[vtkusers] Hardware stereo 3D viewing of confocal images

[Mike Dresser]

Hello Dan.

We've used VTK and related software to visualize LSM510 volumes, though
using Windows boxes, for a couple of years with very good results.  The .lsm
file format is available from Zeiss, so that if you want to read in the data
directly you can generate a reader.  I've written a simple, limited .lsm
file reader for an application that we use in-house - I'm not much of a
programmer, but I'll clip out the relevant parts and send them if you
promise not to laugh in public.  Alternatively, the LSM510 software can
export single-channel data to a series of .tifs, and VTK includes a TIFF
file reader that may be able to handle these files relatively easily.
You'll have to enter spacing, wavelength, etc., manually if you go the .tif
route.

If you're not interested in writing the code, then I highly recommend
VolView from Kitware, which does run in Linux, and does handle the
LSM510-output .tifs.  We've been using VolView for a year or more and have a
number of labs that use it regularly.  We have not tried to use
stereo-viewing hardware, so I can't address that part of your question.  If
you can afford it, I would highly recommend getting a VolumePro board from
TeraRecon (don't know if it works in Linux) which allows very rapid zooming,
rotating, etc. with large datasets.  The VolumePro board is supported by VTK
and by VolView.  (I don't work for any of the companies involved.)

Mike

------------
Michael E. Dresser, MD/PhD
Assoc. Member, Molecular and Cell Biology
Director, Core Facility for Imaging
405-271-7682

Oklahoma Medical Research Foundation
825 NE 13th St.
Oklahoma City, OK 73104

-----Original Message-----
From: Dr. Dan White [mailto:dan at chalkie.org.uk]
Sent: Friday, August 16, 2002 5:37 AM
To: vtkusers at public.kitware.com
Cc: ppkank at cc.jyu.fi
Subject: [vtkusers] Hardware stereo 3D viewing of confocal images


Hi All,

I'm new to this list, so hope I'm directing these questions to the 
right people.

I have a linux workstation primarily set up for viewing 3D models of 
proteins using Stereographics crystal eyes hardware.

We have many people doing confocal microscopy with multiple stains 
using LSM 510 imaging software.
We want a good way to reconstruct 3D images from layers of confocal 
image "slices", and be able to look at the 3D representations in 
hardware stereo on this linux workstation.

Am I right in thinking VTK has the right tools for this job? If so, 
can anyone give me any tips on how to get started?

I have the current VTK sources and docs and examples. What is the 
right way to use the cake complier tool to get VTK up and running? I 
see stuff about Tcl and Tk , and also python wrapping, which I know 
very little about. Does this give the GUI? Is there a GUI? Or is it a 
command line interface?

Does VTK allow you to spin and zoom a 3D image around on the screen 
in any direction with the mouse, and use crystal eyes stereo 
viewing??????

Hope someone can help!!!!

Dan White


dan at chalkie.org.uk
http://www.chalkie.org.uk

Daniel James White PhD.
Cell Biology
Department of Biological and Environmental Science
University of Jyväskylä
FIN-40351
Jyväskylä
Finland

+358 (0)14 260 4183 (office)

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