From: bloch@pasteur.fr (Laurent Bloch)
Newsgroups: bionet.software
Subject: Microscope Image Processing
Date: 29 Sep 92 16:14:52 GMT

Forwarded message:
From sourdive Tue Sep 29 17:21:09 1992
Date: Tue, 29 Sep 1992 16:21:07 +0100
From: David Sourdive <sourdive>
Message-Id: <199209291521.AA23978@mendel.sis.pasteur.fr>
To: bloch@pasteur.fr
Subject: resume des reponses recues


 Voisci 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@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
operations.

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

==========================================================================
>From hauch@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
USA

Doug Benson, President
David Fine sales rep
Image analysis software for sun.
ISee, RatiotoolJ
919-361-4609J
919-361-5876 FaxJ

==========================================================================
>From mangalam@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,..)*
>
>
>
>OPTIONALLY
>
>- 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
machine!) 
   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
software.  
   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@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...

Cheers,

Harry

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

==========================================================================
From: s.budd@imperial.ac.uk :


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

description.
RRegards
sinclair Budd


     KHOROS  1.0 (Patch Level 4) RELEASE  ANNOUNCEMENT

INTRODUCTION

     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.


KHOROS DISTRIBUTION METHODS

1)  Anonymous FTP

Khoros is available via anonymous ftp from pprg.eece.unm.edu
(129.24.24.10).  Use your e-mail address as the password
(for example, ralph@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
steps:

     a.   Use ftp to connect to pprg.eece.unm.edu.
          % ftp pprg.eece.unm.edu
               -or-
          % ftp 129.24.24.10

     b.   Use "anonymous" or "ftp" as the user name.
          Name (pprg.eece.unm.edu:login): anonymous
               -or-
          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@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@chama.eece.unm.edu.
Once you have the system and want to report bugs, mail to
khoros-bugs@chama.eece.unm.edu.

KHOROS REQUIREMENTS AND LIMITATIONS

     To run Khoros, you must have a UNIX platform running
the X11R3, X11R4, X11R5, or OpenWindows servers. The Khoros
system consists of ~450,000 lines of C code;  you will need
a maximum of 120 Megabytes of storage for source, documenta-
tion and binaries.  To compile Khoros, the system requires
X11R4 (patch levels 1-18) or X11R5 client software from MIT
and an additional 50 Megabytes of storage.

-----------------------------------------------------------------------------
         Khoros 1.0, patch level 4 Compiles On These Machines

                   (MIT X unless otherwise noted)
------------------------------------------------------------------------------
Vendor     Name                       Configuration
--------+--------------------------+-------------------------------------------
Apollo  |  DN10000                 |  OS 10.3, Fortran 10.8, cc 6.8 
        |                          |
CRAY    |  XMP, YMP, Cray 2        |  UNICOS 6.1                   
        |                          |
DEC     |  5000/3100               |  Ultrix 4.2, mips cc 2.0, DEC f77 V3.0-2

        |                          |
DEC     |  Vax 3600                |  Ultrix 4.1, cc1.37.1
        |                          |
HP      |  HP9000/*                |  HP-UX 7.05, HP-UX 8.05
        |                          |
IBM     |  RS/6000                 |  AIX v3.x
        |                          |
OMRON   |  Luna88k                 |  Mach 2.5, gcc 1.37, f77 1.8.5
        |                          |
MIPS    |  Magnum 3000             |  RISCOS 4.51, cc 2.11, f77 2.11, X 4.0
        |                          |
NeXT    |  68030,40                |  MACH 2.0, gcc 1.37, Absoft f77 2.0,

        |                          |  Pensoft X
        |                          |
SGI     |  All                     |  OS 3.3.2, OS 4.0, X11 1.2, f77 3.3
        |                          |
SUN     |  SPARCstations, SUN4/*   |  SUN OS 4.1.1, f77 1.3.1
        |                          |
SUN     |  SUN3/*                  |  SUN OS 4.1.1, f77 1.3.1, gcc 1.39
-------------------------------------------------------------------------------

     The Khoros user community has ported Khoros to various
other platforms such as the Convex, the Sequent, Data Gen-
eral Aviion, MacII, and 386/486 machines. At this time,
these platforms are not directly supported by the Khoros
Group.

KHOROS CONSORTIUM

     If your organization is interested in distributing the
Khoros software system, and/or supporting further research
and development of software environments for data processing
and visualization please contact Tom Sauer at the address
below or e-mail consort@chama.eece.unm.edu.

                Tom Sauer, Khoros Consortium
   Department of EECE, Room 110, University of New Mexico
                   Albuquerque, NM 87131

===========================================================================================
                    C U T  H E R E
===========================================================================================

                           KHOROS
                          Room 110
                     Department of EECE
                  University of New Mexico
                   Albuquerque, NM 87131

        SHIP TO:


                 -----------------------------------------------------------


                 -----------------------------------------------------------


                 -----------------------------------------------------------

                 -----------------------------------------------------------

        PHONE NUMBER:


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        E-MAIL ADDRESS:


                 -----------------------------------------------------------

        PURCHASE ORDER NUMBER:


                 -----------------------------------------------------------

        CREDIT CARD ORDERS -    Please include the type of credit card, your

                                credit card number, and its expiration date.
                                In order to process your order, we
                                need to have your full name (as it
                                appears on the card) and also a number
                                where we can reach you during the day.

           NAME (as it appears on credit card):


                 -----------------------------------------------------------

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                 -----------------------------------------------------------

        Media:  (Please circle one of the following types of media)

                1) DC600A cartridge tape
                2) DC6250 cartridge tape
                3) 9-track tape (1/2 inch, 1600bpi)
                4) 9-track tape (1/2 inch, 6250bpi)
                5) DAT 4mm tape

        Binaries: (If you would like a compiled version of Khoros,
                   please circle one of the following machine architectures)

                1) DEC MIPS (Ultrix 4.2)
                2) SUN3  (SunOS 4.1.1)
                3) SUN4, SPARCstation  (SunOS 4.1.1b)
                4) SGI (OS 4.0)

==========================================================================
==========================================================================
==========================================================================


Our own investigations led us to choose the following equippement :

- camera : CCD cooled, 1018 x 1000 pixels x 10-12/14 bits (depending on the
           grabbing speed). Ref : C4880 by HAMAMATSU Photonics.
           (In AMERICA : 360 Foothill Road, Bridgewater, N.J.

            08807-0910, USA. tel: 908-231-1116 Fax: 908-231-0852
            Also present in FRANCE,GERMANY, UNITED KINGDOM, ITALY, SPAIN,
            "NORTH EUROPE" (i.e. SWEDEN))

- Grabbing boards : series 150/151 with VSI (Variable Scan Interface),
                    FB (Frame Buffer), ALU150 (Arythmetyic/Logic Unit),
                    DP150 (high resolution Display). By Imaging Technology
                    (in AMERICA: 55 Middlesex Turnpike Bedford, MA 01730-1421
                    tel : 800-532-3500  fax: 617-275-9590)
                    (in Europe, an excellent dealer and developper is

                     IMASYS 68 av. CARNOT 92150 SURESNES FRANCE
                     tel : (33)(1) 46 97 82 42   Fax (33)(1) 40 99 11 88)

- Monitor : NEC 5FG (17" color, able to display 1280 x 1024 pixel images)


- computer : Sun SPARCstation IPX (19" color monitor, 16 Mb RAM, 424 Mb hard
             drive, with a GX graphics accelerator).

- Software : VISILOG 4.0 by NOESYS
            ( In Europe : immeuble Nungesser, 13 av. Morane Saulnier 78140
              Velizy.
              tel : (33)(1)34650895   fax : (33)(1)34659914

              In North America : Noesys in Quebec, CANADA ...)


The reasons were the following :

1- Our priorities were resolution and sensitivity, not real time or video
   imaging. The best camera available with these criteria is the C4880 by
   HAMAMATSU.

2- Due to internal constraints, such as compatibility with networks on our
   campus, already available service for workstations, etc. , and in order to
   have a system able to evolve with new technologies and new demands on the
   experimental side, we chose to use a workstation rather than a PC (it is
   noteworthy that there is NOT A SINGLE BOARD FOR MACINTOSH that can handle
   the images delivered by this camera), and we chose SUN for commercial
reasons.

3- The only boards able to handle the images delivered by this camera are :
   -the VSI (mentionned above) part of a series 150/151 box (containing 7 or 12
    slots with an internal VME bus and a VME/Sbus translator to be hooked up to
    the workstation, or another translator for PCs ) by Imaging Technology.
    This box is accessible at variable levels with a complete set of routines
    grouped in the "ITEX" package
   -the AFG board (but the 1024x1024 pixels can only be 12 bits deep) for PCs,
by
    Imaging technology, again !!!

4- The best softwares for our purposes are
   - OPTIMAS (in AMERICA by : 
     BIOSCAN 170 West Dayton, suite 204 Edmonds, Washington 98020
     tel : (206) 775. 8000  fax : (206) 775. 3640,
              in EUROPE by  :
     IMASYS 68 av. CARNOT 92150 SURESNES FRANCE
     tel : (33)(1) 46 97 82 42   Fax (33)(1) 40 99 11 88)
     Runs only on PCs, under Windows. Does not take advantage of all
     the built-in goodies in the AFG board or in the series 150/151
     (does not know of ITEX).
   - VISILOG by NOESYS (mentionned above) Runs on PCs, under Windows,
     on Helwett Packard Workstations, and SUN SPARCstations. It is the
     only software able to handle the series 150/151 or the AFG board. It uses
     ITEX routines and takes advantage of all the built-in goodies of these
boards.
     It is therefore much faster for all classical image operations.
   Both softwares can do a lot more than what we intend to do. They can handle
   calcium real time measurements, be used for granulometry, astronomy, 3-D
   reconstruction and other medical purposes, etc. The only drawback of VISILOG
   is its price : about twice as much as OPTIMAS, but it handles more
sophisticated
   hardware.

5- We JUST LIKED the NEC 5FG when we saw it, besides its very bright and flat
which
   lets us take direct photographs of the screen. There are, of course, other
   monitors that can display 1280 x 1024 pixel images, such as SONY Trinitrons
for
   example, its basically a matter of taste ... and money.


Should we have chosen *a PC based solution* our investigations would have led
us to choose :

- The same camera.

- The AFG board.

- A fast PC (486/50 MHz or even 100 MHz) with a lot of RAM and Disk space.

- The same High resolution monitor.

- OPTIMAS to run the whole thing.



 Any questions or comments are welcome at sourdive@pasteur.fr




David SOURDIVE                     !
Unite des virus oncogenes          !
Departement des Biotechnologies    !
INSTITUT PASTEUR                   !
FRANCE                             !
tel : (33)(1) 45 68 85 25          !
fax : (33)(1) 40 61 30 33          !



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