Leica CW4000 Quick Start Guide
Contents
1. 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 mage 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 CW 4000 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 s2. 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 99 99 9 Leica CW 4000 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 CW 4000 Quick Start Guide CGH Features 99 99 99 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 M FISH research Leica CW 4000 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 thresh
3. Issue 1 Printed in UK Table of Contents Chapter One Introduction 1 Chapter OVBIVIGW sansir in ce ke Dad rt nates 1 INIFOGUCHORmrga TEMP E a 2 Style RETEFENC Oui lena 3 Welcome satana aetate ta iat erica 4 What is Leica CW 4000 rr 5 e A E A tah 5 Leic a CWAO0OKaFy Oen ecce rt tte a tren dal 5 Leica CW 4000 FISH s ssssssisststrstrstrtrststrsrstestrttstrsnrnnntrsnrnnrntsnr ahd beak 6 Lera CU AO CO Haase dett racc rear 6 Leica CW 4000 M FISH rental 7 Leica CW 4000 Satellite Capture 8 M inimum System RequirementSs ii 8 Software Requilemments inscite inhalant 9 Chapter T wo Installation 11 Chapter OvervieW assertio ebrii RISE ub pa ipu UR TI A dane 11 introduction Rael Pp o ele ede onte Pa Ee ad 12 Installation ProCedUre a n cocti n o tee me ep e n 13 D neiistalla OI etus rev edis Dvd iaia 15 Chapter Three System Configuration 17 Chapter OVBTVIBW sanirana a 17 Configuring Your SySteM rasoio 18 Language and Database Settings 18 Image Acquisition Settings 18 Microscope Settings 3 5 denique E 19 Chapter Four Using Leica CW4000 21 Chapter VO GW uis retia exi iere Apr papa Yos d tune 21 INTOGUE LOTES na Coetus ncn ala 22 Starting the Applications atr ra FI ale 22 The Leica CW 4000 Karyotyping Desktop s 23 The M ain CW 4000 Karyo M NUS eem 24 The M ain CW 4000 FISH Menus senem 25 The Main CW 4000 Karyo T
4. Karyotyping FISH CGH and M FISH require a screen resolution of 1280 x 1024 for comfortable operation This will normally be provided by a 19 or greater monitor size Leica CW 4000 SatCap will normally be operated at a screen resolution of 1024 x 768 on a 17 monitor Leica CW 4000 Quick Start Guide Software Requirements I wn adi 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 e Microsoft Windows 2000 service pack 2 with Internet Explorer 5 5 or later installed e Microsoft Office 2000 XP Small Business Edition SBE e Leica Server software Version 2 1 or later is required to support image acquisition and peripheral hardware e Leica DC Camera software Version 4 1 1 or later is required if you are to use one of these cameras e 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 CW 4000 Quick Start Guide Page 9 Page 10 Leica CW 4000 Quick Start Guide Chapter T wo Installation Chapter Overview This chapter contains the following topics e Introduction Installation Procedure e Un installation Leica CW 4000 Quick Start Guide Page 11 Introduction Page 12 If yo
5. Leica CW 4000 Quick Start Guide This document describes the installation procedure for the Leica CW 4000 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 Windows the Windows logo the Windows NT logo and the Windows 2000 logo are trademarks of Microsoft Corporation Date April 2002 Part Number 12724007
6. Make FISH Image Produces merged FISH image 5j Add Record to Archive A dds current record to FISH database Import record from Archive A lows record to be recalled from r1 FISH database Print Archive report Prints report of specified cases directly amp from FISH database i Note You can customise the main toolbar so that it contains the options you use most frequently Leica CW 4000 Quick Start Guide Page 29 Obtaining Leica CW 4000 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 CW 4000 User M anual CW 4000help pdf Both Adobe Acrobat and the Leica CW4000 User Manual are supplied on the installation CD 1 To install Adobe Reader 3 1 Inthe Windows START menu click Run You see the Run dialog Insert the Leica CW 4000 CD and browse for the program acrobat exe in the Adobe folder 2 Click OK to install the reader 1 To view the Leica CW4000 User Manual 3 1 Inthe Windows START menu click Run You see the Run dialog The filename is Leica CW 4000 User Manual It is installed in the following folder Program files Leica CW Leica CW 4000 Karyo 2 Click OK to view the manual Page 30 Leica CW 4000 Quick Start Guide
7. and then press OK Leica CW 4000 Quick Start Guide Page 19 Page 20 Leica CW 4000 Quick Start Guide Chapter F our Using Leica CW 4000 Chapter Overview This chapter contains the following topics Introduction Starting the Applications The Leica CW 4000 Karyotyping Desktop The Main CW 4000 Karyo M enus The M ain CW 4000 FISH Menus The M ain CW 4000 Karyo Toolbar The M ain CW 4000 FISH Toolbar Obtaining Leica CW 4000 Help 999 99 99 Leica CW 4000 Quick Start Guide Page 21 Introduction As Leica CW 4000 uses the conventions of Microsoft Windows 2000 TM 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 canrun the Leica Cytogenetics Ta Applications by clicking on the icons in the fd 4 Hn 1 1 Pal Leica Cytogenetics folder as shown opposite Leica CW4000 Karyo Or 1 Run the Leica Cytogenetics Applications 3 1 Select the application in the istas Leica Cytogenetics item in the Windows Start M enu Click on the START button 2 Select Programs from the Start menu and then Leica Cytogenetics from the submenu 3 Click on Leica CW40000r CW 4000 FISH to run the program 4 The Start Up screen will gt appear for either Karyo or FISH fei Page 22 Leica CW 4000 Quick Start Guide The Leica CW 4000 K aryotyping Desktop The Leica CW 4000 Karyotyping Desk
8. ding CGH and M FISH karyotyping applications e Support for Leica DC500 and DC350F to provide high resolution karyotyping resulting in improved image quality and more confidence in analysis and results e Easy to use Karyotyping toolbar e Karyotyping of FISH images 2 or 3 colour FISH images for improved analysis Leica CW 4000 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 CW 4000 Quick Start Guide Page 5 K aryotyping F eatures e Dynamic presentation of separation and overlap cuts in metaphase editing saves time e Camera control in live window saves time while providing optimal camera adjustment e Automatic include function R banded ideograms e Accurate display of outline of chromosomes in thresholding display Leica CW 4000 FISH Leica CW 4000 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
9. e If you have already installed some of the Leica Cytogenetics Applications we recommend that you uninstall them before reinstalling this software 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 CW 4000 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 da by step Instructions 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 CW 4000 Application Solutions for Cytogenetics CD is cor
10. e image to enable whole area to be seen Import M etaphase Allows import of metaphase from Cybase for subsequent modifications Leica CW 4000 Quick Start Guide Add Result Allows the addition of a new result to Cybase me Review Result Allows import of metaphase and karyogram from CD Cybase for review purposes Note You can customise the main toolbar so that it contains the options you use most frequently Leica CW 4000 Quick Start Guide Page 27 The Main CW 4000 FISH Toolbar The Leica CW 4000 FISH main toolbar provides a quick way of accessing commonly used functions The functions of the buttons on this toolbar are described below D amp se a 8 8 5 E Tm mo Page 28 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 M icroscope 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 Leica CW 4000 Quick Start Guide yy Acquire All Probes Acquisition of all specified probes L3
11. el by selecting the Start menu Settings Control Panel 2 Click onthe 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 then uninstall these as well Leica CW 4000 Karyo Leica CW 4000 FISH Leica Cybase 3 Delete the Leica CW 4000 Folder in Windows Explorer and desktop shortcut icons using conventional Windows functionality Leica CW 4000 Quick Start Guide Page 15 Page 16 Leica CW 4000 Quick Start Guide Chapter Three System Configuration Chapter Overview This chapter contains the following topics e Configuring Your System Language and Database Settings Image Acquisition Settings Microscope Settings Leica CW 4000 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 M enu Language and Database Settings The
12. ging on and off e Printing e Exiting The EDIT menu allows you to e Undoactions e Copy and paste images The VIEW menu enables you to specify which items are displayed on the desktop and offers access to the Chromosome Editor Acts as the control centre for the microscope and fluorochromes The IM AGE menu allows you to Setup the camera e Grabalive image e Annotate images Allows direct interaction with the FISH database Allows interaction with automatic capture procedure The WINDOW menu allows you to rearrange the application windows on the screen The HELP menu provides access to online help Leica CW 4000 Quick Start Guide Page 25 The Main CW 4000 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 DI ui LE Page 26 BAREDE 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 karyogram windows Undo Reverses your previous action Re do Re does previous action Zoom in Zooms in on image Zoom out Zooms out on image Fitto Window Scales th
13. le R eference The following conventions have been used to make this manual easier to read M enus FILE bold capitals M enu Commands Buttons Dialogs Open OK bold References Chapter 1 italics Notes Tips Warnings References Appear as follows and and Instructions contain additional information So Note Additional information that should be noted A Refer to References to other relevant material ef Tip Tips to help you use the program more productively A WARNING Important information to which you should pay careful attention One Step instructions Operations that can be performed in a single step 34 Step by step instructions Numbered instructional steps Information that only applies in certain situations is enclosed in boxes Leica CW 4000 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 plea
14. olded objects M FISH classification of telomeres Optimum enhancement of M FISH True colour and classification image Optional pixel shiftfeature Support for high resolution cameras Leica CW 4000 Quick Start Guide Page 7 Leica CW 4000 Satellite Capture The Leica CW 4000 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 CW 4000 system Minimum System R equirements Soi Page 8 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 e This software requires Microsoft Windows 2000 e Pentium or equivalent CPU is used with a speed of at least 900 M Hz e This product requires approximately 120 M bytes of disk space for a full installation and an additional free space of 200 M bytes 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 e Itis strongly recommended that at least 256 M bytes of system RAM is installed for FISH CGH and MFISH applications e
15. oolbar sene 26 The Main CW 4000 FISH Toolbar 28 Obtaining Leica CW 4000 Help enne 30 Chapter One Introduction Chapter Overview This chapter contains the following topics e Introduction e Style Reference Welcome e Whatis Leica CW 4000 General Leica CW 4000 Karyo Leica CW 4000 FISH Leica CW 4000 CGH Leica CW 4000 M FISH Leica CW 4000 Satellite Capture e Minimum System Requirements Software Requirements Leica CW 4000 Quick Start Guide Pagel Introduction Iw Page 2 This document describes the V1 0 release of the Leica CW 4000 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 CW 4000 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 READM E 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 Leica CW 4000 Quick Start Guide Sty
16. rectly loaded into your CD ROM drive and then the autorun facility on the CD should bring up the Leica CW 4000 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 CW 4000 Quick Start Guide Page 13 Page 14 and typing D INSTALL EXE in the Open box where D is the drive letter of your CD ROM drive 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 Select installation settings such as the language for the user interface Note that not all languages are supported by all applications When you have selected the items that you require you should click the Install button to start the installation process When the installation process is complete 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 Leica CW 4000 Quick Start Guide Un installation Should it be necessary to un install the software for any reason the procedure below should be followed 1 Step by step Instructions 3 1 Access the control pan
17. se 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 and 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 CW 4000 Quick Start Guide W hat is Leica CW 4000 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 e CW4000 provides a common karyotyping framework for G banding R ban
18. top appears as show below ia We Pose due ew tee ee e D SME GEREI 48x The Main M enu Barprovides access to all the features File Edit View Image Analysis Cybase Settings Help The Main Toolbar provides shortcuts to the most frequently used features DC SehidcRe aaWMngaser Leica CW 4000 Quick Start Guide Page 23 The Main CW 4000 Karyo Menus The main Leica Karyo CW 4000 menus are described below FILE EDIT VIEW IMAGE ANALYSIS CYBASE SETTINGS HELP The FILE menu contains commands for e Managing files e Logging on and off e Printing e Exiting The EDIT menu allows you to e Undoactions e Copy and paste images The VIEW menu enables you to specify which items are displayed on the desktop and offers access to the Chromosome Editor The IMAGE menu allows you to e Setup the camera e Graba live image The ANALYSIS menu allows you to e Perform an analysis e Editan existing karyogram The CYBASE menu allows you to directly interact with the Cybase Database The SETTINGS menu gives you options to change the underlying system settings and to train a new classifier The HELP menu provides access to online help Leica CW 4000 Quick Start Guide Page 24 The Main CW 4000 FISH Menus The main Leica CW 4000 FISH menus are described below FILE EDIT VIEW SETUP IMAGE ARCHIVE ACapS WINDOW HELP The FILE menu contains commands for e Managing files Log
19. u 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 Leica CW 4000 Quick Start Guide Installation Procedur
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