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 [e-mail] 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

Leica CW4000 Satellite Capture

The Leica CW4000 Satellite Capture module is a complete network
solution designed specifically for cytogenetics image acquisition and
data entry in network configurations. The module allows you to
acquire metaphase images for successive analysis to occur on a
Leica CW4000 system.

Minimum System Requirements

Note: Note that a back-up device and a back-up strategy for images and
data are essential. The user must ensure that regular and reliable backup
of databases and important files is performed.

It is strongly recommended that the following basic system
requirements are correct before installing any Leica software.

♦ This software requires Microsoft Windows 2000.
♦ Pentium or equivalent CPU is used with a speed of at least 900

MHz.

♦ This product requires approximately 120 Mbytes of disk space

for a full installation and an additional free space of 200 Mbytes
for efficient operation. Further space is required for data and
image storage, which depends on the application and frequency
of use. The free space must be checked regularly.

♦ It is strongly recommended that at least 256 Mbytes of system

RAM is installed for FISH, CGH and MFISH applications.

♦ Karyotyping, FISH, CGH and MFISH require a screen resolution

of 1280 x 1024 for comfortable operation. This will normally be
provided by a 19" or greater monitor size. Leica CW4000 SatCap
will normally be operated at a screen resolution of 1024 x 768 on
a 17" monitor.

Page 8 Leica CW4000 Quick Start Guide

Software Requirements

Note: A back-up device and a back-up strategy for images and data are
essential. The user must ensure that regular and reliable back-up of
important files is performed.

For Leica Software to function correctly the following Software is
required.

♦ Microsoft Windows 2000 service pack 2 with Internet Explorer

5.5 or later installed.

♦ Microsoft Office 2000/XP Small Business Edition (SBE).
♦ Leica Server software Version 2.1 or later is required to support

image acquisition and peripheral hardware.

♦ Leica DC Camera software Version 4.1.1 or later is required if

you are to use one of these cameras.

♦ A dongle licensing the applications purchased to run.
♦ Adobe Acrobat Reader is required for Release Notes, Manuals

and Help files, this can be installed from the Adobe Directory on
the CD

Leica CW4000 Quick Start Guide Page 9

Page 10 Leica CW4000 Quick Start Guide

Chapter Two:
Installation

Chapter Overview

This chapter contains the following topics:

♦ Introduction

Installation Procedure

♦ Un-installation

Leica CW4000 Quick Start Guide Page 11

Introduction

If you have just received a new image analysis workstation from
Leica, the appropriate software will have already been installed and
configured. This configuration will enable the applications that you
are licensed to use to operate in a fully functional manner; please do
not change this configuration.

This CD, along with the Leica Q550 Servers CD contains all the
software that you need to run the Leica range of cytogenetics
application solutions. These instructions outline the actions needed
to re -install the software or to upgrade an existing system.

If you are installing Leica DC cameras you also need the Leica DC
Camera CD.

WARNING: The installation of Leica Servers and Leica PC interface cards
is a task that should only be undertaken by, or under the direct instruction
of, trained Leica personnel. Installing incorrect options can cause
significant problems that may be difficult to rectify.

Note: Interfering with the factory-set Server options may invalidate the
warranty.

Note: If you choose to uninstall an existing installation, you may lose data
that you have saved, we recommend that you save the current
configuration before making any changes to the installation. See the
section ‘Save Peripheral Settings’.

Note: If you have a Leica Microscope or Image Acquisition peripheral
connected to your PC, then you must install the ‘Leica Q550 Server CD’
before you install this CD.

Page 12 Leica CW4000 Quick Start Guide

Installation Procedure

If you have already installed some of the Leica Cytogenetics
Applications, we recommend that you uninstall them before
reinstalling this soft ware.

Refer to: the un-installation instructions on page 15.

Note: if you do not uninstall, you should ensure the ‘Cybase’ option is

unchecked (otherwise you will get a message warning you that Cybase
cannot overwrite an existing installation). The CW4000 Karyo installation
will warn you that there are existing databases.

Note: If you are to use a Leica DC camera, you must install the Leica DC
Twain software before installing this CD.

WARNING: If you choose to uninstall an existing installation, you may
loose data that you have saved in one of the Leica Cytogenetics
databases.

If you have a Software Protection Device (‘Dongle’), you should
install this in the parallel port of your PC or USB port depending on
the type supplied. If you have a USB dongle, you will have to firstly
install USB dongle support from the Leica Q550 Server CD, part
number 723791. If you do not have a dongle, the application will run in
‘Preview Mode’ only, with some functions disabled.

Step-by-step Instructions:

1. Before installing this CD, you must install the Leica Q550 Server
CD Version 2.1 or later if you have any Leica Microscope or
Image Acquisition peripherals connected to your PC. Then you
must restart your PC.

2. You should ensure that the 'Leica CW4000 Application Solutions
for Cytogenetics' CD is correctly loaded into your CD-ROM drive,
and then the 'autorun' facility on the CD should bring up the
Leica CW4000 Installation Screen. If this screen does not appear
when you insert the CD, you should run the INSTALL.EXE
program on the CD by selecting the ‘Start’ menu ‘Run…’ option

Leica CW4000 Quick Start Guide Page 13

and typing ‘D:\INSTALL.EXE’ in the ‘Open:’ box (where ‘D:’ is the
drive letter of your CD-ROM drive).

3. Select the software applications options that you require. If you
have installed a dongle, the software applications will be
automatically set to match the items licensed by the dongle. If
you do not have a dongle then you should select the options that
you wish to preview.

4. Select installation settings such as the language for the user
interface. Note that not all languages are supported by all
applications.

5. When you have selected the items that you require, you should
click the 'Install' button to start the installation process.

6. When the installation process is comp lete, you should click the
‘Exit’ button to close the application. Before using your Leica
Cytogenetics Applications, you should configure your system as
described in the section entitled ‘Configuring Your System ’.

Page 14 Leica CW4000 Quick Start Guide

Un-installation

Should it be necessary to un-install the software for any reason the
procedure below should be followed.

Step-by-step Instructions:

1. Access the control panel by selecting the ‘Start’ menu ‘Settings’,
‘Control Panel’.

2. Click on the ‘Add/Remove programs’ icon, then select and
uninstall the following applications, following the instructions
displayed on the screen:

Leica Cytogenetics Workstation
Leica Image Servers (if you have no other Leica Imaging
applications installed on your PC).
If the following options were installed th en uninstall these as
well:
Leica CW4000 Karyo
Leica CW4000 FISH
Leica Cybase

3. Delete the Leica CW4000 Folder in Windows Explorer and
desktop shortcut icons using conventional Windows
functionality.

Leica CW4000 Quick Start Guide Page 15

Page 16 Leica CW4000 Quick Start Guide

Chapter Three:
System Configuration

Chapter Overview

This chapter contains the following topics:

♦ Configuring Your System

Language and Database Settings
Image Acquisition Settings

Microscope Settings

Leica CW4000 Quick Start Guide Page 17

Configuring Your System

Again, if you have just received a new system the appropriate
software will have been installed and configured. Please do not
change this configuration.

If you have installed this software yourself, you may need to tell the
software what hardware items you are using. To do this, you should
run the ‘Cyto Administrator’, by clicking on the icon in the ‘Leica
Cytogenetics’ window, or the item in ‘Leica Cytogenetics’ in the
Windows Start Menu.

Language and Database Settings

The installation procedure should have ensured that the language
and database settings are correct. You can use the ‘Cyto
Administrator’ to create and/or select another database and to
change the user interface language.

Image Acquisition Settings

If you have an Image Acquisition device (e.g. an Image capture
board), you should click on the ‘Image Acquisition Settings…’ button
and ensure that the device and camera selected correspond to those
installed on your system.

If you have a Photometrics PVCAM/SenSys camera, we recommend
that you first select the ‘Settings…’ button and then ‘PCISetup…’
button. This should run the Photometrics Setup program. You should
ensure that this shows the correct camera name (e.g. ‘SenSys’) with
the status ‘OK’. You can then use the ‘Preview’ button to see the
image from the camera.

Page 18 Leica CW4000 Quick Start Guide

Microscope Settings

If you have any Microscope automation (e.g. motorised X/Y Stage, or
Focus), you should click on the ‘Microscope Settings…’ button and
then select the items that you require. You can click ‘Test’ to verify
these settings before closing the dialog.

Saving Settings

Once you have selected and verified the settings, we recommend
that you save these settings by clicking on the ‘Microscope
Settings…’ button and then on the ‘Save Settings…’ button. Enter a
name for your settings (for example your own name or your
department’s), and then press ‘OK’.

Leica CW4000 Quick Start Guide Page 19

Page 20 Leica CW4000 Quick Start Guide

Chapter Four:
Using Leica CW4000

Chapter Overview

This chapter contains the following topics:

♦ Introduction
♦ Starting the Applications
♦ The Leica CW4000 Karyotyping Desktop
♦ The Main CW4000 Karyo Menus
♦ The Main CW4000 FISH Menus
♦ The Main CW4000 Karyo Toolbar
♦ The Main CW4000 FISH Toolbar
♦ Obtaining Leica CW4000 Help

Leica CW4000 Quick Start Guide Page 21

Introduction

As Leica CW4000 uses the conventions of Microsoft Windows 2000
, it is a good idea to familiarise yourself with the basic operations
of the Microsoft Windows 2000  user interface before you begin.

Starting the Applications

You can run the Leica Cytogenetics
Applications by clicking on the icons in the
‘Leica Cytogenetics’ folder as shown opposite.

Or:

Run the Leica Cytogenetics Applications

1. Select the application in the
‘Leica Cytogenetics’ item in
the Windows Start Menu.
Click on the START button.

2. Select Programs from the
Start menu, and then Leica
Cytogenetics from the
submenu.

3. Click on Leica CW4000 or
CW4000 FISH to run the
program.

4. The Start-Up screen will
appear for either Karyo or
FISH.

Page 22 Leica CW4000 Quick Start Guide

The Leica CW4000 Karyotyping Desktop

The Leica CW4000 Karyotyping Desktop appears as show below:

The Main Menu Bar provides access to all the features.

The Main Toolbar provides shortcuts to the most frequently used
features.

Leica CW4000 Quick Start Guide Page 23

The Main CW4000 Karyo Menus

The main Leica Karyo CW4000 menus are described below:

FILE The FILE menu contains commands for:

♦ Managing files.
♦ Logging on and off.
♦ Printing.
♦ Exiting.

EDIT The EDIT menu allows you to:

♦ Undo actions.
♦ Copy and paste images.

VIEW The VIEW menu enables you to specify which items are

displayed on the desktop, and offers access to the
Chromosome Editor.

IMAGE

ANALYSIS The ANALYSIS menu allows you to:

The IMAGE menu allows you to:

♦ Set up the camera.
♦ Grab a live image.

♦ Perform an analysis.
♦ Edit an existing karyogram.

CYBASE The CYBASE menu allows you to directly interact with

the Cybase Database.

SETTINGS The SETTINGS menu gives you options to change the

underlying system settings, and to train a new
classifier.

HELP The HELP menu provides access to online help.

Page 24 Leica CW4000 Quick Start Guide

The Main CW4000 FISH Menus

The main Leica CW4000 FISH menus are described below:

FILE The FILE menu contains commands for:

♦ Managing files.
♦ Logging on and off.
♦ Printing.
♦ Exiting.

EDIT The EDIT menu allows you to:

♦ Undo actions.
♦ Copy and paste images.

VIEW The VIEW menu enables you to specify which items are

displayed on the desktop, and offers access to the
Chromosome Editor.

SETUP

IMAGE

ARCHIVE
ACapS Allows interaction with automatic capture procedure.
WINDOW The WINDOW menu allows you to rearrange the

HELP The HELP menu provides access to online help.

Leica CW4000 Quick Start Guide Page 25

Acts as the control centre for the microscope and
fluorochromes.

The IMAGE menu allows you to:

♦ Set up the camera.
♦ Grab a live image.
♦ Annotate images.

Allows direct interaction with the FISH database.

application windows on the screen.

The Main CW4000 Karyo Toolbar

The Leica CW4000 Karyo main toolbar provides a quick way of
accessing commonly used functions. The functions of the buttons on
this toolbar are described below:

New Window—Opens a new image window.

Live— Displays the Camera Live Dialog.

Acquire —Grabs the live image from the camera.

Search Window—Sets the size of the analysis window.

Start Analysis—Starts the analysis sequence.

Edit Karyogram—Allows interaction and modifications to

Karyogram display.
Metaphase Karyogram—Toggles view between the metaphase

and karyog ram windows.

Undo—Reverses your previous action.

Re-do—Re-does previous action.

Zoom in—Zooms in on image.

Zoom out—Zooms out on image.

Fit to Window —Scales the image to enable whole area to be

seen.
Import Metaphase—Allows import of metaphase from Cybase for

subsequent modifications.

Page 26 Leica CW4000 Quick Start Guide

Add Result—Allows the addition of a new result to Cybase.

Review Result—Allows import of metaphase and karyogram from

Cybase for review purposes.

Note: You can customise the main toolbar so that it contains the options you
use most frequently.

Leica CW4000 Quick Start Guide Page 27

The Main CW4000 FISH Toolbar

The Leica CW4000 FISH main toolbar provides a quick way of accessing
commonly used functions. The functions of the buttons on this toolbar
are described below:

New Window—Opens a new image window.

Open Image — Opens an image file from disk.

Save Image— Saves an image to file.

Close Image— Closes current image.

Print—Prints an Image.
Undo—Reverses your previous action.

Copy Image—Copies the current image to the clipboard.

Paste Image—Pastes an image from the clipboard to the desktop.

Setup Microscope —Displays Microscope Setup.

Setup Filters —Displays Filter Setup.

Setup Video —Displays camera live dialog.

Reference Data—Allows input of sample details.

Run ACapS—Runs Automated Capture Sequence.

Acquire Probe—Acquisition of single probe.

Page 28 Leica CW4000 Quick Start Guide

Acquire All Probes—Acquisition of all specified probes.

Make FISH Image—Produces merged FISH image.

Add Record to Archive—Adds current record to FISH database.

Import record from Archive—Allows record to be recalled from

FISH database.
Print Archive report —Prints report of specified cases directly

from FISH database.

Note: You can customise the main toolbar so that it contains the options you
use most frequently.

Leica CW4000 Quick Start Guide Page 29

Obtaining Leica CW4000 Help

The Leica CW4000 Cytogenetics Workstation is fully supported by
on-line help. Clicking the HELP menu will start Adobe Acrobat Reader
and the Leica CW4000 User Manual (CW4000help.pdf).

Both Adobe Acrobat and the Leica CW4000 User Manual are
supplied on the installation CD.

To install Adobe Reader:

1. In the Windows START menu, click Run.
You see the Run dialog. Insert the Leica CW4000 CD and browse
for the program acrobat.exe in the Adobe folder.

2. Click OK to install the reader.

To view the Leica CW4000 User Manual:

1. In the Windows START menu, click Run.
You see the Run dialog. The filename is Leica CW4000 User
Manual. It is installed in the following folder:

Program files\Leica CW \Leica CW4000 Karyo

2. Click OK to view the manual.

Page 30 Leica CW4000 Quick Start Guide