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Help in Selecting 3D Measurement Software

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Earl_Sanford

Help in Selecting 3D Measurement Software

I am sorry if this topic has been discussed recently but I checked the archives
and did not find anything too recent.

I am currently trying to determine which software package to acquire in order
to make volumetric measurements from z-stacks collected on a confocal
microscope. I want a package that is rather intuitive and straight forward to
obtain size information (length, width, volume, etc.). Unfortunately I am not
familiar with many of the packages available. I am currently using using ImageJ
but am looking to find something that is a little more refined. However since
the commercial packages are not inexpensive, I need to make sure I get the
best package available to make the above measurements.

Please let discuss the stregths and weakness of the software packages you
are familiar with.

Thanks for your help
Earl

Armstrong, Louise

Re: Help in Selecting 3D Measurement Software

*COMMERCIAL RESPONSE*

Hi Earl

There are a number of commercial software packages for 3D analysis of
confocal images and your choice is likely to depend on what it is you
want to do.

Both Volocity from PerkinElmer and Imaris from Bitplane are strong in 3D
visualization and analysis and both have slightly different areas of
strength depending upon the types of measurements you want to make.

If you would like to contact me off list then I can arrange for one of
our imaging specialists to contact you to discuss your application.
Having worked with Volocity and the team since before it was launched 10
years ago, I know they will give you an honest opinion on where our
strengths and weaknesses lie.

If you want to try it for yourself then we recently introduced a free
demonstration version of Volocity which you can download from our
website. Accompanying it there is some demo data and web-based
tutorials and notes to guide you through how to recreate the steps such
as selecting 3D objects and measuring volumes. I hope this will let you
try it out on your own images. You can always ask for a specialist to
contact you at any point.

www.cellularimaging.com/products/volocity/demo

Best wishes

Louise

Louise Armstrong-Denby PhD | Global Product Manager, Bio-discovery
PerkinElmer | For the Better
[hidden email]
Phone: +44 24 7669 2229 | Fax: +44 24 7669 0091 |
Viscount Centre II, University of Warwick Science Park, Millburn Hill
Road, Coventry CV4 7HS, UK
www.perkinelmer.com
Please consider the environment before printing this e-mail.
This e-mail message and any attachments are confidential and proprietary
to PerkinElmer, Inc. If you are not the intended recipient of this
message, please inform the sender by replying to this email or sending a
message to the sender and destroy the message and any attachments.
Thank you.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of Earl Sanford
Sent: 09 September 2010 20:23
To: [hidden email]
Subject: Help in Selecting 3D Measurement Software

I am sorry if this topic has been discussed recently but I checked the
archives
and did not find anything too recent.

I am currently trying to determine which software package to acquire in
order
to make volumetric measurements from z-stacks collected on a confocal
microscope. I want a package that is rather intuitive and straight
forward to
obtain size information (length, width, volume, etc.). Unfortunately I
am not
familiar with many of the packages available. I am currently using using
ImageJ
but am looking to find something that is a little more refined. However
since
the commercial packages are not inexpensive, I need to make sure I get
the
best package available to make the above measurements.

Please let discuss the stregths and weakness of the software packages
you
are familiar with.

Thanks for your help
Earl

Michael Weber-4

Re: Help in Selecting 3D Measurement Software

Louise, good to hear that there is finally a Volocity demo!

Earl, you can also ask your local Andor/Bitplane representative for a demo
license of Imaris. A hands-on demo is always the best choise, especially
if you already have samples to analyze. Both Imaris and Volocity can
perform volume measurements, although the approach is a bit different. The
price model might also be of interest for you, as it is different as well.

Michael

> *COMMERCIAL RESPONSE*
>
> Hi Earl
>
> There are a number of commercial software packages for 3D analysis of
> confocal images and your choice is likely to depend on what it is you
> want to do.
>
> Both Volocity from PerkinElmer and Imaris from Bitplane are strong in 3D
> visualization and analysis and both have slightly different areas of
> strength depending upon the types of measurements you want to make.
>
> If you would like to contact me off list then I can arrange for one of
> our imaging specialists to contact you to discuss your application.
> Having worked with Volocity and the team since before it was launched 10
> years ago, I know they will give you an honest opinion on where our
> strengths and weaknesses lie.
>
> If you want to try it for yourself then we recently introduced a free
> demonstration version of Volocity which you can download from our
> website. Accompanying it there is some demo data and web-based
> tutorials and notes to guide you through how to recreate the steps such
> as selecting 3D objects and measuring volumes. I hope this will let you
> try it out on your own images. You can always ask for a specialist to
> contact you at any point.
>
> www.cellularimaging.com/products/volocity/demo
>
> Best wishes
>
> Louise
>
>
> Louise Armstrong-Denby PhD | Global Product Manager, Bio-discovery
> PerkinElmer | For the Better
> [hidden email]
> Phone: +44 24 7669 2229 | Fax: +44 24 7669 0091 |
> Viscount Centre II, University of Warwick Science Park, Millburn Hill
> Road, Coventry CV4 7HS, UK
> www.perkinelmer.com
> Please consider the environment before printing this e-mail.
> This e-mail message and any attachments are confidential and proprietary
> to PerkinElmer, Inc. If you are not the intended recipient of this
> message, please inform the sender by replying to this email or sending a
> message to the sender and destroy the message and any attachments.
> Thank you.
>
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Earl Sanford
> Sent: 09 September 2010 20:23
> To: [hidden email]
> Subject: Help in Selecting 3D Measurement Software
>
> I am sorry if this topic has been discussed recently but I checked the
> archives
> and did not find anything too recent.
>
> I am currently trying to determine which software package to acquire in
> order
> to make volumetric measurements from z-stacks collected on a confocal
> microscope. I want a package that is rather intuitive and straight
> forward to
> obtain size information (length, width, volume, etc.). Unfortunately I
> am not
> familiar with many of the packages available. I am currently using using
> ImageJ
> but am looking to find something that is a little more refined. However
> since
> the commercial packages are not inexpensive, I need to make sure I get
> the
> best package available to make the above measurements.
>
> Please let discuss the stregths and weakness of the software packages
> you
> are familiar with.
>
> Thanks for your help
> Earl

Vitaly Boyko

Re: Help in Selecting 3D Measurement Software

Earl, I guess there should be much cheaper and more intuitive options than Volocity, Metamorph or Imaris...

Cheers,

Vitaly

From: Michael Weber <[hidden email]>
To: [hidden email]
Sent: Fri, September 10, 2010 7:36:06 AM
Subject: Re: Help in Selecting 3D Measurement Software

Louise, good to hear that there is finally a Volocity demo!

Earl, you can also ask your local Andor/Bitplane representative for a demo
license of Imaris. A hands-on demo is always the best choise, especially
if you already have samples to analyze. Both Imaris and Volocity can
perform volume measurements, although the approach is a bit different. The
price model might also be of interest for you, as it is different as well.

Michael

Chris Guerin

Re: Help in Selecting 3D Measurement Software

In reply to this post by Earl_Sanford

Hello Earl:

As someone who runs a core facility I can comment that my users find Volocity to be very powerful, intuitive and easy to use. I also agree with the comment made before though that depending on what you want to do specifically another program might be better at certain tasks. The other thing I can comment on is the support offered by Perkin Elmer after you've bought the product. Volocity support is simply outstanding. It is also great that it's multi platform (PC and Mac) and that it can run under 64 bit operating systems and if you're dealing with large data sets this is a great advantage. We frequently use it on gigabyte data sets which choke other programs and it performs very well. Finally I also agree with the others who have suggested "try before you buy". it's the only way to know if what others find easy and powerful will work as well for you.

Good luck,

Chris

Christopher Guérin, Ph.D.

Leader, Microscopy Core

V.I.B., D.M.B.R., Univ. Gent

Fiers-Schell-Van Montagu' building
Technologiepark 927, B-9052 Ghent (Zwijnaarde) - Belgium
tel : +32-9-33 13 611

[hidden email]

web:http://www.dmbr.ugent.be/ext/public/microscopy/index.html

Neeraj Gohad-2

Re: Help in Selecting 3D Measurement Software

In reply to this post by Michael Weber-4

Hi Earl,

We were in the same boat couple of months ago. We evaluated Bitplane's Imaris and Visage Imaging's amira. Both the companies offered us demo licenses and gave us webminars to get us started. People from both these companies were very helpful and knowledgeable. At the end of our evaluation we found Imaris to be more intuitive and suited for our application. Imaris has many modules and the price goes up as you add modules, we have the confocal standard and statistics package that helps us do all sorts of measurements on confocal datasets, the statistics package allows you to color code objects using features like area, volume etc. We also like the key frame animation feature where you can create fly through movies with your datasets, it's a very effective way of communicating 3D data.

As always, no commercial interest,

Best,

Neeraj.

Neeraj V. Gohad, Ph.D.
Postdoctoral Fellow
Okeanos Research Group
Department of Biological Sciences
132 Long Hall
Clemson University
Clemson,SC-29634
Phone: 864-656-3597
Fax: 864-656-0435

Website: http://www.clemson.edu/okeanos

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Weber
Sent: Friday, September 10, 2010 7:36 AM
To: [hidden email]
Subject: Re: Help in Selecting 3D Measurement Software

Louise, good to hear that there is finally a Volocity demo!

Earl, you can also ask your local Andor/Bitplane representative for a demo
license of Imaris. A hands-on demo is always the best choise, especially
if you already have samples to analyze. Both Imaris and Volocity can
perform volume measurements, although the approach is a bit different. The
price model might also be of interest for you, as it is different as well.

Michael

Arvonn Tully

Re: Help in Selecting 3D Measurement Software

In reply to this post by Earl_Sanford

*COMMERCIAL RESPONSE*

Dear Earl,

I think that you will find that there are three main commercial packages, Amira (Avizo? ), Imaris and Volocity. Each package should be able provide those results, but due to the different workflows, you will find that certain software is easier than others to use.

Depending on the complexity of the image, you will find each software package has very different segmentation (feature extraction) tools for analyzing the objects of interest. I urge you to pay attention to these tools, which are critical for accurately defining your objects, and subsequently measuring those objects.

If you would like to try using the Imaris software, please either give us a call at:

1-888-332-4879 or visit our demo download webpage:

http://www.bitplane.com/go/download/imaris-evaluation.

Someone from Bitplane will get in touch with you shortly thereafter, and they will provide you with a personalized demonstration of the software. Please note that the Imaris demonstration version software will work with any of supported Image formats, and Imaris is not limited to demo data sets (although we provide a few to get you started).

We strongly encourage you to evaluate all of the products, side by side if possible, to see what works best for your needs.

Best Regards,

Arvonn Tully

Technical and Application Support

Western United States
[hidden email]
Support Telephone:+1-888-332-4879 ext 12
fax: 866-691-9112
Bitplane, Inc.
http://www.bitplane.com

On Thu, Sep 9, 2010 at 12:23 PM, Earl Sanford <[hidden email]> wrote:

I am sorry if this topic has been discussed recently but I checked the archives
and did not find anything too recent.

I am currently trying to determine which software package to acquire in order
to make volumetric measurements from z-stacks collected on a confocal
microscope. I want a package that is rather intuitive and straight forward to
obtain size information (length, width, volume, etc.). Unfortunately I am not
familiar with many of the packages available. I am currently using using ImageJ
but am looking to find something that is a little more refined. However since
the commercial packages are not inexpensive, I need to make sure I get the
best package available to make the above measurements.

Please let discuss the stregths and weakness of the software packages you
are familiar with.

Thanks for your help
Earl

Bob Nienhuis

Re: Help in Selecting 3D Measurement Software

In reply to this post by Earl_Sanford

How do these packages do volumetric measurement differently than stereological

approaches? I understand that several groups are now applying stereological methods

to confocal image stacks.

Bob Nienhuis

VA / UCLA Neurobiological Research

North Hills, CA

Mika Hukkanen

Re: Help in Selecting 3D Measurement Software

We have done some volumetric measurements on podosomes and invadopodia in epithelial-mesenchymal transition; some points to keep in mind – deconvolution to take into account for the psf, and standard curves generated of beads of known sizes (different sizes related to the volume of interests). The packages that have been mentioned most likely do the job ok, however, if you go for a commercial one the license maintenance fees per annum can be quite high. Initial purchase price may not seem that high but are you willing, for the years to come, to pay some 1000;- eur per each module just for bug fixes and upgrades?

Mika Hukkanen

Biomedicum Imaging Unit

Helsinki, Finland

http://research.med.helsinki.fi/biu/

Guy Cox-2

Re: Help in Selecting 3D Measurement Software

In reply to this post by Bob Nienhuis

Stereology essentially uses a random approach – you count how your sampling pattern intersects with the structure you are measuring. It can therefore get you measurements of (eg) organelle volume or membrane area from random slices. Maybe you can use a full stack of optical sections but there is no need for it. What you end up with is an estimate based on sampling statistics.

What these programs (and others) do is apply standard segmentation methods in three dimensions, so you get an exact measure of what is in the sampled volume (or at least, as accurate as your original segmentation, and that’s another can of worms).

Guy

Optical Imaging Techniques in Cell Biology

by Guy Cox CRC Press / Taylor & Francis

http://www.guycox.com/optical.htm

______________________________________________

Associate Professor Guy Cox, MA, DPhil(Oxon)

Australian Centre for Microscopy & Microanalysis,

Madsen Building F09, University of Sydney, NSW 2006

Phone +61 2 9351 3176 Fax +61 2 9351 7682

Mobile 0413 281 861

______________________________________________

http://www.guycox.net

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Bob Nienhuis
Sent: Saturday, 11 September 2010 10:28 AM
To: [hidden email]
Subject: Re: Help in Selecting 3D Measurement Software

How do these packages do volumetric measurement differently than stereological

approaches? I understand that several groups are now applying stereological methods

to confocal image stacks.

Bob Nienhuis

VA / UCLA Neurobiological Research

North Hills, CA

Vincent Schoonderwoert

Re: Help in Selecting 3D Measurement Software

In reply to this post by Earl_Sanford

*commercial response*

Dear all,

We would like to respond to the initial request that Earl Sanford posted, concerning an interest in comparing inexpensive 3D visualization and analysis software packages.

As was also mentioned in previous comments, we very much encourage testing the available software.
This is why we would like to bring our Huygens software under attention, since it was not specifically mentioned yet.
Huygens is known for its high quality deconvolution but offers also advanced 3D visualization and analysis tools.
Huygens can be downloaded from http://www.svi.nl/download using the 'request license on-line' button.

Best,
Vincent Schoonderwoert

Scientific Volume Imaging bv
Imaging Specialist/Account Manager
[hidden email]

Laapersveld 63
1213 VB Hilversum, The Netherlands
Tel: + 31 35 646 8216
Fax: + 31 35 683 7971
www.svi.nl
FAQ: http://support.svi.nl

Earl Sanford wrote:

I am sorry if this topic has been discussed recently but I checked the archives 
and did not find anything too recent.

I am currently trying to determine which software package to acquire in order 
to make volumetric measurements from z-stacks collected on a confocal 
microscope. I want a package that is rather intuitive and straight forward to 
obtain size information (length, width, volume, etc.). Unfortunately I am not 
familiar with many of the packages available. I am currently using using ImageJ 
but am looking to find something that is a little more refined. However since 
the commercial packages are not inexpensive, I need to make sure I get the 
best package available to make the above measurements.

Please let discuss the stregths and weakness of the software packages you 
are familiar with.

Thanks for your help
Earl

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