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Analysis of 1-D Gels

PUN Thierry pun at cui.unige.ch
Tue Jan 5 03:16:27 EST 1993

In article <1993Jan5.065024.15769 at hippo.ru.ac.za> mimq at hippo.ru.ac.za (Molapo Qhobela) writes:
>Can anyone out there help me out. I am looking for a DOS based software
>package that can be used to analyse 1-D gels, with the ultimate aim of
>perantage determination of samples. I currently use a package called
>GelManager by Peter Jackman, but it only calculates similarities between
>samples. I saw a similar posting on this subject a few months back, but
>I never saw the responses.


Our software LaboImage (public domain, general purpose image analysis,
see doc below) includes a comprehensive 1D gel analysis program. This
program is based on work I performed at the NIH in 1982-1985, but has 
been rewritten for Sun, then for Motif/X11. 

We have not had the resources to run LaboImage on PC/DOS, but since it
is now based on Motif/X11, it is feasible.

Best regards,

     Prof. Thierry Pun, Computer Vision Group
     Computing Science Center, University of Geneva
     24, r. General Dufour, CH-1211 Geneva 4, SWITZERLAND  
     Phone : +41(22) 705 7627; secr: x7660; fax: x7780
     E-mail: pun at cui.unige.ch [or pun at cgeuge51.bitnet]


Original notice

March 8th, 1989: LaboImage 2.0 (SunView)
August 24th, 1990: LaboImage 3.0 (SunView)
March 19th, 1991: LaboImage 3.1 (SunView)
December 1st, 1992: LaboImage 4.0 (X11 / OSF Motif)
Computer Science Center, University of Geneva, Switzerland

Thank you for your interest in LaboImage!

General description
Labo Image is a window based software for image processing and analysis. It
contains a comprehensive set of operators as well as general utilities. It
is designed to be open-ended; new modules can easily be added. The software,
written in C, is now based on X11 / OSF Motif. The current version has been
developped and tested on a Sun SPARC station, with X11r4 and Motif 1.1.
LaboImage has been extensively used by students as well as researchers from
various domains: computer science (image analysis), medicine, biology, physics.
It is distributed free of charge (source code).

Version 4.0, 1st December 1992:

    - hosts: Sun SPARC station;
    - OS: 4.1.1;
    - window system: X11r4 / Motif 1.1;
    - language: C;
    - approx. code size: source 2.5MB (80'000 lines), executable 2.5MB;
    - documentation: interactive help (english)

Means of distributions

LaboImage source code is available by anonymous ftp at:
1) ftp.ads.com, login name anonymous, in pub/VISION-LIST-ARCHIVE/SHAREWARE.
2) peipa.essex.ac.uk, login name anonymous, in ipa/proc-src.
If you have no access to ftp, please contact the author.
If you wish to be kept current with update, error reports, ..., please send
us a mail with your full name, regular and electronic addresses.

Distribution policy
In essence:
    - this is a non-profit software, but it is our property and the copyright
      notice must appear;
    - the reference to cite in case of published results obtained with Labo
      Image is: "A. Jacot-Descombes, M. Rupp, T. Pun: `LaboImage: A portable
      window-based environment for research in image processing and analysis',
      SPIE Symposium on Electronic Imaging Science and Technology, Image
      Processing: Implementation and Systems, San Jose, California, USA,
      Feb. 9-14, 1992.
    - no responsibility is assumed;
    - not to be used for profit making purposes;
    - bugs will usually be corrected since we use the software intensively ;
    - modifications should be communicated to us, with (normally) allowance
      for redistribution.

Athough LaboImage has undergone many upgrades and suffered in the hands of 
many users, the current version is certainly not bug free. For the time being,
we require NO prepayment, return postage or anything. 
We may however change this policy in the future, and ask for nominal fees to
cover material expenditures. HOWEVER, if you are satisfied with the product,
why not send us some "souvenir" (post card, drink, etc.)) from your country...??!!

Labo Image is an interactive software, whose interface is menu, mouse and 
window based. Its main features are:
    - input-output: LaboImage format file, SUN raster file; postscript;
    - display: mono, RGB, dithering, color table editor;
    - preprocessing: filters (median, high pass, low pass: hamming, gauss, etc),
	    background subtraction, histogram equalization;
    - processing: thresholding, Fourier transforms, edge extractions: various
	    operators, ridge-riding, zero-crossing; segmentation into regions,
	    binary and gray tone mathematical morphology;
    - measures: histograms, image statistics, power, region outlining, 
	    object counting;
    - auxiliary: conversions, arithmetic & logical operations, noise addition,
	    image generation, magnification, convolution/correlation with
	    masks, image; padding;
    - elementary interactive operations: region outlining, statistics and
	    histogram computation, etc.;
    - special tools: 
	    - modify image at pixel level interactively,
	    - one-dimensional gel analysis,
	    - expert system for image segmentation (not implemented in LaboImage 4.0);
    - macros definitions, save and replay (not implemented in LaboImage 4.0);
    - on line documentation.

Image formats
Own format: descriptor file + data file (binary, byte, int, float, complex;
mono or RGB). Supports also Sun raster format. Conversions to various other 
Data structures:
    - iconic (pixel-based), with each image having its own parameter list;
    - vectors (histograms, look-up tables);

Miscellaneous remarks (answers to commonly asked questions)

 - FILE FORMAT: we decided to go for: 1) a machine independant format; 2) a
   simple, data (ie. signal) oriented format. At the beginning of the
   development (summer 1987), we were not aware of any image format used by
   the whole community. There seems now to be some progress on the matter
   (TIFF, etc.), but they are still not that widely used in the community.
   Also, due to development priorities we consider conversion routines a more
   secondary issue as long as our format is simple. 
   In addition, the menu "ACQUISITION=>free byte format" is fairly versatile.
   Also, the SUN raster images can now be read into LaboImage and likewise
   images on system may be stored in SUN raster format.
   However.. we would welcome any software contribution!

 - 3D IMAGE PROCESSING: nothing special for such images.

 - ON LINE HELP: available.

More than 10 people have so far participated in this project, and their
contribution is gratefully acknowledged.
Staff: Pierre-Yves Burgi, Claudia Coiteux-Rosu, Ziping Hu, Alain Jacot-
Descombes, Rene Lutz, Christian Pellegrini, Thierry Pun, Marianne Logean-
Rupp, Krassimir Todorov.
Students: Anne Bobillier, Alain Brunner, Markus Buchi, Christian Girard,
Rene Perrier, Vrinda Shukla. 
Amongst them, A. Jacot-Descombes is responsible for general design issues, 
and is the keystone for implementation; R. Lutz is responsible for display
manipulations (Color Table Editor,etc.); T. Pun is responsible for the 
original layout and general design issues;
V. Shukla is responsible for the upgrade from LaboImage 2.0 to LaboImage 3.0;
Marianne Logean-Rupp is responsible for the portability of LaboImage to X11
(LaboImage 4.0).
We are particularly grateful to Drs. D. F. Hochstrasser and O. Ratib, Digital
Imaging Unit, Computer Center, University Hospital of Geneva, for their
extended support. LaboImage 4.0 could not have been without their help.

Particular problems will be redirected to relevant persons, but we prefer
that all communications be made to the same address:
e-mail: "pun at uni2a.unige.ch" or pun at cgeuge51.bitnet (if this fails,
	"pun at cui.unige.ch").
tel.: +(4122) 705 76 27 (T. Pun), 705 76 30 (A. Jacot-Descombes).
fax:  +(4122) 320 29 27.
postal address: Thierry Pun
                Computing Science Center, University of Geneva
                24, rue du General-Dufour
                CH - 1211 Geneva 4


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