1D gel analysis program
pun at cui.unige.ch
pun at cui.unige.ch
Sun Feb 28 11:29:04 EST 1993
I take the opportunity of Dr. K.W. Clark announcement to mention
that our image analysis software LaboImage also does 1D gel
analysis. LaboImage can be obtained free by anonymous ftp (see
description below); it is described in Cabios, 7, 2, April 1991,
225-232, while the 1D gel algorithm was originaly described in
Electrophoresis, 6, 6, June 1985, 268-274. Some recent adjunctions
to the 1D gel algorithm from 1985 are in the 1991 Cabios paper.
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]
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!
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.
- 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
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,
- 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.
Own format: descriptor file + data file (binary, byte, int, float, complex;
mono or RGB). Supports also Sun raster format. Conversions to various other
- 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
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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