Suggestion for good 3D analysis software

[manojshree]

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Hello friends,
I need to buy a 3D quantification software to analyze data in large z-stack.
Stack is going to be complex where we need to visualize blood vessesl,
artery and neurons and astocytes.  I dont know which is the best software
available in the market. Any suggestion would be great.

Thanks,
Manoj

[Alberto Diaspro]

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we used our www.powermicroscope.com before hackers attacked it... i suggest that packages by Scientific Volume Imaging are excellent...Hans van der Voort, behind them, is one of the best in the field website: www.svi.nl
all the best
alby

do not miss www.maf13.org


Il giorno 05/ago/2012, alle ore 11:40, Manoj Jaiswal <[hidden email]> ha scritto:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello friends,
> I need to buy a 3D quantification software to analyze data in large z-stack.
> Stack is going to be complex where we need to visualize blood vessesl,
> artery and neurons and astocytes.  I dont know which is the best software
> available in the market. Any suggestion would be great.
>
> Thanks,
> Manoj

[John Hyun-2]

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Manoj,

Try the 3D Visualization component of DigitalMicrograph. See: http://gatan.com/products/software/3D_Visualization.php

You can download a full demo version for free. I hope this helps.

Best regards,

John Hyun
Marketing Communications Manager

Gatan, Inc.
5794 W. Las Positas Blvd.
Pleasanton, CA 94588

Tel: [phone]
Fax: [phone]
Email: [hidden email]
Web: www.gatan.com

Manoj Jaiswal <[hidden email]> wrote:


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Hello friends,
I need to buy a 3D quantification software to analyze data in large z-stack.
Stack is going to be complex where we need to visualize blood vessesl,
artery and neurons and astocytes.  I dont know which is the best software
available in the market. Any suggestion would be great.

Thanks,
Manoj

[George McNamara]

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Hi Manoj,

Volocity or Imaris or Huygens (for latter see Alby's reply) can probably
do what you want. Fiji ImageJ might be able to.

FARSIGHT Toolkit has already done it:

http://www.farsight-toolkit.org/wiki/FARSIGHT_Toolkit

Associative image analysis: a method for automated quantification of 3D
multi-parameter images of brain tissue. </pubmed/18294697> Bjornsson CS,
Lin G, Al-Kofahi Y, Narayanaswamy A, Smith KL, Shain W, *Roysam B*.

J Neurosci Methods. 2008 May 15;170(1):165-78. PMID: 18294697

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700351/figure/F4/

Badri Roysam and colleagues have a lot more papers using FARSIGHT, above
was the first.

While I'm thinking about it - request to Fiji ImageJ/ImageJ2 organizers:
Please incorporate FARSIGHT into Fiji.


Blood vessel labeling:

Consider DiA, ~450 nm excitation, ~590 nm emission (so "blue" with
respect to excitation).

Best to learn how to label blood vessels with lipophilic dyes by
starting out with DiI:

Li Y, Song Y, Zhao L, Gaidosh G, Laties AM, Wen R. Direct labeling and
visualization of blood vessels with lipophilic carbocyanine dye DiI. Nat
Protoc. 2008;3(11):1703-8. PubMed PMID: 18846097

Plan BV:

Consider a BV421-antibody conjugate, such as anti-CD31 (anti-PECAM). For
more on BV421 and its siblings, see

http://www.biolegend.com/brilliantviolet

Plan H: you should be able to label all the blood vessel nuclei with
Hoechst or other DNA counterstains. If you want to label just the
endothelial cell nuclei, might be able to do this (somewhat) selectively
by using low concentration and perfusion incubation time.

George



On 8/5/2012 5:40 AM, Manoj Jaiswal wrote:

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

I need to buy a 3D quantification software to analyze data in large z-stack.

Stack is going to be complex where we need to visualize blood vessesl,
artery and neurons and astocytes.  I dont know which is the best software
available in the market. Any suggestion would be great.

Hello folks,

I am looking for a dye for blood vessels labeling in the blue emission
range. Any suggestion. Cascade blue did not work well in our hand and i did
not find any dextean conjugates in blue color.
Thanks,

Manoj

[manojshree]

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Hello Alberto, John and George and other friends,

Thank you so much for the reply. I will soon decide after the demo trial.

Thanks,
Manoj

On Sun, Aug 5, 2012 at 5:40 AM, Manoj Jaiswal <[hidden email]>wrote:

> Hello friends,
> I need to buy a 3D quantification software to analyze data in large z-stack.
> Stack is going to be complex where we need to visualize blood vessesl,
> artery and neurons and astocytes.  I dont know which is the best software
> available in the market. Any suggestion would be great.
>
> Thanks,
> Manoj
>

[Erik von Stedingk]

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(Commercial response, although from my private email)
Hello Manoj
I would think one of my colleagues in the US will have been in contact with
you by now. I don't want to use this space for (overt) sales purposes but I
wanted to point out that our FilamentTracer module could be exquisitely apt
for your application as there are algorithms for both vessels and neurons.
Don't forget to ask my colleague to show you the range of semi-manual
procedures to trace filaments in a data-stack. In a complex stack, this
could be most important.

If you go to http://www.bitplane.com/go/download/imaris-evaluation you can
ask for a demo download of our full package.

Best regards
Erik von Stedingk
(EMEA Distr. Network Sales Exec)

2012/8/5 Manoj Jaiswal <[hidden email]>

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello friends,
> I need to buy a 3D quantification software to analyze data in large
> z-stack.
> Stack is going to be complex where we need to visualize blood vessesl,
> artery and neurons and astocytes.  I dont know which is the best software
> available in the market. Any suggestion would be great.
>
> Thanks,
> Manoj
>

--
****************************************
Erik von Stedingk - [hidden email]
0735 11 29 00 - 08 739 86 87
****************************************

[Sathya]

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Hi Manoj,

Have you tried stereology software for your analysis? You can load z-stacks 
using one and can do various types of analysis like blood vessel density (length per unit 
area -L, or length per unit volume - Lv), or count different types of cells in a 3D stack.
There are a few commercial stereology softwares in the market, just to name a few:
StereoInvestigator from MBF Bioscience (http://www.mbfbioscience.com/), Visiopharm (http://www.visiopharm.com/), 
SRC (http://www.disector.com/), to just name a few. We have used StereoInvestigator from 
MBF Bioscience and we have got good results for blood vessel analysis in 3D stacks obtained 
using confocal microscope. If you are interested in neuron tracing, they also have
Neurolucida, Autoneuron and auto spine modules. Hope it helps.

Sathya

> Date: Mon, 6 Aug 2012 09:23:09 -0400
> From: [hidden email]
> Subject: Re: Suggestion for good 3D analysis software
> To: [hidden email]
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello Alberto, John and George and other friends,
>
> Thank you so much for the reply. I will soon decide after the demo trial.
>
> Thanks,
> Manoj
>
> On Sun, Aug 5, 2012 at 5:40 AM, Manoj Jaiswal <[hidden email]>wrote:
>
> > Hello friends,
> > I need to buy a 3D quantification software to analyze data in large z-stack.
> > Stack is going to be complex where we need to visualize blood vessesl,
> > artery and neurons and astocytes. I dont know which is the best software
> > available in the market. Any suggestion would be great.
> >
> > Thanks,
> > Manoj
> >

     

[manojshree]

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Thanks Josh.
Manoj


On Sun, Aug 5, 2012 at 8:46 AM, John Hyun <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Manoj,
>
> Try the 3D Visualization component of DigitalMicrograph. See:
> http://gatan.com/products/software/3D_Visualization.php
>
> You can download a full demo version for free. I hope this helps.
>
> Best regards,
>
> John Hyun
> Marketing Communications Manager
>
> Gatan, Inc.
> 5794 W. Las Positas Blvd.
> Pleasanton, CA 94588
>
> Tel: [phone]
> Fax: [phone]
> Email: [hidden email]
> Web: www.gatan.com
>
> Manoj Jaiswal <[hidden email]> wrote:
>
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello friends,
> I need to buy a 3D quantification software to analyze data in large
> z-stack.
> Stack is going to be complex where we need to visualize blood vessesl,
> artery and neurons and astocytes.  I dont know which is the best software
> available in the market. Any suggestion would be great.
>
> Thanks,
> Manoj
>

[samuel connell]

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Hello Manoj,

*****Commercial Response*****

I would like to also take the time to offer you a trial of SlideBook
software. SlideBook has detailed analysis, visualization, and presentation
tools for 3D microscopy data sets.

Feel free to contact me off list if you would be interested in exploring
this user-friendly scientist designed software.

Best Regards,
--

Sam

------------------------

Samuel A. Connell

Senior Applications Scientist

Intelligent Imaging Innovations, Inc

Office: [phone] x6926

[hidden email]




On Sat, Aug 11, 2012 at 2:13 PM, Manoj Jaiswal <[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Thanks Josh.
> Manoj
>
>
> On Sun, Aug 5, 2012 at 8:46 AM, John Hyun <[hidden email]> wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Manoj,
> >
> > Try the 3D Visualization component of DigitalMicrograph. See:
> > http://gatan.com/products/software/3D_Visualization.php
> >
> > You can download a full demo version for free. I hope this helps.
> >
> > Best regards,
> >
> > John Hyun
> > Marketing Communications Manager
> >
> > Gatan, Inc.
> > 5794 W. Las Positas Blvd.
> > Pleasanton, CA 94588
> >
> > Tel: [phone]
> > Fax: [phone]
> > Email: [hidden email]
> > Web: www.gatan.com
> >
> > Manoj Jaiswal <[hidden email]> wrote:
> >
> >
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Hello friends,
> > I need to buy a 3D quantification software to analyze data in large
> > z-stack.
> > Stack is going to be complex where we need to visualize blood vessesl,
> > artery and neurons and astocytes.  I dont know which is the best software
> > available in the market. Any suggestion would be great.
> >
> > Thanks,
> > Manoj
> >
>