Visualization challenges in microsocpy

[Richard Superfine]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

We at CISMM would like to understand the community’s biggest challenges in visualization of 3d data. Do people use stereo or immersive (headmount, etc) displays and what is your experience with these? CISMM is an NIH resource for developing new technologies in biological forces, microscopy user interfaces, visualization and analysis. ( ww.cs.unc.edu/Research/nano/cismm). For example, We are developing visualization tools for flow through bloodclots and mucus flow over cell cultures. The phenomena in these cases require tiled z-stacks (time series) that provide long-range, high resolution images for which flexible viewing strategies are necessary. What kinds of specimens are you trying to understand where you would like long range, high resolution 3d data? Are your current visualization tools satisfactory? What else would you like to see? Would you like to “walk through” or “fly-over” your specimen?  We are also porting technologies from medical imaging to microscopy such as cut planes determined from non-planar surfaces defined by data,  and multiple volumetric scalar fields such as those from multiple fluorophores in confocal stacks. Ideas?

 

Richard Superfine

Bowman and Gordon Gray Professor

Department of Physics and Astronomy

Director, Center for Computer Integrated Systems for Microscopy and Manipulation

Phillips Hall CB3255

University of North Carolina

Chapel Hill, NC 27599-3255

919-962-1185; 919-962-0480 (fax)

CISMM: http://www.cs.unc.edu/Research/nano/cismm/index.html

Nanoscale Science Research Group: http://www.cs.unc.edu/Research/nano/index.html

[hidden email]

[Daniel James White]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi Richard,

For visualisation of 3D microscopy data, the free tools have come a  
long way in the recent past.

BioImageXD uses VTK for 3D graphics and ITK for image processing,
and does much of what you suggest below. It can do whatever VYK can,  
which is a lot.
Currently it lacks 3D  stitching but this would be relatively simple  
to implement using existing ITK,
and the hardware stereo using crystal eyes should work, but there is a  
bug presently stopping it.
( we have the lcd shutter glasses and big old CRTs here, and it works  
in imaris for example,
and users like it! I have asked for a demo of one of the newer auto  
stereo 3D lcd displays...)

The BioImageXD graphical user interface is designed for microscopists  
(as opposed to computer scientists),
and it stands up very well against the commercial competition, eg  
imaris and volocity. etc.

BioImageXD makes 3D rendered movies / animations, with key frame or  
camera path modes,
so spinning datasets and fly through, past etc movies, rather similar  
to imaris.

BioImageXD natively reads several confocal microscopy formats,
Zeiss, leica, olympus and more. We hope to leverage the power of LOCI  
bio-formats in the future.

Its written in python using python wrapped C++ libraries VTK, ITK and  
custom libs,
so is fast and simple to develop and add new stuff to. It is free,  
open source and GLPed.

ImageJ now has much better 3D rendering, and work is underway to get N  
dimensional data support.
My colleague here has just written a very good 3D stitching plugin for  
imageJ,
with sophisticated registration and fusion methods. You might want to  
talk to him.
Their solution is very good. It is being presented at a conference soon.

Have a look at BioImageXD, you are welcome to join the project if you  
think it is a good place to get going from.

cheers

Dan (BioImageXD team)

On Aug 19, 2008, at 6:00 AM, CONFOCAL automatic digest system wrote:

>
> Date:    Mon, 18 Aug 2008 07:59:29 -0400
> From:    Richard Superfine <[hidden email]>
> Subject: Visualization challenges in microsocpy
>
> This is a multipart message in MIME format.
>
> ------=_NextPart_000_0046_01C90108.5B35D2F0
> Content-Type: text/plain;
> charset="us-ascii"
> Content-Transfer-Encoding: 7bit
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> We at CISMM would like to understand the community's biggest  
> challenges in
> visualization of 3d data. Do people use stereo or immersive  
> (headmount, etc)
> displays and what is your experience with these? CISMM is an NIH  
> resource
> for developing new technologies in biological forces, microscopy user
> interfaces, visualization and analysis. ( ww.cs.unc.edu/Research/
> nano/cismm
> <http://www.cs.unc.edu/Research/nano/cismm> ). For example, We are
> developing visualization tools for flow through bloodclots and mucus  
> flow
> over cell cultures. The phenomena in these cases require tiled z-
> stacks
> (time series) that provide long-range, high resolution images for  
> which
> flexible viewing strategies are necessary. What kinds of specimens  
> are you
> trying to understand where you would like long range, high  
> resolution 3d
> data? Are your current visualization tools satisfactory? What else  
> would you
> like to see? Would you like to "walk through" or "fly-over" your  
> specimen?
> We are also porting technologies from medical imaging to microscopy  
> such as
> cut planes determined from non-planar surfaces defined by data,  and
> multiple volumetric scalar fields such as those from multiple  
> fluorophores
> in confocal stacks. Ideas?
>
>
>
>
>
> Richard Superfine
>
> Bowman and Gordon Gray Professor
>
> Department of Physics and Astronomy
>
> Director, Center for Computer Integrated Systems for Microscopy and
> Manipulation
>
> Phillips Hall CB3255
>
> University of North Carolina
>
> Chapel Hill, NC 27599-3255
>
> 919-962-1185; 919-962-0480 (fax)
>
> CISMM:  <http://www.cs.unc.edu/Research/nano/cismm/index.html>
> http://www.cs.unc.edu/Research/nano/cismm/index.html
>
> Nanoscale Science Research Group:
> <http://www.cs.unc.edu/Research/nano/index.html>
> http://www.cs.unc.edu/Research/nano/index.html
>
> [hidden email]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany


New Mobile Number!!!

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )