Re: Suggestion for good 3D analysis software- free rendering software from CISMM

[Tim O'Brien Sr.]

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

Dear Manoj-

There are a lot of good packages out there, but I would also try the free  3D rendering software available from our center.  You can find it at either the specific site for Imagesurfer (http://imagesurfer.cs.unc.edu/downloads.html) or go to the CISMM website (https://cismm.cs.unc.edu).  There is even a nice procedure for setting up a pretty inexpensive but very fun stereo view system with glasses and such on the site: (https://cismm.cs.unc.edu/core-projects/visualization-and-analysis/setting-up-a-simple-stereo-system/).  We have several set up in our lab and I use mine regularly.

The ImageSurfer program itself is constantly being updated.  It works on Macs and Windows at present, can output a movie of a rotating image, and can apply many different filters to the data.  Deconvolution is almost ready as well.  There is also a good user's guide.  

Anyway, having the virtue of being free, it is definitely worth looking at.  I use it to render stacks of labeled cells and to reconstruct fibrin clots in 3D.  There are examples on the websites.

Hope it helps!

Tim O'Brien
Computer Integrated Systems for Microscopy and Manipulation
UNC Chapel Hill, NC  







-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Manoj Jaiswal
Sent: Monday, August 06, 2012 9:23 AM
To: [hidden email]
Subject: Re: Suggestion for good 3D analysis software

*****
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
>

[Joe Ping-Lin Hsiao]

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

Hi Manoj,

I am the developer of ImageSurfer. I just want to add more details
regard Tim's post. ImageSurfer has a filter designed specifically for
extracting tube-shape structures, like blood vessels and neurons. As
for the analysis, I don't know what you are looking for, but
ImageSurfer can locate and highlight intersections in the branches and
output the ratio of each type of branch (3-way, 4-way, and etc). The
tutorial is at http://cismm.cs.unc.edu/resources/tutorials/imagesurfer-2-tutorials/imagesurfer2-fibrin-network-structure-analysis/.

There are also more tutorials available at
http://cismm.cs.unc.edu/resources/tutorials/imagesurfer-2-tutorials/.

Go take a look and feel free to shoot me an email if you have any questions.

Thanks,
Joe

On Mon, Aug 6, 2012 at 11:23 AM, O'Brien III, E. Timothy
<[hidden email]> wrote:

> Dear Manoj-
>
> There are a lot of good packages out there, but I would also try the free  3D rendering software available from our center.  You can find it at either the specific site for Imagesurfer (http://imagesurfer.cs.unc.edu/downloads.html) or go to the CISMM website (https://cismm.cs.unc.edu).  There is even a nice procedure for setting up a pretty inexpensive but very fun stereo view system with glasses and such on the site: (https://cismm.cs.unc.edu/core-projects/visualization-and-analysis/setting-up-a-simple-stereo-system/).  We have several set up in our lab and I use mine regularly.
>
> The ImageSurfer program itself is constantly being updated.  It works on Macs and Windows at present, can output a movie of a rotating image, and can apply many different filters to the data.  Deconvolution is almost ready as well.  There is also a good user's guide.
>
> Anyway, having the virtue of being free, it is definitely worth looking at.  I use it to render stacks of labeled cells and to reconstruct fibrin clots in 3D.  There are examples on the websites.
>
> Hope it helps!
>
> Tim O'Brien
> Computer Integrated Systems for Microscopy and Manipulation
> UNC Chapel Hill, NC
>
>
>
>
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Manoj Jaiswal
> Sent: Monday, August 06, 2012 9:23 AM
> To: [hidden email]
> Subject: Re: Suggestion for good 3D analysis software
>
> *****
> 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
>>