Leica CW4000 Quick Start Guide
Leica CW4000 Quick Start Guide
This document describes the installation procedure for the Leica
CW4000, minimum system requirements and information relating to
this release of the Leica Cytogenetics Application Solutions CD. You
should read this document before installing your copy of this CD.
All reasonable steps have been taken to ensure that this publication
is correct and complete, but should any user be in doubt about any
detail, clarification may be sought from Leica Microsystems Imaging
Solutions Ltd, or their accredited representative. The information in
this document is subject to change without notice and should not be
construed as a commitment by Leica Microsystems Imaging
Solutions Ltd. Leica Microsystems Imaging Solutions Ltd accepts no
responsibility for any errors that may appear in this document.
Copyright © Leica Microsystems Imaging Solutions Ltd, Cambridge,
UK, 2002
All rights reserved. The contents of this publication may not be
reproduced in any form, or communicated to a third party without
prior written permission of Leica Microsystems Imaging Solutions
Ltd.
Due to a policy of continuous development, we reserve the right to
change specifications without notice.
Microsoft and MS-DOS are registered trademarks and Windows,
Windows NT, Windows 2000, WindowsXP, the Windows logo, the
Windows NT logo and the Windows 2000 logo are trademarks of
Microsoft Corporation.
Date: April 2002
Part Number: 12724007
Issue: 1
Printed in UK
Table of Contents
Chapter One: Introduction.................................. 1
Chapter Overview ..................................................................1
Introduction...........................................................................2
Style Reference.....................................................................3
Welcome...............................................................................4
What is Leica CW4000?.........................................................5
General .............................................................................................................5
Leica CW4000 Karyo....................................................................................... 5
Leica CW4000 FISH .........................................................................................6
Leica CW4000 CGH.........................................................................................6
Leica CW4000 MFISH .....................................................................................7
Leica CW4000 Satellite Capture.................................................................... 8
Minimum System Requirements ............................................8
Software Requirements .........................................................9
Chapter Two: Installation.................................11
Chapter Overview ................................................................11
Introduction.........................................................................12
Installation Procedure ..................................................................................13
Un-installation.....................................................................15
Chapter Three: System Configuration...................17
Chapter Overview ................................................................17
Configuring Your System.....................................................18
Language and Database Settings ...............................................................18
Image Acquisition Settings.......................................................................... 18
Microscope Settings ....................................................................................19
Chapter Four: Using Leica CW4000..................... 21
Chapter Overview ................................................................21
Introduction.........................................................................22
Starting the Applications .....................................................22
The Leica CW4000 Karyotyping Desktop.............................23
The Main CW4000 Karyo Menus..........................................24
The Main CW4000 FISH Menus...........................................25
The Main CW4000 Karyo Toolbar........................................26
The Main CW4000 FISH Toolbar..........................................28
Obtaining Leica CW4000 Help..............................................30
Chapter One:
Introduction
Chapter Overview
This chapter contains the following topics:
♦ Introduction
♦ Style Reference
♦ Welcome
♦ What is Leica CW4000?
General
Leica CW4000 Karyo
Leica CW4000 FISH
Leica CW4000 CGH
Leica CW4000 MFISH
Leica CW4000 Satellite Capture
♦ Minimum System Requirements
♦ Software Requirements
Leica CW4000 Quick Start Guide Page 1
Introduction
This document describes the V1.0 release of the Leica CW4000
Cytogenetics Application Solutions CD. You should read this
document before installing your copy of this CD.
This document is intended to guide you through the installation
process, setup information and provides an overview of the program
and its features.
Refer to: For further information you should refer to the Leica CW4000 User
Tutorials provided with your system.
If you have just received a new Cytogenetics workstation from Leica,
the software will have been installed and configured and you should
ignore the sections on Installation and Configuration, but please take
the time to read through the remaining sections, and the
README.HLP file on the CD-ROM.
Refer to: For the very latest product enhancements and a release history,
please refer to the Release Notes as provided on the CD.
Page 2 Leica CW4000 Quick Start Guide
Style Reference
The following conventions have been used to make this manual
easier to read:
Menus FILE (bold, capitals).
Menu Commands/ Buttons/ Dialogs
References Chapter 1 (italics).
Notes, Tips, Warnings, References
and Instructions
Note: Additional information that should be noted.
Refer to: References to other relevant material.
Tip: Tips to help you use the program more productively.
WARNING: Important information to which you should pay careful
attention.
One Step instructions: Operations that can be performed in a single step.
Step-by-step instructions: Numbered instructional steps.
Information that only applies in certain situations is enclosed in
boxes.
Open, OK (bold).
Appear as follows and
contain additional information
Leica CW4000 Quick Start Guide Page 3
Welcome
Welcome to your new Leica CW4000 Cytogenetics Image Analysis
Workstation.
We at Leica Microsystems are sure that you will be pleased with
your new system. We hope that you find the software both intuitive
and easy to use. To help with this we have re-organised our user
manual.
This guide, along with the tutorials, outlines the standard tools you
will need to carry out the routine, everyday tasks. In addition, we
have included some helpful tips and hints to help you get the most
out of your workstation.
However, we are sure that there will be some things that you would
like to do that are not covered by this manual. If so, please let us
know your requirements and, if it is possible, we will certainly point
you in the right direction. If your request is not currently covered by
the software functionality, letting us know will help us determine
future product development.
If there is any aspect of the system that you are concerned with,
please do not hesitate to let your local specialist know. Alternatively,
you can e-mail us on imaging.support@leica-microsystems.com and
we will do our very best to help you.
We are always keen to hear about the successes you have had using
our system. If you have any publications in which you have used a
Leica Imaging System we would love to hear about them.
Don’t forget that Leica CW4000 allows you to capture standard
banded images an d analyse G-, R-, and Q- banded cells, along with
CGH and MFISH images; and FISH is the software used for the
capture of all your fluorescence labelled cytogenetic slides, whether
they be metaphase or interphase.
Page 4 Leica CW4000 Quick Start Guide
What is Leica CW4000?
The Leica CW4000 total imaging solution combines a number of
Cytogenetics imaging techniques, with Leica microscopes and
cameras, to offer you a flexible cytogenetics imaging solution that
suits your laboratory needs.
Leica CW4000 comes in a variety of combinations and offers
application solutions for Karyotyping, FISH, MFISH and CGH analysis.
General
♦ CW4000 provides a common karyotyping framework for G
banding, R banding, CGH and MFISH karyotyping applications.
♦ Support for Leica DC500 and DC350F to provide high-resolution
karyotyping resulting in improved image quality and more
confidence in analysis and results.
♦ Easy to use Karyotyping toolbar.
♦ Karyotyping of FISH images (2 or 3 colour FISH images) for
improved analysis.
Leica CW4000 Karyo
The Leica CW4000 Automated Karyotyping Module is a trainable
application solution for both human and non-human chromosome
analysis, making use of neural network technology to increase speed
and reliability. Leica CW4000 has been developed in association with
research and routine analysis laboratories to meet exacting
Karyotyping requirements.
Leica CW4000 Quick Start Guide Page 5
Karyotyping Features
♦ Dynamic presentation of separation and overlap cuts in
metaphase editing – saves time
♦ Camera control in live window – saves time while providing
optimal camera adjustment
♦ Automatic include function
♦ R banded ideograms
♦ Accurate display of outline of chromosomes in thresholding
display
Leica CW4000 FISH
Leica CW4000 FISH is a highly developed imaging and documentation
solution, which gives cytogeneticists the power to produce instant,
impeccable composite FISH images. You can use it for simple image
acquisition of fluorescent samples or for in-depth FISH
experimentation in research.
FISH Features
♦ Sophisticated interface to Leica DMR range of microscopes.
♦ Acquisition of up to 8 different image planes.
♦ Facility to capture in multiple Z-Planes.
♦ Facility to correct for any image shift that occurs.
♦ Acquisition using a wide variety of cameras.
♦ Advanced image enhancement facilities.
Leica CW4000 CGH
Leica CW4000 CGH is a specialist cytogenetics application module,
which operates within Leica CW4000. It is an image processing and
measurement application involving profile ratio level determination
for comparative genomic hybridisation.
Page 6 Leica CW4000 Quick Start Guide
CGH Features
♦ Unique “two -scale” CGH gain and loss bars.
♦ Improved correction of centromere position.
♦ Improved CGH midline correction of chromosomes.
♦ Editable CGH gain and loss bars - better presentation of data.
♦ Select individual profiles – improved analysis.
♦ Chromosome, cell and multiple case profile comparison.
♦ Ability to threshold image using combined DAPI/Reference
image – more accurate.
♦ Save CGH profiles as a .tif – more flexible.
♦ Support for high-resolution cameras.
Leica CW4000 MFISH
Leica CW4000 MFISH is an application module for multi-coloured
Karyotyping, developed in close collaboration with scientists
pioneering MFISH research. Leica CW4000 MFISH uses proprietary
analysis techniques to give superior image quality and unique
chromosome classification results.
MFISH Features
♦ Intelligent-dynamic separation and overlap positions in
metaphase editing.
♦ Accurate display of thresholded objects.
♦ MFISH classification of telomeres.
♦ Optimum enhancement of MFISH True colour and classification
image.
♦ Optional pixel shift feature.
♦ Support for high-resolution cameras.
Leica CW4000 Quick Start Guide Page 7
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