IQTL Getting Started Manual
Contents
1. Browse View Log WV Start Server at Power Up The field Path to the license file is the directory where the floating license file should be placed The default directory for floating license files is C Program Files GE Healthcare eLicense Server Licenses Do not change the default path The floating license file which has been collected from the Web lin section Section 1 3 3 must be placed in the directory that is set here We recommend that you select Use Services to run the license server as a Windows Service We also recommend that you select Start Service at Power Up to automatically start the license server when the machine boots Click Save Service even if you made no changes in steps 3 4 ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 6 Select the Start Stop Reread tab to control the license manager Information about the license file is displayed at the bottom of the dialog LMTOOLS by Macrovision Corporation http www macrovision com File Edit Mode Help Service License File System Settings UtiltieX Start Stop Reread Server Status Server Diags Config Services Borrowing FLEXnet license services installed on this computer Start Server Stop Server ReRead License File Force Server Shutdown hasist NOTE This box must be checked to shut down a license server when licenses are borrowed Using License File C Program Files GE Healthcare2. Edit A Eat standard x Mapping Units FS DRigest III E5 Lambda Hind III Phi 1 4 Hine II Mappings List ER Phix174 Hae Ill 3 Lambda pfge FB DNA pfge EZ 1 Kb Ladder EZ 250 Bp Ladder EZ 100 Bp Ladder E5 50 Bp Ladder S 8 32 Bp Oligo sizing EB 0 16 1 77 Kb RNA x 4 lim Alx Edit standard Create a duplicate of the existing standard before editing the values Create new standard Click the button select the mapping units and add the standard values ES 1d_mwpi tif Zoomed to fit m lol x EURE kg cTEPRE LE ble Base Pairsikb x 103 E 100 150 200 Pixel Position Lear log cur nie 012674 10 06 Wa DE ae Pi er Cures i 3 Select the curve type that best fits the data in the example you see a linear log curve 4 Click within a lane to assign standards right click to deselect ImageQuant TL Getting Started 28 9184 96 Edition AA 35 4 1D gel analysis 4 5 Molecular Size Calibration 5 If there are distortions in the gel that were compensated for when creating the lanes then use Rf to propagate 6 Deselect any values in the Parameters tab that you do not want to use The software retains these settings until you change them 7 Click Compute and the calibrated figures appear in the Measurements Table If all the bands are nicely separated selecting a lane should result in perfect automatic assignment from top down If there is a problem you can move the assigned
3. File Exit 22 ImageQuant TL Getting Started 28 9184 96 Edition AA 2 Getting started Getting started 2 To start ImageQuant TL double click the ImageQuant TL icon on the desktop Alternatively select ImageQuant TL v7 0 from the Start Programs menu The Control Centre window appears IQ ImageQuant TL Control Centre ImageQuant TL 1D gel analysis Analyze a 1D electrophoresis gel image Analysis Toolbox Analyze a dot slot blot microtiter plate or macroarray Colony Counting Coun AIT colonies or detect 2D electrophoresis spots analysis Analyze an image using area and profile based tools Online Help Look up queries in the comprehensive reference guide Also contained in this installation FluorSep IQ Tools ImageQuant TL Getting Started 28 9184 96 Edition AA 22 Getting started 2 2 1 Opening an image ImageQuant TL can analyse 8 to 16 bit grey scale Tiff images gel files and ds files from most types of image capture devices currently available Open 1 E Look in E Images e ace Array_Blot tif Array_Microtitre tif Colony Petri tif Colony _Spots tif i 1d_MWPLTIF ie 1d_norm tif i 1d_Tiers tif E 2channel ds File name fi d_Basic tif Files of type All ImageQuantTL image files tif tiff gel Cancel Analyse this image using IV Preview E 1D ma gt 3 wee ee gt for analysis of many types of 1D elect
4. eLicense server Licenses 7 Select the Start Server button to start the license server 8 Toconfirm that the License Server is operating with the selected license select the Server Status tab and press the Perform Status Enquiry button Then scroll to the bottom of the text box The information given here will confirm that the License has been accepted and the License Server is operable LMTOOLS by Macrovision Corporation http Avww macrovision com File Edit Mode Help Service License File System Settings Utilities Start Stop Reread Server Status Server Diags Config Services Borrowing Helps to monitor the status of network licensing activities gt Options Individual Daemon Perform Status Enquiry edud Feaure oo Server Name Flexible License Manager status on Wed 3 23 2005 15 58 Detecting lmgrd processes License server status Z7000 SEHC C4081B86 D License file s on SEHC C4081B86 D C Program Files GE Healthcare eLicense Server Licenses DeCyder MS 1 0 DUP_GROUP SEHC C4081B86 D 5 Expiring 050331 lic v Using License File C Program Files GE Healthcare eLicense Server Licenses DeCyder MS 1 0 DUP_GROUP SEHC C4081B86 ImageQuant TL Getting Started 28 9184 96 Edition AA 17 1 Introduction and installation instructions 1 4 Testing e License 9 Select File Exit and continue with section Section 1 4 Note Using LMTOOLS to control the floating license server is covered in detail in the Macrovision Licen
5. ladder by dragging the yellow line in the image window For the demo image 1D_MWEPI TIF the standard is Lambda Hind Ill and the standard lane is lane 12 Click Next to open the Quantity Calibration mode or use the Next menu to choose an alternative mode Note Molecular weight calibration must be performed in the Single channel view When the standard is applied to a lane click Compute and ImageQuant TL calculates the molecular weight across all the channels The Measurements Table shows the data relating to the channel selected in the main image window 36 ImageQuant TL Getting Started 28 9184 96 Edition AA 1D gel analysis 4 4 6 Quantity Calibration This mode allows calibration of bands on a gel to Known volumes also accounting for nonlinear staining effects A standard curve is produced and the software automatically calculates values for the unknowns 1 Click the bands where the quantities are known from the experimental set up 2 Add the known volume in the box that appears You select the units in the Parameters tab 3 Selecta curve method and click Calibrate The volumes appear in the Measurements Table 4 Click Next to open the Normalisation mode or use the Next menu to choose an alternative mode Note Quantity Calibration must be performed in the Single channel view You can assign known quantities to the bands on a channel click Calibrate and the volumes appear in the Measurements Table for that channel Qu
6. want to use background correction The lane profile window displays visual confirmation of the background subtraction Click Next to advance to the Band Detection mode or use the Next menu to choose an alternative mode Note Background subtraction is performed simultaneously across all the channels of a multichannel image and can be performed in either the Single or Overlay view If the Manual Baseline method is selected you change each individual channel in Single view but you view all channels in Overlay view The manual baselines cannot be edited in Overlay view 32 ImageQuant TL Getting Started 28 9184 96 Edition AA 1D gel analysis 4 4 4 Band Detection Click the Detect button and the software automatically detects the bands and band edges using the currently selected parameters an oO 2 a Es 2 oO Band detection has three parameters e Minimum Slope A value that represents how pronounced a band must be from its surrounding area to be recognised You adjust the value using the slider e Noise Reduction Sets the level to determine the difference between noise and band presence You can adjust the value in the Parameters tab e Percentage Maximum Peak Measures the relationship between each band in comparison to the tallest band and determines at what level to include a faint band You can adjust the value in the Parameters tab Band edges can be determined automatically o
7. will start automatically before the installation dialog appears ImageQuant TL Getting Started 28 9184 96 Edition AA 5 1 Introduction and installation instructions 1 3 E licensing IQTL Installation ImageQuant TL Install IOTL Not Installed Getting Started Install License Server Not Installed License Activation Homepage ImageQuant is a trademark of GE Healthcare Companies Adobe and Adobe Reader are trademarks of Adobe Systems Inc Any use of this software is subject to GE Install Adobe Reader Not Installed Healthcare Standard Software End User License Agreement for Life Sciences Software Products GE Healthcare Life Sciences AB a General Electric Company 2007 General Electric Company All rights reserved Close 2 Install each component by clicking the buttons in the installation dialog Follow the instructions for each installation part 1 3 licensing ImageQuant TL software requires an electronic license e license to use the program Once all installations have been performed ImageQuant TL should be activated with a license file 1 3 1 _ E license types There are two main types of e licences Machine node locked license A machine license also called node locked license is used for a single computer This type of license is useful when only one or a few computers are used for working with ImageQuant TL When using node locked licenses one e license per computer is needed Im
8. 0 Korea T 82 2 6201 3700 F 82 2 6201 3803 Latin America T 55 11 3933 7300 F 55 11 3933 7304 e Middle East amp Africa T 30 210 96 00 687 F 30 210 96 00 693 Netherlands T 0800 82 82 82 1 F 0800 82 82 82 4 e Norway T 47 815 65 777 F 47 815 65 666 Portugal T 21 417 7035 F 21 417 3184 Russia CIS amp NIS T 7 495 956 5177 F 7 495 956 5176 e Spain T 902 11 72 65 F 935 94 49 65 e Sweden T 018 612 1900 F 018 612 1910 e Switzerland T 0848 8028 10 F 0848 8028 11 e UK T 0800 515 313 F 0800 616 927 e USAT 1 800 526 3593 F 1 877 295 8102 Imagination at work 28 9184 96 AA 05 2007
9. 3 Colony counter analysis 6 1 Feature Detect ee ee 44 02 Feature EdIUNO euere 45 GS BACKGTOUNG SUDO EOC HON ner 46 Toolbox 71 SSO OCS TIMUOM en n cascada tone ee 47 72 SOO EAN en 48 1 3 TBOCKGROUNG SUDITOCHON sure 49 ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 1 Introduction and installation instructions 1 1 Introduction This booklet provides a quick introduction to ImageQuant TL and guides you through the analysis process in each module The figures that accompany each section help you work through your analysis and relate to the provided tutorial images This Getting Started does not describe all the features in ImageQuant TL For more information view the online Help available within the software If you have any questions or feedback on ImageQuant TL please contact GE Healthcare Technical Support at igtlsupport ge com or your local GE Healthcare representative 1 2 Installation Note Local administrative privileges must be obtained for installation of ImageQuant TL software The ImageQuant TL disc contains the installation files for all the items required to run ImageQuant TL software 1 Insert the disc The Autostart opens the Installation page in your browser If autostart is disabled select the DVD CD in Windows Explorer and launch setup exe Note Ifthe target computer does not have NET framework installed an installation of NET framework
10. GE Healthcare ImageQuant TL 7 0 Image Analysis Software Getting Started ED G3 O O i lt n e EEe T j Contents 1 Introduction and installation instructions Ll 1 2 L3 1 3 1 1 5 2 123 3 1 3 4 1 4 1 4 1 1 9 1 6 INLLOAUCLON zent 5 MS tallati eanan N A 5 Be H CVS IV o n E 6 PalCOMSC LV DCS i nn seen 6 Activation steps for ImageQuant TL sssrin 6 Collecting and placing a License file 9 Installation of GE Healthcare e license Server Program11 Tesung license I7 TOSI OCCU en a E 17 Finishing tHe installat One 19 Changing license configuration neee 20 2 Getting started 2 1 ODEHIDG ANIME ee 23 3 ImageQuant TL interface oral 3 2 53 3 4 3 9 3 6 Sur 4 1D gel analysis 4 1 4 2 4 3 4 4 4 5 4 6 4 TAS generally oUt ssena 25 TEMOJ ION are 25 Image VISWING TOONS sense een 26 KOHLASL Ausser 27 EOOUF oenen 27 EAIE Image aan nen ann ee 27 OPLIONS Eee N 27 QING ChEGTION een 29 EAN EANO ee en ne 30 Background SUD UACHON a ee 31 BOM CDOT CHOOT Ange 33 Molec lar SIZE C CIID QUOD ee 55 Quanti yC AlDrat O IN ise e csr ee 37 INORG SCO ass ea ats 38 ImageQuant TL Getting Started 28 9184 96 Edition AA 3 Array analysis Dake DCTS SOS cscs scr cle ie see 39 ord Create and Stretch GHGS nneeeleskhtsie 39 5 1 2 PCIOSENICIIES zen 39 5 13 Move and Resize SPOS nn 40 52 Background SUDACUON nes 41 53 NOIMAISOLON Eee 42 S4 SIPFESENCETNIOING een 4
11. OI you draw the area on the image before clicking Automatic After an automatic analysis is completed you can review and edit the data in each analysis mode by selecting the mode button You access the option to display multiple profiles in the Parameters tab Note Automatic analyses all channels simultaneously You can edit the image in the individual modes To draw an AO on a multichannel image prior to Automatic analysis use the Overlay view so that all the lanes are analysed Stepwise Proceed mode by mode through the analysis using the Next and Previous buttons to access the analysis modes ImageQuant TL Getting Started 28 9184 96 Edition AA 28 Select adt made Creata Lanes hai MP Manual The whole image G e Bo y Previous Mest Number of Tiers fi ImageQuant TL Getting Started 28 9184 96 Edition AA 1D gel analysis 4 4 1 Lane creation To create lanes automatically or manually select the appropriate button in the Navigator If you select Automatic e Click Create and the software automatically detects the lanes You access the edit mode from the list in the Navigator e For automatic analysis within an AOI drag from the top left to the bottom right on the image and then click Create The software automatically detects the lanes within this area e Select multiple tiers in the Parameters tab before clicking Create If you select Manual e Define the lane template in the Parameters tab Drag
12. Refer to the Help pane throughout the analysis process or refer to the footnotes throughout this document that describe how an analysis would be carried out on a multichannel image ImageQuant TL Getting Started 28 9184 96 Edition AA ImageQuant TL interface 3 3 ImageQuant TL interface 3 1 The general layout The appearance of the program remains the same throughout each analysis module A toolbar appears at the top of the window that contains the following buttons Og Single Overlay Sie sh gt HB DB Open Export Print Preview Annotate Contrast Colour Options Edit Image Additional windows such as the Image View Analysis Measurements Table MW Curve Report and Second Image Window to be used when analysing multichannel images can be selected from the buttons at the bottom of the Navigator Channel Channel Channels Channelg 3 2 The navigator The pane at the left of the screen is the Navigator The Navigator contains the tools required for the current mode of the analysis ImageQuant TL uses a wizard interface Next and Previous buttons allow easy navigation through the analysis modes The Restart button allows you to begin the analysis again ImageQuant TL Getting Started 28 9184 96 Edition AA 25 3 ImageQuant TL interface 3 3 Image viewing tools A Help pane is also present that provides information and tips relevant to the current analysis x x Action Clear Action Clear Previou
13. Standard Time I Include Domain Username Jettcile GMT Time Tue Mar 22 10 53 25 2005 CPU ID Difference From UCT 4294967236 IP Address euer he MSDOS Time 11 53 25 Ethernet Address OOO fBe8c60 Local Time f 111488805 Disk Volume Serial 94716f304 Number Windows Directory Ic WINDOWS FLEXID i Save HOSTID Info to a File 2 The physical address is displayed in the Ethernet Address text box P Host iD Notepad File Edit Format View Help Username cttcile CPU ID IP Address 3 183 240 95 Ethernet Address ooof1lFsescs6a ImageQuant TL Getting Started 28 9184 96 Edition AA 15 1 Introduction and installation instructions Viewing configuration settings 1 3 E licensing 1 2 a 4 5 16 Click the Config Services tab to display the configuration of the e license server The configuration displayed below should be used for ImageQuant TL LMTOOLS by Macrovision Corporation http www macrovision com Fie Edit Mode Help Service License File System Settings Utilities Start Stop Reread Server Status Server Diak Conta Services Boroning Configure Service Save Service Service Name GE healthcare eLicense server v Remove Service Path to the Imgrd exe file C Program Files GE Healthcare elicense serve _ Browse Path to the license file 1 Files GE Healthcare elicense server Licenses __ Browse Path to the debug loa file C Program Files GE Healthcare elicense serve
14. ageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 Concurrent floating license A concurrent license also called floating license is a license that can be used by all computers connected via network to a computer running a license server This type of license is useful when many users but not all at the same time need access to ImageQuant TL The number of computers that simultaneously can use ImageQuant TL depends on the license and is administered via the license server The license server can be installed on any computer in the network 1 3 2 Activation steps for ImageQuant TL To activate ImageQuant TL 1 Receive the access code see Access code 2 Find the physical address Ethernet MAC address of a physical network card of the computer see Finding the physical address of the computer 3 Collect and place a license file see Section 1 3 3 4 For a floating license Install the e license server program see Section 1 3 4 5 Launch ImageQuant TL to test the e license see Section 1 4 Access code After ordering ImageQuant TL a letter including an access code AC will be sent with a courier to the order s shipment address Store the access code ina safe place The access code is necessary for collecting license files see Collecting and placing a License file Note If the access code has not been delivered within 5 days of the order contact customer service to get
15. antity calibration data can be calculated for each channel individually ImageQuant TL Getting Started 28 9184 96 Edition AA 37 4 1D gel analysis 4 7 Normalisation 38 4 7 Normalisation The normalisation protocol allows the use of known values or the bands can be expressed as a percentage or a proportion of one or more selected bands If actual volumes are not known the band volume can be set to 100 ignore units and the unknown bands expressed as a percentage of the known band s 1 2 Select one or several known band s right click to deselect Select the required units in the Parameters tab Type the amount to be associated with the known bands Select either their average volume or collective volume Click Normalise Note Normalisation must be performed in the Single channel view Normalised values can be calculated for each channel individually ImageQuant TL Getting Started 28 9184 96 Edition AA Array analysis 5 5 Array analysis From the Control Centre click Array analysis and select an image or go to the Images directory and select either Array_Blot tif or Array_Microtitre tif Click Open to launch the Array analysis module Array analysis can be performed in either the Single or Overlay view Each stage of the analysis is performed on all the channels 5 1 Define Spots 5 1 1 Create and Stretch Grids Ee Image Window Array_Blot tif Zoomed to Fi oj x 12 tee e Select the gr
16. are calculates the unknown spots in relation to that spot 1 2 Select one or more known spots on the image window Select the required units in the Parameters tab and type the amount associated with the known spot s Select average volume or collective volume Click Normalise Click Next to advance to the Presence Flagging mode or use the Next menu to choose an alternative mode ImageQuant TL Getting Started 28 9184 96 Edition AA Array analysis 5 5 4 Presence flagging Tt x Estimate Clear Flagging threshold 50 Be Define spots as present Ye Define spots as absent Flagging threshold 50 u Previous Next This mode sets limits above which a spot is deemed to be present on the image which is indicated in a table as a spot presence 1 or absence 0 Detection is automatic if you select Estimate or you can manually adjust the value using the slider Alternatively you can define a spot as absent or present using the buttons in the Navigator ImageQuant TL Getting Started 28 9184 96 Edition AA 43 Colony counter analysis 6 6 Colony counter analysis From the Control Centre select Colony Counting and then select an image or go to the Images directory and select Colony_Petri tif Click Open to launch the Colony Counter Analysis module Note Multichannel images cannot be analysed using this module 6 1 Feature Detection 53 Image Window Colony_Petri tif 1 1 07 You select the
17. area of interest AOI shape in the Parameters tab and then draw an AOI on the image window The information about the detected features automatically appears in the Measurements Table You can change the following parameters e Detection parameters Modify using the sliders for sensitivity and operator size Selecting Initialize Sensitivity automatically determines the sensitivity for a given operator size e Background noise factor and spot splitting Can be adjusted in the Parameters tab ImageQuant TL Getting Started 28 9184 96 Edition AA 44 Colony counter analysis 6 You can use the zoom tool to determine if editing is necessary Click Next to open the Edit mode or use the Next menu to choose an alternative mode 6 2 Feature Editing 2 X Renumb Clear Pern eraser size at 1 1 Ble cco Draw or Erase Features Ek Delete Features Ge Split Features ne P Previous Next The Navigator contains the following controls e Drawor Erase Features Left click and drag to draw a feature using the selected pen size Right click and drag to erase part of a feature e Delete Features Click a feature if you want to delete e Split Features Manually split a feature by dragging a line at the required position Use Draw or Erase to make minor changes After editing the Measurements Table can be updated by clicking Renumber Spots Click Next to open the Background Selection mode or use the Next menu to
18. choose an alternative mode ImageQuant TL Getting Started 28 9184 96 Edition AA 45 6 Colony counter analysis 6 3 Background subtraction 6 3 Background subtraction Select a method from the Parameters tab The methods are e Mode of Non Spot Calculates the background based on the most common pixel value in the region around the feature You can adjust the margin in the Navigator e Image Rectangle Requires you to draw a rectangle on the part of the image that represents the background The results are displayed in the Measurements Table 46 ImageQuant TL Getting Started 28 9184 96 Edition AA 7 Toolbox X Calculate Clear Areas Lines Selector Tt NN R ce A 3 a Autotrace at Y g H e aya gt a Previous Next Autotrace Parameters Edge pixel intensity Threshold 50 Region of Interest Width 100 pixels Height 100 pixels Parameters f Instructions Toolbox 7 From the Control Centre click Analysis Toolbox and then select an image Click Open to launch the Toolbox analysis module 7 1 Shape definition Select a drawing tool from the choice of Areas Lines or Autotrace in the Navigator Areas and Lines Drag to create the object on the image window Some objects require multiple clicks right click to complete the object Grid Type the grid dimensions in the box that appears Drag the grid on the image window Autotrace Right click the outer edge of the feature to de
19. e by adding handles and dragging the handles ImageQuant TL Getting Started 28 9184 96 Edition AA 1D gel analysis 4 Click Next to advance to the Background Subtraction mode or use the Next menu to choose an alternative mode Note Lane creation is carried out simultaneously across all the channels of a multichannel image and can be performed in Single or Overlay view Any edits are applied to all the channels When editing lanes or drawing the AOI the Overlay view should be selected so that all the lanes are visible 4 3 Background Subtraction The selected background subtraction method is displayed in the Navigator To choose a different method select the method from Parameters tab KM Lane 12 100 olx 100 150 Pixel Position The following methods are available e Rubber Band Select and the software automatically removes the background e Minimum Profile Select and the software automatically removes the background e Rolling Ball Select and then adjust the radius of the ball in the Navigator the software automatically removes the background ImageQuant TL Getting Started 28 9184 96 Edition AA 31 4 1D gel analysis 4 3 Background Subtraction e Image Rectangle Select and then draw a rectangle on the part of the image that represents the background e Manual Baseline Select and then add or delete the handles in the profile window Drag a handle to adjust the baseline e None Select if you do not
20. e on request Sweden All third party trademarks are the property of their respective owners All goods and services are sold subject to the terms and conditions of sale of the company within GE Healthcare which supplies them A copy of these terms and conditions is available on request Contact your local GE Healthcare representative for the most current information 2007 General Electric Company All rights reserved First Published May 2007 GE Healthcare Europe GmbH Munzinger Strasse 9 D 79111 Freiburg Germany GE Healthcare UK Ltd Amersham Place Little Chalfont Buckinghamshire HP7 9NA UK GE Healthcare Bio Sciences Corp 800 Centennial Avenue P O Box 1327 Piscataway NJ 08855 1327 USA GE Healthcare Bio Sciences KK Sanken Bldg 3 25 1 Hyakunincho Shinjuku ku Tokyo 169 0073 Japan Asia Pacific T 85 65 62751830 F 85 65 62751829 e Australasia T 61 2 8820 8299 F 61 2 8820 8200 e Austria T 01 57606 1613 F 01 57606 1614 Belgium T 0800 73 890 F 02 416 8206 Canada T 1 800 463 5800 F 1 800 567 1008 Central amp East Europe T 43 1972 720 F 43 1972 722 750 e Denmark T 45 70 25 24 50 F 45 45 16 2424 e Eire T 1 800 709992 F 44 1494 542010 e Finland amp Baltics T 358 9 512 3940 F 358 9 512 39439 France T 01 69 35 67 00 F 01 69 41 98 77 e Germany T 0800 9080 711 F 0800 9080 712 Greater China T 852 2100 6300 F 852 2100 6338 Italy T 02 26001 320 F 02 26001 399 e Japan T 81 3 5331 9336 F 81 3 5331 937
21. from the top left to the bottom right on the image window and ImageQuant TL draws the lanes 29 4 1D gel analysis 4 2 Lane Editing x Accept Clear Select edit mode edit Multiple Lanes H Bend Resize Lane Box f Move Lane Box Edges Fr Add Lanes The whole image gt y Previous Next Half lane width 15 gt pixels Apply X Delete Current Lane _ Instructions A Parameters 30 4 2 Lane Editing Select the edit mode from drop down menu If you make changes click Accept to update the lane profile window To delete the current lane highlight the lane you want to delete and then click on the Delete button in the Parameters tab Edit multiple lanes Select from the following options in the Navigator e Bend Resize Lane Box For fine control of badly distorted gels left click to add a handle and then drag the handle Right click to remove a handle e Move Lane Box Edges Drag to move lane box edges on image window e Add Lanes Click the location on the image window within the lane box where you need to add the lane Edit single lanes Select from the following options in the Navigator e Bend Resize Left click to add a handle and then drag the handle Right click to remove a handle e Move Select the lanes and then drag the lanes to a new location e Add Grimaces Grimaces account for band distortions Click a band to apply the grimace and then alter the grimac
22. id type spot shape and spot size from the Parameters tab and then click Detect to automatically define the spots To auto size spots select the checkbox e Alternatively select the grid type spot shape and size and then define the grid by positioning the pointer in the centre of the top left well Drag the pointer to the centre of the bottom right well 5 1 2 Adjustments e Drag to move the entire grid e Reshape the grid by dragging a handle ImageQuant TL Getting Started 28 9184 96 Edition AA 39 5 Array analysis 5 1 Define Spots 40 5 1 3 Move and Resize Spots Spot Properties FE Identification Spot ID more than one spot selected Label Size and shape Radius 3 E pixels Y Radius CD 29 pixel Shape JO Circle Miscellaneous Exclude from analysis To move individual spots click a spot Ctrl click each spot or drag out an area to choose multiple spots Then reposition the spot s exactly over the well Clear the Show Spot Numbers check box in the Options window To alter the diameter of a spot change the spot radius in the Parameters tab make sure you clear the auto size check box Alternatively right click the spot and open the Spot Properties window and change the size and shape using the pixel values In addition you can add the Spot Label in this field Alternatively click the spot and drag the perimeter to the required size as shown in the figure You should use a
23. ing concurrent license e Select the I am using a Floating E license radio button e Click Next The next page in the wizard is displayed ImageQuantIL License Setup Wizard License Server lt lt lt IF vou do not have a license file please collect one using the Software Licensing System tool available on the GE Healthcare E Licensing Webpage www BliCensing amershambiosciences com gthwebslogin Please see the IQTL Getting Started guide for instructions on how to set up a license server MAC address For this computer 001 185ded38a lt Back Finish Help e Enter the network name of the machine that is running the GE Healthcare Software Licensing Server e Click Finish Once the license file is found ImageQuant TL will start displaying the license agreement ImageQuant TL Getting Started 28 9184 96 Edition AA 19 1 Introduction and installation instructions 1 5 Finishing the installation 3 If using a node locked machine license e Select the I am using a Node Locked E license radio button e Click Next The next page in the wizard is displayed ImageQuantIL License Setup Wizard Node locked License File Browse If you do not have a license file please collect one using the Software Licensing System tool available on the GE Healthcare E Licensing Webpage waw elicensing amershambiosciences com gtlweb login MAC address For this computer 001185ded38a lt Back Finish Help e Ente
24. ll making sure Ea Een you leave a space between the gand the Kicker zei 1 gt ipconfig all Command Prompt 4 Press Enter 8 ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 This will create an output of this type Host Name eo ee ee a AEBDEW ESUL Primary Dna suffix ko ae u ee Node Type oe oe we ew ue Hybrid IP Routing Enabled 2 ee ae a Ele WINS Proxy Enabled a No Ethernet adapter Local Area Connection Connection specific DNS Suffix Description as a 2 s o IntelfR PRO 100 Alert on LAN Manage sus aCe Dhep P TEE YES ee Enahled ee amp 2 Fes IF Address gt Een Sue amp ow e l 10 255 160 20 subnet Mask 2 a a a amp 2 a a 106 193 0 1 Default Gateway a s 2 a 22 a o 20 397 052 DHCP Server z 20 37 2 3 5 Makea Hote sf the avec address of the computer The physical address is the number to the right of Physical Address but without any dashes or colons Inthe above case the physical address for the computer is 10A2B307B077 Note Ifa computer has several physical addresses there can be one for each Ethernet card in the computer any physical address not associated with a VPN can be used for identification Note A computer can also have virtual physical addresses for example if connected to a VPN software Make sure that an address related to the physical network card is selec
25. nfirm Collection Product Selected DeCyder MS 1 0 machine license only beta Hostid Type ETHERNET Host ID Address Entered 900d05982592c Collect License ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 Make sure that your e license is configured correctly and if so confirm your e license collection by pressing Collect license Otherwise press Back to perform corrections g Save license to file Save license to file We recommend you use the Save license to file alternative A floating license file must be placed on the computer running the e License server Place the license file in the folder C Program Files GE Healthcare eLicense Server Licenses on the License server see also section Section 1 3 4 step Section 2 A node locked license file must be placed on the computer running the ImageQuant TL program Send by e mail not recommended If you use the Send by e mail alternative the license contents are delivered as raw text in the e mail body You must copy the license text and paste it as an ASCII text file in for example Notepad Then save the License with the extension lic in your e license folder 4 For a floating license continue from section Section 1 3 4 For a node locked license continue from section Section 1 4 ImageQuant TL Getting Started 28 9184 96 Edition AA 11 1 Introduction and installation instructions 1 3 E licensing 12 1 3 4 In
26. or daemon status on SEHC C4081B86 D gehealth UP vl0 1 Feature usage info users of ImageQuant TL Total of 5 licenses issued Total of O licenses in use mage Quan v7 U vendor gehea floating license Using License File C Program Files GE Healthcare eLicense Server Licenses DeCyder MS 1 0 DUP_GROUP SEHC C4081B86 3 Click the Start Stop Reread tab and stop the Stop Sever e license server by pressing the Stop Server button 4 Update the set of licenses that should be used by the e license server for example if a new license shall be added copy it to the folder where the current set of e licenses resides by default C Program Files GE Healthcare eLicense Server Licenses Please ImageQuant TL Getting Started 28 9184 96 Edition AA 21 1 Introduction and installation instructions 1 6 Changing license configuration observe that all licenses in this folder must be valid and have the same vendor name in our case gehealth Imageluant TL v7 0 vendor gehealth 5 Inthe LMTOOLS Start Stop Reread tab press the Start server button to restart the e license server 6 To confirm that the new set of licenses has been accepted and are available as expected select the Server Status tab and press the Perform Status Enquiry button Then scroll to the bottom of the text box The information given here will confirm that the License has been accepted and the License Server is operable see the screen dump in step 2 7 Select
27. r all the edges can be set to a fixed width You can edit the bands and edges either on the image or lane profile window The pointer changes according to its proximity to the bands and edges e Toremove a band edge right click ImageQuant TL Getting Started 28 9184 96 Edition AA 33 4 1D gel analysis 4 4 Band Detection 34 e Toadda band edge left click e To move an edge position the pointer over an existing edge and drag the pointer The image and profile windows can be viewed in greater detail by zooming in The Measurements Table window contains the current results You can alter the fields displayed in the table using the Options from the main toolbar Click Next to open the Molecular Size Calibration mode or use the Next menu to choose an alternative mode Note Band detection must be performed on each channel individually in the Single view Edits can be performed on the main image window and lane profile window The second image window can be used for visual comparisons between the channels When band detection is complete all the channels can be viewed in Overlay mode ImageQuant TL Getting Started 28 9184 96 Edition AA 1D gel analysis 4 4 5 Molecular Size Calibration Before you can perform molecular size calibration you must set up the molecular size reference lane in the Parameters tab 1 Select the standard from the library or create a new standard 2 Tocreate a new or edit an existing standard click
28. r or browse for the location where you have stored the license file on the machine e Click Finish Once the license file is found ImageQuant TL will start displaying the license agreement 1 5 Finishing the installation 1 Eject the DVD 2 Restart the computer 20 ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 1 6 Changing license configuration If the set of licenses needs to be changed on an e license server that is already installed and in operation perform the following steps 1 Open the LMTOOLS utility by locating the folder where the license server installation is stored and double click Imtools exe LMTOOLS opens 2 Make sure that all licenses offered by the e license server are checked in All e license server users must have returned their license to the server that is closed their program windows Control this by opening the Server Status tab Press the Perform Status Enquiry button Then scroll to the bottom of the text box The information given here will confirm that no license is in use LMTOOLS by Macrovision Corporation http Avww macrovision com File Edit Mode Help Service License File System Settings Utilities Start Stop Reread Server Status Server Diags Config Services Borrowing Helps to monitor the status of network licensing activities Options Individual Daemon Perform Status Enquiry indvidual Feature IT Server Name Vend
29. rophoresis gel ee ee eee To open an image in an analysis module click the button in the Control Centre or if already in the analysis module select Open from the File menu The Open Image window appears The demonstration images are located in the Images folder of the ImageQuant TL program group Select the image and the analysis module you want to use and click on Open The software automatically saves your analysis throughout the process ImageQuant TL can perform a full analysis of multichannel images ds format When a multichannel image is loaded the interface changes to allow access to the multichannel analysis features Note Colony counter module cannot load multichannel images ImageQuant TL Getting Started 28 9184 96 Edition AA 23 2 Getting started 2 1 Opening an image 24 The Overlay and Single buttons on the main tool bar allow you to select the image view If you select Overlay you choose the channels to be viewed using the channel selector buttons This determines which channel data appears in the main image window the lane profile window and the measurements table To assist with the analysis you can access a second image window using the buttons under the Navigator The second image window allows you to visually compare the channels you select using the buttons in the window If you want to edit the image you use the main image window The software updates the second image window automatically
30. s Mext Previous est Selected Mode Parameter selection This pane contains step by Parameter one step help on the selected mode f Parameter two Parameters Instructions Instructions A Parameters e Click the Parameters tab to view any additional parameters 3 3 Image viewing tools You access the image viewing tools from the buttons on the Image window q e Zoom Drag a rectangle on the image window and then left click to increase or right click to decrease the image magnification Alternatively you can drag the scroll bar edges 1 1 Zoom 1 1 View the image at a 1 1 ratio Eh e Fitto window View the whole image fs Magnify Allows magnification of a portion of the image m e Panning The image can be moved around the image window when part of the image is not visible if for example the zoom tool has been used 26 ImageQuant TL Getting Started 28 9184 96 Edition AA ImageQuant TL interface 3 3 4 Contrast The contrast window allows you to improve the way the image is displayed The values are based on the image calibration during scanning The contrast can be altered in either the Single or Overlay view When analysing in Overlay you select the channels for contrast adjustment from the drop down menu The original data remains unaltered 3 5 Colour The colour window allows you to change the colour of the displayed image You cannot make alterations to the colour display in the Overla
31. sing End User Manual 1 4 Testing e License To be able to start ImageQuant TL the correct license file must be found ImageQuant TL will at every login check that the license file is available 1 4 1 Test procedure After installation of ImageQuant TL software downloading and placing the license file start ImageQuant TL to test that the license file can be found Test ImageQuant TL software on all computers where the program is installed Note The previous sections must have been successfully completed to start ImageQuant TL 1 Start ImageQuant TL 2 Ifa valid license file is available ImageQuant TL will start displaying the license agreement Note ImageQuant TL will use the last used license if it is still available and valid If you want it to use another license disable make sure the program cannot find the license type s that should not be used by for example changing the name for a node locked license or disconnecting the network for a floating concurrent license during log in 18 ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 License failure 1 If one or more of the requested licenses are not available the ImageQuant TL License Setup Wizard dialog is displayed ImageQuantIL License Setup Wizard Please select which type of License you intend to use Tam using a Node Locked E license i I am using a Floating E License 2 If using a float
32. smaller diameter with microtitre plates not necessarily including the perimeter of each well s contents With a blot you should use a wider diameter Click Next to advance to the Background Subtraction mode or use the Next menu to choose an alternative mode ImageQuant TL Getting Started 28 9184 96 Edition AA Array analysis 5 5 2 Background subtraction Select a method from the Parameters tab You can choose from the following five methods e Spot Surface Minimum Select and the software automatically removes the background e Spot Edge Average Select and the software automatically removes the background e Negative Controls Select and then define the negative controlls in the image window e Image Rectangle Select and then draw a rectangle on the part of the image that represents the background e None Select if you do not want to use background subtraction The values appear in the Measurements Table You can change the fields using the Options window Click Next to advance to Normalisation mode or use the Next menu to choose an alternative mode ImageQuant TL Getting Started 28 9184 96 Edition AA 41 5 Array analysis 5 3 Normalisation 42 5 3 Normalisation The Normalisation protocol allows the use of Known values or the spots can be expressed as a percentage or a proportion of one or more selected spots If the actual volumes are not known the spot volume can be set to 100 percent and the softw
33. stallShield Wizard Ready to Install the Program The wizard is ready to begin installation Click Install to begin the installation IF you want to review or change any of your installation settings click Back Click Cancel to exit the wizard ImageQuant TL Getting Started 28 9184 96 Edition AA 13 1 Introduction and installation instructions 1 3 E licensing 4 Click Finish i GE Healthcare Software Licensing Server InstallShield Wizard x InstallShield Wizard Completed The InstallShield Wizard has successfully installed GE Healthcare Software Licensing Server Click Finish to exit the wizard Launch GE Healthcare Software Licensing Server 5 If the check box Launch GE Healthcare Software Licensing Server Launch GE Healthcare Software Licensing Server was checked in step Section 4 it is checked by default LMTOOLS a dialog containing information and tools for the e license server is automatically opened 14 ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 To find the physical address of the computer 1 Click the System Settings tab LMTOOLS by Macrovision Corporation http Avww macrovision com File Edit Mode Help Service License File System Settings Utilities Start Stop Reread Server Status Server Diags Contig Services Borrowing Hostid Settings Time Settings Computer Hostname SEHC HS1 BCIJ D System Time Zone Central Europe
34. stallation of GE Healthcare e license Server Program The installation in this section should only be performed when using a floating license If only node locked licenses are used continue from Section 1 4 Select the computer on the network where the license server should be installed All computers running ImageQuant TL must have network access to this computer in order to run 1 On the ImageQuant TL Installation page click License Server An Install shield wizard dialog is displayed If not locate the cd drive and double click setup exe i GE Healthcare Software Licensing Server InstallShield Wizard Welcome to the InstallShield Wizard for GE Healthcare Software Licensing Server The InstallShield R Wizard will install GE Healthcare Software Licensing Server on your computer To continue click Next WARNING This program is protected by copyright law and international treaties Click Next ImageQuant TL Getting Started 28 9184 96 Edition AA Introduction and installation instructions 1 2 Click Next to accept the default destination folder i GE Healthcare Software Licensing Server InstallShield Wizard Destination Folder Click Next to install to this Folder or click Change to install to a different Folder Install GE Healthcare Software Licensing Server to C Program Files GE Healthcare eLicense server 3 Click Install to start the installation i GE Healthcare Software Licensing Server In
35. ted for the installation 6 Close the DOS prompt window 1 3 3 Collecting and placing a License file 1 Make sure you have the access code and the physical address available 2 Onthe ImageQuant TL Installation page click License Activation Homepage The Software Licensing System home page opens ImageQuant TL Getting Started 28 9184 96 Edition AA 9 1 Introduction and installation instructions 1 3 E licensing 3 Collect the License file according to the instructions on the web site The collection includes the following steps q f 10 Enter the Access Code and press Continue Inthe License Administration Center Collect Licenses page that opens press Collect Licences The Select Product and Register Product page opens Perform step1 7N Select productto collect Please Select Product to Collect Here Perform step 2 l i gt Register your Please Register Your Product Here product Perform step 3 Enter the physical address Host ID of the computer Please Enter Your Host ID The host ID will be an Ethernet MAC address for example 02 45 ee f4 32 02 Please enter it without any separator characters For example enter 0245eef43202 For help and more information please refer to the Host ID Help Page Expected Type of Host ID ETHERNET Please Enter the Machine Host ID Press Continue to proceed to Collection Confirmation Co
36. termine the Edge pixel intensity the value appears in the Parameters tab and then left click the centre of the feature to detect and draw the object Selector Allows you to select objects for editing Drag through an area to select multiple objects ImageQuant TL Getting Started 28 9184 96 Edition AA 47 7 Toolbox 7 2 Shape Editing 7 2 Shape Editing e Click the Selector button and then click the object or CTRL click for multiple objects that you want to edit e Drag a handle to resize the object e Drag an object to a new location e Right click to copy and paste objects Click Next to open the Background Subtraction mode Note Shape definition must be performed on each channel individually in the Single view You can edit the image in the main image window and compare the channels in the second image window When shape definition is complete all the channels can be viewed in the Overlay mode 48 ImageQuant TL Getting Started 28 9184 96 Edition AA Toolbox 7 7 3 Background subtraction Select the method from the Parameters tab You can use different methods on different features on the same image e Local Average Select and the software automatically performs the background subtraction on the selected feature e Local Median Select and the software automatically performs the background subtraction on the selected feature e Histogram Peak Select and the software automatically performs the background sub
37. the access code via telephone Finding the physical address of the computer Note Itis possible to use Macrovision LMTOOLS utility for finding the physical address The LMTOOLS utility is installed when installing the e license server program but can also be installed ImageQuant TL Getting Started 28 9184 96 Edition AA 7 1 Introduction and installation instructions 1 3 E licensing separately from the Access Code home page For instructions see Chapter 1 3 4 Installation of GE Healthcare e license Server Program 1 The physical address of the computer also called Ethernet MAC address is necessary for identification of the computer when collecting the appropriate e license file An example of a computer physical address is 00 3E F4 E4 44 76 FE 56 The physical address can only contain digits 0 9 and letters a f A F Dashes or colons should be removed to be used as the physical address Note The computer s Internet IP number is NOT the physical address of the computer For questions regarding physical addresses or e licensing refer to http www elicensing amershambiosciences com gtlweb tag html 2 Onthe computer where the e license file should be placed select Start All Programs Accessories Command Prompt Note A floating license file should be placed on the License server a node locked license file should be placed on the computer running ImageQuant TL 3 When the DOS prompt appears enter the command ipconfig a
38. traction on the selected feature e Image Rectangle Ellipse Select and draw an object on the part of the image window that represents the background If multiple objects are drawn select the object to apply from the drop down menu in the Parameters tab and the software automatically subtracts the background In Selector mode click the feature that requires background subtraction Choose a method from the Parameters tab and the software automatically subtracts the background To simultaneously subtract the background from multiple objects click the Selector button and drag an area Choose a method from the Parameters tab and the software automatically subtracts the background Background subtraction must be performed on each channel individually in the Single view When background subtraction is complete all the channels can be viewed in Overlay mode ImageQuant TL Getting Started 28 9184 96 Edition AA 49 7 Toolbox 7 3 Background subtraction 50 ImageQuant TL Getting Started 28 9184 96 Edition AA www gel ifesciences com GE imagination at work and GE monogram are trademarks of General Electric Company ImageQuant is a trademark of GE Healthcare companies GE Healthcare Bio Sciences AB Any use of this software is subject to GE Healthcare Standard Bj rkg atan 30 Software End User License Agreement for Life Sciences Software Products A copy of this Standard Software End User License 19 1 84 U ppsala Agreement is availabl
39. y view 3 6 Edit Image The image manipulation tools are available from the main tool bar and allow you to edit the image All the edits are logged for a specific image and can be viewed in the Image Properties window Editing can be performed in either the Single or Overlay view All the edits appear in all the channels of a multichannel image 3 7 Options You can access a variety of options using the button on the main tool bar These options are specific to the selected analysis module and allow customisation of the Image Window and Measurements Table ImageQuant TL Getting Started 28 9184 96 Edition AA 27 1D gel analysis 4 4 1D gel analysis N Automatic Stepwise Automatic analysis steps IV Lane Creation IV Background Subtraction IV Band Detection Manual only analysis steps Molecular Size Calibration Quantity Calibration Normalisation 1D Analysis lf required select an area of interest in the Image window Press the Automatic button to run through the selected steps Press the Stepwise button to run through the steps one by one Click for help From the Control Centre click 1D gel analysis Select the image or go to the Images folder and select 1D_MWPI tif to follow this example Click Open to launch the 1D analysis module Automatic Performs an automatic analysis using the selected modes Select or clear the modes in the Navigator If the analysis requires an area of interest A
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