ImageQuant TL 7.0
Contents
1. yl ii GE Healthcare HI HI A HI g Mai ee i ll E l Ho gt ImageQuant TL 7 0 i Mo Image Analysis Software l E E Getting Started 4 Il i Il HI HI Il Contents 1 Introduction and installation instructions LI VOU CHO Me ariana ai 5 1 2 INSOlO tO RG nia 5 MS ESC OT VSI nn ibiccros ali iii i 6 bs ESIICCNSC WD acli 6 1 3 2 About GE Healthcare s e license server program 1 3 3 Installation of GE Healthcare s e license server program 1 3 4 ACC COSS COO Olii nei 9 135 Collect and place a License file 10 UZ Start OTL forthetirst tiime Os eater ee reese 11 1 4 1 RoG NENCO SOTO a a e lai 12 2 Getting started el AODEIMMONNIMOO Sense ica ese Lana 15 3 ImageQuant TL interface sd TInegeneralioyvout anale alba 17 52 INGMNOVIGOOr ella 17 55 Image VIEWING tools sin essences Nore ln 18 BE CONO seh eee eee oe 19 Ge COQUE silla 19 36 ECE MING Cascade divi irrita 19 ST ODORE lena ae 19 4 1D gel analysis 4 1 LONE Creton Rea 21 de Lone id gru 22 4 3 Background Subtraction uate chee ee ts 25 Ae BONOMDETOCIION acari hi 25 45 MOlECUIGISIZe CONDRARON inun 27 o QUARINvcgalpialone elle 29 A NOOO gioia dai 30 5 Array analysis Sil Delne sSpotShinoalii ibid 31 ImageQuant TL Getting Started 28 9184 96 Edition AB 3 511 Create and Stretch Gus anres nN 31 5 1 2 AGUSTINO Nees Re EN CREE RMT rs CIPRSAA FERRI PIE TOT2. 1 4 Start IQTL for the first time To be able to start an IQTL software the correct license file must be found IQTL will at every login check that the license file is available ImageQuant TL Getting Started 28 9184 96 Edition AB 11 1 Introduction and installation instructions 1 4 Start IOTL for the first time 1 4 1 Find the license file After installation of an IQTL software downloading and placing the license file start IQTL on all computers where the program is installed to let the computers find the license file on the network Note The previous sections must have been successfully completed to Start IOTL Note QTL 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 disconnecting the relevant network during log in 1 Start ImageQuant TL and or IQTLSecurlTy 1D Gel Analysis tool by clicking Its icon 2 The ImageQuant TL License Setup Wizard dialog is displayed ImageQuant IL License Setup Wizard Please select which type of License you intend to use f I am using a Node Locked E license i I am using a Floating E License 12 ImageQuant TL Getting Started 28 9184 96 Edition AB Introduction and installation instructions 1 3 Select the I am using a Floating E license radio button and click Next The next page in the wizard is displayed ImageQu
3. 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 AB 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 Edit a Edit standard x Standards Mapping Units ES DRigest Ill YJ ES Lambda Hind III FAI Phi x174 Hine Il Mappings List FR PhiX174 Hae Ill FS Lambda pfge FE DNA pfge E5 1 Kb Ladder E5 250 Bp Ladder E5 100 Bp Ladder E5 50 Bp Ladder FAI 8 32 Bp Oligo sizing ES 0 16 1 77 Kb RNA x 4 B 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
4. e Spot Edge Average Select and the software automatically removes the background e Negative Controls Select and then define the negative control s 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 AB 33 5 Array analysis 5 3 Normalisation 54 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 software 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 AB Array analysis 5 5 4 Presence flagging se x Estimate Clear Flagging threshold 50
5. We Define spots as present We Define spots as absent Flagging threshold 50 ao Previous Mext 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 AB 35 6 Colony counter analysis 6 1 Feature Detection 6 Colony counter analysis 36 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 Image Window Colony_Petri tif 1 1 07 You select the 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 G
6. 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 ImageQuant TL Getting Started 28 9184 96 Edition AB 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 subtraction 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
7. Channel Channel4 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 PAE 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 AB 17 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 Dm cb D y Previous Mext Previous Next Selected Mode Parameter selection e This pane contains step by Parameter one step help onthe selected mode f Parameter two Parameters f Inziructione Instructions A Parameters j 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 S 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 ata 1
8. LORIA 31 5 1 3 Move and Resize SPOtS eccsecssessssessssessssesssessssecssessssessseesseesseeen 32 5 2 BUCKIIOUNOASUDEActoni aula ilialenee 33 55 INeFMOlSdton alal alla 34 54 Presencetlogging ahi el aleialale 55 Colony counter analysis 6 1 Feature DETCCUION machete ridin eects Bator id 36 6 20 Feature Edinet 37 625 BacCkoround subtract eenen e E 38 Toolbox elk SOPE OEO e beet tees pie bated 39 LA 010 0456 REA NEO 40 TS IBAGKOPOUPO SUDTOCHON ascella 41 Licensing Server administration ol OpenNet azera lalla 43 8 2 View the Host ID of the computer 443 6 5 View configuration settings cxicsirncidincccadiblenl ween 44 8 4 Change license configuration o eeceeesessssessstsssesstecstessseessees 46 ImageQuant TL Getting Started 28 9184 96 Edition AB 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 igtisupport ge com or your local GE Heal
9. known band s 1 2 Select one or several known bandis 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 AB 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 e Select the grid 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 AB 31 5 Array analysis 5 1 Define Spots 532 S
10. 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 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 Move Lane Box Edges Drag to move lane box edges on image window 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 Bend Resize Left click to add a handle and then drag the handle Right click to remove a handle Move Select the lanes and then drag the lanes to a new location Add Grimaces Grimaces account for band distortions Click a band to apply the grimace and then alter the grimace by adding handles and dragging the handles ImageQuant TL Getting Started 28 9184 96 Edition AB 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 i
11. 1 ratio e Fit to window View the whole image i e Magnify Allows magnification of a portion of the image lm 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 18 ImageQuant TL Getting Started 28 9184 96 Edition AB 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 Overlay 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 Editi
12. Help Look up queries in the com nsive reference guide Also contained in this installation FluorSep lQ Tools 14 ImageQuant TL Getting Started 28 9184 96 Edition AB Getting started 2 2 1 Open 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 Se tag 2 xi Look in Images ee OD 2Channel DIR i Array_Blot tif DI 1d_Basic tif Array_Microtitre tif i 1d_MWPI TIF i Colony _Petri tif 1d_norm tif Colony_Spots 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 M Preview Ea 1 D i 9909 n a ceo for analysis of many types of 1D electrophoresis gel bagna e ee ee se To open an image in an analysis module click the button in the Control Centre or it 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
13. Nm 1 6 8 6 lol tL Lee B BERGE BELF T a a wo u HE de nm im Ga SI 100 150 200 Pixel Position Ls 12999 Lea log cur y D167 10 06 RI Value 9850 AE i M Curse 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 AB 27 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 ladder by dragging the yellow line in the image window For the demo image 1D_MWPI TIF the standard is Lambda Hind III 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 Measurement
14. ant IL License Setup Wizard License Server e 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 www elicensing amershambiosciences comigitvebilogin Please see the IQTL Getting Started guide for instructions on how to set up a license server MAC address for this computer 001185ded38a lt Back Finish Help Note The node locked e license is only used for demo versions 4 By default Local host the computer you are using is entered as License Server If the license file and the GE Healthcare Software Licensing Server are placed on another computer enter the network name of the machine Click Finish Once the license file is found the IQTL software will start Note For further information about the license see Chapter 8 ImageQuant TL Getting Started 28 9184 96 Edition AB 13 2 Getting started 2 Getting started 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 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 Count colonies or detect 2D electrophoresis spots Array analysis Analyze an image using area and profile based tools Online
15. ath 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 By default Use Services is selected to run the license server as a Windows Service By default Start Service at Power Up is also selected to automatically start the license server when the machine boots 3 Click Save Service even if you made no changes in step 2 44 ImageQuant TL Getting Started 28 9184 96 Edition AB 4 5 Licensing Server administration 8 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 Avww macrovision com File Edit Mode Help Service License File System Settings Utilitie Start Stop Retead Server Status Server Diags Config Services Borrowing FLEXnet license services installed on this computer GE healthcare eLicense server Start Server Stop Server ReRead License File i Force Server Shutdown Sinti lt NOTE This box must be checked to shut down a license server when licenses are borrowed Using License File C Program Files GE Healthcare eLicense server Licenses Click the Reread License File button to update the license file information Then it displays Reread Server License File Completed LMTOOLS by Macrovi
16. be 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 2008 General Electric Company All rights reserved Close 2 Install each component by clicking the buttons in the installation dialog Follow the instructions for installation of ImageQuant TL and or IQTLSecurlTy and Adobe Reader in the windows that open Installation of the license server is described in 1 3 1 3 E licensing IQTL softwares require an electronic license e license to use the program To activate ImageQuant TL or IQTLSecuriTy you must install the e license server program receive the access code collect and place the license file on the computer running the license server program and launch the IQTL software 1 3 1 E license type A concurrent license also called floating license is used for IQTL softwares This license can be used by all computers connected via network to a computer running a license server ImageQuant TL Getting Started 28 9184 96 Edition AB Introduction and installation instructions 1 This type of license is useful when many users but not all at the same time need access to IQTL The number of computers that simultaneously can use IQTL depends on the license and is administered via the l
17. code in a safe place The access code is necessary for collecting license files see Collect and place a License file Note Ifthe access code has not been delivered within 7 days of the order contact technical support to get the access code via telephone ImageQuant TL Getting Started 28 9184 96 Edition AB 9 1 Introduction and installation instructions 1 3 E licensing 1 3 5 Collect and place a License file 1 Onthe ImageQuant TL Installation page click License Activation Homepage The Software Licensing System home page opens 2 Collect the License file according to the instructions on the web site The collection includes the following steps a Enter the Access Code and press Ee 1 Continue Inthe License Administration Center page press Collect Licences The Select Product and Register Product page opens Collect Licenses _ Please Select Product to Collect Here Perform step 1 Selectproductto collect Perform step 2 1 Register your Please Register Your Product Here product Perform step 3 Enter the Ethernet 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 Pl
18. eLicense Server Licenses DeCyder MS 1 0 DUP GROUP SEHC C4081B86 D 5 Expiring 050331l lic v Using License File C Program Files GE Healthcare eLicense Server Licenses DeCyder MS 1 0 DUP_GROUP SEHC C4081B86 7 Select File Exit 8 4 Change 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 Make sure that all licenses offered by the e l Perform Status Enquiry 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 46 ImageQuant TL Getting Started 28 9184 96 Edition AB Licensing Server administration 8 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 Fedra Server Name Vendor daemon status on SEHC C4081B8S6 D gehealth UP vl0 1 Feature usage info er A mel ecex eiaaexmnms e gt gt Users of ImageQuant TL Total
19. ease Enter the Machine Host ID The correct Host ID is found in the IQTL Installation window under the Install License Server button see Chapter 1 2 Installation Press Continue to proceed to Confirm Collection Note The computer s Internet IP number is NOT the Host ID of the 10 computer ImageQuant TL Getting Started 28 9184 96 Edition AB Introduction and installation instructions 1 f Make sure that the Host ID is correctly entered and if so confirm your e license collection by clicking Collect License Otherwise click Back to perform corrections Confirm Collection Product Selected IQTL 7 0 1 concurrent network license Hostid Type ETHERNET Host ID Address Entered 0019b92916cf Collect License Back g Save license to file Save license to file recommended We recommend you to 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 Send by e mail 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 3 Restart the computer The license server reads the license file during the restart
20. etting Started 28 9184 96 Edition AB 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 X Fenumb Clear Pengeraser size at 1 1 i e E Draw or Erase Features Ek Delete Features ie Split Features e Previous Next The Navigator contains the following controls e Draw or 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 choose an alternative mode ImageQuant TL Getting Started 28 9184 96 Edition AB 57 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 dis
21. icense server The license server can be installed on any computer in the network but the license file must be placed on the computer running the license server 1 3 2 About GE Healthcare s e license server program All computers running an IQTL software must be connected on the same network as the computer that you install the e license server program on The e license server program and file can be installed on a local computer when using ImageQuant TL This provides flexibility to use the software outside the office network However the e license server program and file must be installed on the network when using IQTLSecurlTy The SecurlTy features of IQTLSecuriTy demand a network connection as the analyses are stored in a Secure folder on the network 1 3 3 Installation of GE Healthcare s e license server program e If you previously have installed a GE Healthcare Software Licensing Server on a computer on your network or for ImageQuant TL it could be a local computer continue from 1 3 4 e If the licensing server is not installed follow the instructions below ImageQuant TL Getting Started 28 9184 96 Edition AB 7 1 Introduction and installation instructions 1 3 E licensing 1 Onthe IQTL Installation page click Install License Server An InstallShield wizard dialog is displayed i GE Healthcare Software Licensing Server InstallShield Wizard x Welcome to the InstallShield Wizard for GE Healthcare Software Licens
22. ing 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 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 8 ImageQuant TL Getting Started 28 9184 96 Edition AB Introduction and installation instructions 1 3 Click Install to start the installation i GE Healthcare Software Licensing Server InstallShield Wizard x 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 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 1 3 4 Access code After ordering ImageQuant TL a letter including an access code will be sent with a courier to the order s shipment address Store the access
23. is modes ImageQuant TL Getting Started 28 9184 96 Edition AB Accept fal Select adt mode Create Lanas k E Automatic DP Manual The whole image Previous Mes Number of Ties T ImageQuant TL Getting Started 28 9184 96 Edition AB 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 from the top left to the bottom right on the image window and ImageQuant TL draws the lanes 21 4 1D gel analysis 4 2 Lane Editing x Accept Clear Select edit mode Edit Multiple Lanes QR Bend Resize Lane Box F Move Lane Box Edges fe Add Lanes The whole image E Previous Next Half lane width 15 pixels Apply X Delete Current Lane Instructions Parameters 22 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
24. n Overlay view 24 ImageQuant TL Getting Started 28 9184 96 Edition AB 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 ioj 11 a oO mi m3 a c K 2 oO Pixel Position 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 or 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 AB 25 4 1D gel analysis 4 4 Band Detection 26 e To add a 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
25. n the Navigator To choose a different method select the method from Parameters tab Lane 12 100 Of x ity N 3 o S N 3 5 f v o a a 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 AB 23 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 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 i
26. of 5 licenses issued Total of 0 licenses in use _ F _ O ImageQuant TL v7 0 vendor gehealt floating license S Using License File C Program Files GE Healthcare eLicense Server Licenses DeCyder MS 1 0 DUP_GROUP SEHC C4081B86 2 Click the Start Stop Reread tab and stop the StepSever e license server by pressing the Stop Server button 3 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 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 4 IntheLMTOOLS Start Stop Rereadta b press the Start server button to restart the e license DOSE server 5 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 ImageQuant TL Getting Started 28 9184 96 Edition AB 47 8 Licensing Server administration 8 4 Change license configuration that the License has been accepted and the License Server is operable see the screen dump in step 1 6 Select File Exit 48 ImageQuant TL Getting Sta
27. on AB 19 4 1D gel analysis 4 1D gel analysis Automatic Stepwise Automatic analysis steps V Lane Creation V Background Subtraction V Band Detection Manual only analysis steps Molecular Size Calibration Quantity Calibration Normalisation 1D Analysis If 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 Instructions 20 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 AOI 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 analys
28. played in the Measurements Table 38 ImageQuant TL Getting Started 28 9184 96 Edition AB 7 Toolbox Calculate Rai Areas Lines Selector DI Di R La va Coi i Autotrace S Y 04 E Previous Next Autotrace Parameters Edge pixel intensity Threshold 50 Region of Interest Height 100 pixels Parameters 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 determine 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 AB 39 7 Toolbox 7 2 Shape Editing 40 7 2 Shape Editing e Clickthe 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
29. pot Properties 5 13 Move and Resize Spots Identification Spotl more than one spot selected Label Po Size and shape Radius 3 E pixels Radius CD 39 Shape PI E Circle Miscellaneous i pixels T Exclude from analysis Cancel Apply 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 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 AB 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
30. rowing Hostid Settings Time Settings Computer Hostname SEHC HS1 BC14 D System Time Zone Central Europe Standard Time Include Domain Username cttcile GMT Time Tue Mar 22 10 53 25 2005 CPUID Difference From UCT 4294967236 IP Address MSDOS Time 11 53 25 Ethernet Address OOF fSe8c60 Local Time 1111488805 Disk Volume Serial 2416fa04 Number Windows Directory C AWINDOWS FLEXID Save HOSTID Info to a File 2 TheHost IDis displayed in the Ethernet Address text box ImageQuant TL Getting Started 28 9184 96 Edition AB 43 8 Licensing Server administration 8 3 View configuration settings 8 3 View configuration settings 1 Click the Config Services tab to display the configuration of the e license server 2 The configuration displayed below should be used for IQTL LMTOOLS by Macrovision Corporation http Avww macrovision com File Edit Mode Help Service License File System Settings Utilities Start Stop Reread Server Status Server Diag Config Services Borrowing Configure Service Save Service Remove Service Service Name GE healthcare eLicense server Path to the Imard exe file C Program Files GE Healthcare eLicense serve __Browse Path to the license file h Files GE Healthcare eLicense server Licenses Browse Path to the debug log file C Program Files GE Healthcare eLicense serve Browse View Log MV Start Server at Power Up The field P
31. rted 28 9184 96 Edition AB For contact information for your local office please visit www gelifesciences com contact GE Healthcare Bio Sciences AB Bj rkgatan 30 751 84 Uppsala Sweden www gelifesciences com imagination at work GE imagination at work and GE monogram are trademarks of General Electric Company ImageQuant is a trademark of GE Healthcare companies Any use of this software is subject to GE Healthcare Standard Software End User License Agreement for Life Sciences Software Products A copy of this Standard Software End User License Agreement is available on request 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 2008 General Electric Company All rights reserved First Published June 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 28 9184 96 AB 06 2008
32. s Table shows the data relating to the channel selected in the main image window 28 ImageQuant TL Getting Started 28 9184 96 Edition AB 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 Select a 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 ona channel click Calibrate and the volumes appear in the Measurements Table for that channel Quantity calibration data can be calculated for each channel individually ImageQuant TL Getting Started 28 9184 96 Edition AB 29 4 1D gel analysis 4 7 Normalisation 30 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
33. sion 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 FLEXnet license services installed on this computer Start Server Stop Server ReRead License File Force Server Shutdown ee NOTE This box must be checked to shut down a license server when licenses are borrowed Reread Server License File Completed To confirm 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 ImageQuant TL Getting Started 28 9184 96 Edition AB 45 8 Licensing Server administration 8 4 Change license configuration information given here will confirm that the License has been accepted and the License Server is operable LMTOOLS by Macrovision Corporation http Awmww 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 Individual Feature lr SC Server Name Flexible License Manager status on Wed 3 23 2005 15 58 Detecting lmgrd processes License server status 27000 GSEHC C4081B86 D License file s on SEHC C4081B86 D C Program Files GE Healthcare
34. thcare representative Information about IQTLSecurlTy is found in QTLSecurlTy 8 0 User Manual for SecurlTy features The user manual is placed on the DVD under Installation Support lOTLSecurITy Installation and can be purchased as a printed version However e license information for ImageQuant TL also applies to IQTLSecurlTy and is provided in this Getting started in chapters 1 and 8 12 Installation Note Local administrative privileges must be obtained for installation of ImageQuant TL or IQTLSecurlTy software The IQTL disc contains the installation files for all the items required to run both IQTL softwares 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 will start automatically before the installation dialog appears ImageQuant TL Getting Started 28 9184 96 Edition AB 5 1 Introduction and installation instructions 1 3 E licensing IQTL Software Installation _ Install ImageQuant TL Not Installed Getting Started Readme User manual Install IQTLSecurlTy Not Installed Readme User manual ImageQuant TL eet mua Install License Server Not Installed License Activation Homepage Computer Ethernet Address 00188B60CC23D ImageQuant is a trademark of GE Healthcare Companies Ado
35. 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 AB 41 7 Toolbox 7 3 Background subtraction 42 ImageQuant TL Getting Started 28 9184 96 Edition AB Licensing Server administration 8 8 Licensing Server administration GE Healthcare Software Licensing Server tools LMTOOLS is a dialog for the advanced user containing information and tools for the e license server program The most useful tabs are System Setting Config Services Start Stop Reread and Server Status Note Using LMTOOLS to control the license server is covered in detail in the Macrovision Licensing End User Manual 8 1 Open the tool Open the LMTOOLS utility by locating the folder where the license server installation is stored and double click Imtools exe LMTOOLS opens 8 2 View the Host ID of the computer The Host ID also called Ethernet MAC address identifies the computer and is used to activate the e license 1 Clickthe 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 Config Services Bor
36. to the multichannel analysis features Note Colony counter module cannot load multichannel images ImageQuant TL Getting Started 28 9184 96 Edition AB 15 2 Getting started 2 1 Open an image 16 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 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 AB 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 eis g aioli e FH YW O Ol Open Export Print Preview Annotate Contrast Colour Options Edit Image Single Overlay Channel Channel2
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