resume des reponses recues

David Sourdive sourdive
Tue Sep 29 10:21:07 EST 1992

 Voisci un resume des reponses que j'ai recues suite a ma demande
 d'information :

 Here is a summary of the answers I have received so far on a image processing
program for quantitative fluorescence microscopy :

>From knosp at sarah.iaf.uiowa :

Vaytek, Inc. offers a line of products that run on pcs, mac II's, HP
workstations, and Silicon Graphics workstations.  They
can be reached at 515-472-2227 (Fairfield, IA).

Their microtome software performs deconvolution and other useful microscopy

Their volume rendering software, Voxblast, operates on SGI, HP, Dec, IBM, Sun
workstations and they also have a version which operates on PC's and Mac II's.

Voxblast allows several 3d quantitative operations in addition to an array
of display and data manipulation techniques.

Vaytek has demos of their software they can send you.

Boyd Knosp				319-335-6715
University of Iowa			knosp at tessa.iaf.uiowa.edu
Image Analysis				77 EMRB Iowa City, IA 52242

>From hauch at cheme.washington.edu :

You will undoubtedly want
to contact the Inovision Corp. 

Inovision CorporationJ
PO Box 12539
2810 Meridian Parkway Ste 100
Research Triangle Park  NC    27709-2539J

Doug Benson, President
David Fine sales rep
Image analysis software for sun.
ISee, RatiotoolJ
919-361-5876 FaxJ

>From mangalam at salk-sc2.sdsc.edu :

Regarding your request for information regarding the capture and processing
of video images from a microscope at 1000X1000X12-16 bits, for an
application running on a *nix workstation.

>The application should meet these requirements
>(or at least part of them) :
>- deliver a good and fast video display of the image(s)* (see below)
>- standard operations on images (+, x, -, convoluation,*
>  noise reduction, linear or non linear LUTs)*(with the free NCSA PALedit)
>- counting cells*
>- numbering nuclei as objects (contours, areas, ...)* (I think)
>- integrating the signal within these objects*
>- define masks and apply them to other images*
>- show the data in statistical format (histograms,
>  correlations, ...) or export it in a format compatible with  
>  standard statistics processing applications (Macintosh
>  or MS/DOS Excel,Cricket Graph, or Unix based applications,..)*
>- print the images to a thermal/laser printer *
>- drive the microscope stage (z axis, or even 3 axes)
>- perform 3-D reconstruction and display from a user
>  defined angle. *(sort of)

   There are number of answers, none of which (of course) answers all your
requirements.  Surprisingly, many of them can be met by Wayne Rasband's
(free) NIH Image running on a Mac.  It can perform all the points marked by
a * above, including direct support for at least 2 video frame grabbers. 
The major limitation is that it was not built to handle the _huge_ image
files that you mention and it has the unfortunate limitation that it will
only handle 8bits of color/greyscale.  If you can reduce the amount of
data, or you are willing to write the modifications to his routines (Pascal
source code is freely available)), then you could save a great deal of
money. (If you were to re-write the source code you could also link in the
routines to use a very fast coprocessor like the Tuplex i860 for the
graphic convolutions/transformations.) The first thing to do is to download
the documentation and the program to see if it is worth the effort. Image
is available from alw.nih.gov in /pub/image.
   If you absolutely demand the size of files you state, only a _very_ fast
workstation will be able to handle them in a 'real-timely' manner, an SGI
Indigo R4000/Elan at minimum and up. SGI recently released it's Reality
Engine - 8 i860 superscalar processors dedicated to graphics processing at
(only!) $60,000 academic on top of whatever VME box you put it in (AMAZING
   The SGI recently released a set of video manipulation tools for the
Indigo - it requires a $2500 board (that only fits into the R3000 based
Indigo because of the size of the R4000 board) but some software tools are
included in the system software. I rather doubt that this board will handle
1Kx1Kx16 bit video capture, though - ask SGI about it.  
   At any rate, to do the analysis, you will have to use some additional
   After digitization, you can reconstruct the image with a program called
SYNU (SYnthetic UNiverse) from UCSD and the San Diego Supercomputer Center
(costs ~$100 to cover costs) which can handle huge data sets and render
beautiful reconstructions (call David Hessler @ 619 534 7968 or Steve Young
@ 619 534 3539 - unfortunately, it only runs on SGI hardware)
   There is also a horrendously expensive (~$20,000), but quite capable 3D
volume rendering/analysis package called VoxelView (Vital Images; phone:
515-472-7726 Ext 118, fax: 515-472-1661, email: userserv at vitalimages.com)
which can do some of the other kinds of image analysis that you require
(also requires SGI hardware).
   Summary - try NIH Image first, rewriting that code that you need to,
then use SYNU if you need it for better reconstruction.

Std Disclaimers Apply...



Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                             mangalam at salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                        mangalam at salk-sgi.sdsc.edu
La Jolla CA 92037                                    mangalam at salk.bitnet

From: s.budd at imperial.ac.uk :

I would suggest you look at the KHOROS software.  I enclose a short

sinclair Budd

     KHOROS  1.0 (Patch Level 4) RELEASE  ANNOUNCEMENT


     Khoros is an integrated software development environ-
ment for information processing and visualization, based on
X11R4.  Khoros components include a visual programming
language, code generators for extending the visual language
and adding new application packages to the system, an
interactive user interface editor, an interactive image
display package, an extensive library of image processing,
numerical analysis and signal processing routines, and 2D/3D
plotting packages.

X Windows Applications

Animate - Interactive Image Sequence Display Tool
Cantata - Extensible Visual Programming Language
Concert - A system for distributed X user interfaces (groupware)
Editimage - Interactive Image Display & Manipulation Program
Xprism2 and Xprism3 - Comprehensive 2D and 3D Plotting Packages
Viewimage - A basic interactive program for surface rendering
Warpimage - An interactive program for registering and warping images

Data Processing Algorithms

     Khoros contains over 260 programs, in the following
categories: arithmetic, classification, color conversion,
data conversion, file format conversion, feature extraction,
frequency filtering, matrix algebra (LINPACK and EISPACK),
spatial filtering, morphology filtering, geometric manipula-
tion, histogram manipulation, statistics, signal generation,
linear operations, segmentation, spectral estimation, sub-
region, and transforms. Khoros supports the following file
formats: TIFF, pbm, BIG, DEM, DLG, ELAS, FITS, MATLAB, Sun
raster, TGA, and xbm.

User Interface Tools

Preview - Graphical User Interface Display Tool
Composer - Interactive Graphical User Interface Editor
Conductor - Code Generation Tool for a Graphical User Interface
Ghostwriter - Code Generation Tool for a Command Line User Interface
Source Configuration & Management - Tools to install and maintain a

                                    distributed source tree.


1)  Anonymous FTP

Khoros is available via anonymous ftp from pprg.eece.unm.edu
(  Use your e-mail address as the password
(for example, ralph at whizbang.wmu.edu).  Once you have logged
in, cd to the "pub/khoros/release" directory and  get the
ascii file install.ftp.  This file will give you complete
instructions on how to get Khoros and install it on your
system.  To get this file, execute the following commands or

     a.   Use ftp to connect to pprg.eece.unm.edu.
          % ftp pprg.eece.unm.edu
          % ftp

     b.   Use "anonymous" or "ftp" as the user name.
          Name (pprg.eece.unm.edu:login): anonymous
          Name (pprg.eece.unm.edu:): ftp

     c.   Use your e-mail address as the password; please
          carefully use a valid e-mail address, as this ver-
          sion site logs all anonymous ftp's.
          Password (pprg.eece.unm.edu:user): {your valid e-
          mail address}
          331 Anonymous login ok, use your E-MAIL address as
          the password.
          230 Guest login ok, access restrictions apply.

     d.   Get the release notes for acquiring Khoros via
          anonymous ftp (note that "install.ftp" is the
          plain text file - both ".ms" and ".ps" files are
          available for those who would like them).
          ftp> cd /pub/khoros/release
          ftp> get install.ftp

 2)  Tape and Printed Documentation

     If you would like to have a tape and printed documenta-
tion sent to you, fill out the order form below (last page)
and include a $250.00 check or purchase order (payable to
UNM EECE Dept., in U.S. funds).  If you need additional
information or confirmation of your order, call the answer-
ing machine at 505-277-0806 and leave a message.

     All communication to the Khoros group should be via e-
mail.  If you have questions, comments or problems of a gen-
eral nature, then either mail the Khoros mailing list
(khoros at chama.eece.unm.edu), or post to the Khoros USENET
news group (comp.soft-sys.khoros).  To subscribe to the
mailing list, mail to khoros-request at chama.e

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net