Bitmap converter needed (Confocal microscope to TIFF etc.)

Bitmap converter needed (Confocal microscope to TIFF etc.)

Post by William Calv » Fri, 14 Sep 1990 03:58:05



I need a bitmap converter (to run under MSDOS, e.g., Quickbasic) that
will take confocal microscope image files (from Bio-Rad's) and make
a standard format like TIFF or PCX.  I have the file specs but hope
to avoid writing the program!

  William H. Calvin


  Seattle WA 98195    206/328-1192  206/543-1648

 
 
 

1. 3-D images from confocal microscope

I cannot suggest any software that accomodates 3D reconstruction of confocal
data, but I will mail you a copy of the Survey of Methods for 3-Dimensional
Reconstruction 1991-1993 (26 kilobytes long) that was posted in the newsgroup
comp.graphics.  Here is what that survey says about confocal data:
----------------------------------------------------------------------------
If you can access an SGI then

1) Bring the images over to the SGI.  You have to know the format they are in.
The best form would be a LxM file of bytes.  Each byte representing an
intensity.

2) Then do

 cat img.1 img.2 imn.n > imgLxMxN.bin

3) view the "volume" using bob.  This program is free and available from
several sites.  its home is at ftp.arc.umn.edu.  This is very useful for
viewing the whole volume.  This of course does not reconstruct the image in
the sense of extracting structural info, but by cleverly manipulating the
colormap one can "see" surprising amounts of detail.

I have helped a person who studies embryo development using confocal
microscopy.  He needed roughly 20 pictures (the N dimension) to get reasonable
info.  The more slices you have the better it is :)

<begin blurb>

The Army High Performance Computing Research Center (AHPCRC) and the
Minnesota Supercomputer Center, Inc., have been developing a set of
tools to work with large time dependent 2D and 3D data sets.  In the
Graphics and Visualization Lab (GVL) we are using these tools along
side standard packages, such as SGI Explorer and the Utah Raster
Toolkit, to render 3D volumes and create digital movies.  A couple of
the more general purpose programs have been bundled into a package
called "GVLware".

GVLware, currently consisting of Bob, Raz and Icol, is now available
via ftp.  The most interesting program is probably Bob, an interactive
volume renderer for the SGI.  Raz streams raster images from disk to
an SGI screen, enabling movies larger than memory to be played.  Icol
is a color map editor that works with Bob and Raz.  Source and
pre-built binaries for IRIX 4.0.1 are included.

To acquire GVLware, anonymous ftp to:
        machine - ftp.arc.umn.edu
        file    - /pub/gvl.tar.Z

<end blurb>


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