSG's Avizo visualization software
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi David,
>
> but perhaps you have heard of amira? It's the same base. Don't know
> exactly why and how but in the meantime there seem to be two companies
> selling it - Visage Imaging calls it amira (the "original" name) and VSG
> calls it Avizo.
>
> It's an excellent visualization tool and used by a large number of
> groups around the world. The user interface is, let's say, something you
> need to get used to because it's quite different from everything else
> but you can have quite good visualizations out of it.
>
> Hope that helps
> Christian
>
> Am 10.02.2011 16:48, schrieb David Knecht:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Does anyone have experience with Avizo software for visualization and measurement? We are having a presentation by them tomorrow but I have never heard of the package before. Thanks- Dave
>>
>> Dr. David Knecht
>> Department of Molecular and Cell Biology
>> Co-head Flow Cytometry and Confocal Microscopy Facility
>> U-3125
>> 91 N. Eagleville Rd.
>> University of Connecticut
>> Storrs, CT 06269
>> 860-486-2200
>> 860-486-4331 (fax)
>
> --
> Christian Götze
>
> arivis - Multiple Image Tools GmbH
> Kröpeliner Straße 54, D-18055 Rostock
>
> http://www.arivis.com

--
Christian Götze

arivis - Multiple Image Tools GmbH
Kröpeliner Straße 54, D-18055 Rostock

Web : http://www.arivis.com