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User Manual - Bio-Rad

1. Intensity Int Background T T P T Band 0 00 0 25 050 R 075 1 00 boundaries Rf Int D The Lane Profile option shows a cross section view of a single lane rotated 90 To explore the Lane Profile window m Use the Next and Previous buttons at the top of the window to page through profiles of the lanes in your image Click on a lane in your image to see its profile The title bar identifies which lane profile is in view Lane 1 Lane 2 and so on There are several settings in the title bar m Scale to fit graph Include Background Identify Bands by These settings as well as the zoom tools are global They apply to all the profiles The zoom tools work the same way they work elsewhere in the software For more information see Zoom Tools on page 139 User Guide 149 9 150 Viewing Images with Image Lab In addition to the graph of the lane intensities the Lane Profile tool also shows an image of the selected lane below the graph The transform and color map are applied to the gray scale image As you move your cursor over the profile the current relative front Rf value and the average value at the Hf value display in the lower right corner of the Lane Profile window Scale to Fit Graph You can choose the highest point of the display to define the range of the graph This provides the best view of the lane profile You can clear the Scale to
2. lle 108 Setting Up Image Lab Security Edition liess 109 Activating and Deactivating Security Edition 200 000 109 Enabling and Disabling Image Lab Secure Mode sulsssuss 115 Setting Security Preferences 1 20 ec tee 119 Renaming Security GroupS 2 0 ee ee 122 Using Groups on a Local Domain 0 cee ee 122 Changing Security Preferences 0000 eee eee eee eee 123 Chapter 8 Image Lab Software Overview 125 Interface Overview 0 0 0 ehe 127 Main MIDdOW eut eet beans pads te RUE TE S 127 Main Toolbar uneven Remate MER eI Bia Sa 128 Results Data x vxor oes t PHAREe IM REI Did UEM ENS E REY 128 Display Toolbox tsosa vt ex Rx eed Fi oe dede etu ee xe ee glo 128 Start Pagers en reote en erbe ge vad yeh faba BRE Sele oe EE 129 Analysis ool Box x des Ret le dies as sad eae tee PENAS 129 Status Bai MO pP PrIE 131 Menu Commands ssssllleelee ehh rn en 131 Chapter 9 Viewing Images with Image Lab 137 Displaying Gel lmageS 00 ee Ih 138 Display Gel Options 0 00 eee ee 138 Zoom To0lSs v ise eels 2 Glee elate ebbe teftetalr usce a sate ae dees 139 Fitin Window sg niea a E et elds eile han Me RR ea 140 Image Transform siu veu e wu HER be eee Weekend ee awe cote eee 140 Image Colors soviele exe Rp nd aed eaten a ee ghe e 142 3 D Projection 2 ef Eee Rut eR No Ee a IS
3. ve View Qu May 15 2014 3 44eu tB Chemi Blot_30sec This image s zoom settings are copied to the other images x go Transom Image Info seu GED Value Chemi Blot_Ssec Chemi Blot_15sec pip Nae Copy Zoom User Guide 81 4 Viewing Images with the ChemiDoc Touch Imager To copy transform settings to the other images 1 2 Select the image whose transform settings you want to copy Tap Copy Transform The transform settings of the selected image are copied to the other images 2 May 15 2014 631 m d 2 o so EZY eVer Galery lt Back to Gallery Chemi Blot 30sec ChemiDoc Touch X Y Value Chemi Blot 30sec Chemi Blot 5sec s es Chemi Blot 15sec amm Copy Lo Hnos transform E Log Histogram amp amp s e 124 invert image display Q A Bl Highignt saturated pixels e Rh Tuy Iz DRE Pit Ddde Senso Tip As you tap each image the settings in the Transform dialog box automatically update to show the settings of the selected image You do not have to close the dialog box between selections Searching for Images in the Gallery Over time you may acquire a large number of images in the Gallery Use the search feature to find particular images To search for an image 1 2 Tap the search box to display the keyboard Enter the search text 82 ChemiDoc Touch Imaging System with Image Lab Touch Software Printing Images The search text is
4. ChemiDoc Touch Imaging System with Image Lab Touch Software Krypton Oriole Fluorescent Gel Stain Qdot 525 Qdot 565 Qdot 625 SYBR Green SYBR Gold SYBR Safe SYPRO Ruby Stain free gels Stain free blots Silver stain Zinc stain Fluorescein GelGreen SYBR Green SYBR Gold SYBR Safe Technical Specifications Technical Specifications Applications Chemiluminescence Fluorescence Colorimetry densitometry Gel documentation Hardware Specifications Touch screen functionality Onboard computer system Sample thickness Maximum image area Excitation source Detector Pixel size Cooling system Filter selector Emission filters Dynamic range Pixel density gray levels Yes Yes Yes Yes Multitouch capable Display resolution 1024 x 768 pixels 12 1 30 73 cm display 4 GB RAM 60 GB disk space 4 USB ports Maximum thickness of 5 mm is supported m Length 16 8 cm m Width 21 cm Trans UV 302 nm standard m Epi white standard Trans white optional Trans blue optional Deeply cooled CCD 4 54 x 4 54 um Thermoelectric setpoint 25 C Automated 1 included 535 645 nm gt 4 0 orders of magnitude 65 535 User Guide 23 1 Introduction Instrument size Instrument weight Operating Ranges Operating voltage Operating temperature Operating humidity Automation Capabilities Workflow automated selection Autofocus patent pending Image f
5. User Guide 163 10 164 Analyzing Images Bend bends a lane to better fit the gel image Click Bend then drag square anchor points to fit the lane to the image Note To add anchor points left click within the lane Drag these anchor points to adjust the lane to fit the gel image To remove an anchor point right click on it Move moves a lane to a new position on a gel image Click Move then click the lane you want to move Drag it to a new location The lanes are renumbered according to their new positions Width changes the width of a lane Click Width then click within the lane Click on the anchor points to adjust the lane width You can also change the lane width by specifying the size of the lanes Click the Width button enter a number in mm in the box and click Apply Note You might notice that the number in the box changes after you click Apply For example you enter 5 75 and the number changes to 5 71 The image is composed of pixels and the software can draw a boundary only in the lane between pixels If the number you specify would cause the boundary to fall anywhere on the pixels Image Lab moves the boundary so that it falls between two pixels and updates the number accordingly Lane Background Subtraction To perform lane based background subtraction gt Select Enable Subtraction in the Background Subtraction field Use the Lane Profile view to see the subtracted lane background
6. User Guide 79 4 Viewing Images with the ChemiDoc Touch Imager Comparing Images You may want to compare multiple images of a gel or blot to decide which is the best one From the Gallery you can open up to four images to view at a time For more information see To open an image from the Gallery on page 75 The selected images appear in Image View each image identified with its name The blue border identifies the currently selected image a gt May 15 2014 3 44eu w o GERD lt Back to Gallery Chemi Blot_30sec ChemiDoc Touch X Value Chemi Blot 30sec Chemi Blot 5sec Chemi Blot 60sec Chemi Blot 15sec eses es x g 9e 8 Blue border indicates current selection Trassform image info Tap the image to select it You can pan or zoom the image view and edit the transform settings view and edit the image information and delete print or export the image to a USB flash drive or network drive It may be easier to compare the images if their transform and zoom settings are identical You can copy the settings from one image to the others 80 ChemiDoc Touch Imaging System with Image Lab Touch Software To copy zoom settings to the other images 1 2 Tap Copy Zoom Comparing Images Select the image whose zoom settings you want to copy Tip The Copy Zoom icon is located on the right side of the screen The pan and zoom settings of the selected image are copied to the other images
7. Volume m Absolute Quantity Relative Quantity Band m Lane Volumes If you drew volume boundaries on the gel you can display the boundaries and their volume labels Zoom Tools P The zoom tools resize the gel image Click the magnifying glass with the plus sign to make the image larger Click the magnifying glass with the minus sign to make the image smaller You can also zoom in on an area using the right mouse button Right click and drag to select the area you want to magnify You can also resize the image by right clicking and using the scroll wheel on your mouse Tip You can return to the original view by right clicking anywhere on the image User Guide 139 9 Viewing Images with Image Lab Fit in Window 4 If you zoomed in on an area of an image this button brings the entire image back into view Image Transform The Image Transform dialog box adjusts image brightness and contrast optimizing the image display so faint details can be seen Image Transform E3 e High L 3562 ww i 39 Gamma n 1 00 Min 0 Max 3984 Units Int Options Invert image display Log histogram v Highlight saturated pixels Auto Scale The minimum to maximum range varies depending on the light and dark values present in the image These adjustments do not change the data They change only the way the data are displayed The human eye cannot see as great a range as the image contains The freque
8. Click a user name in the list to select it or press the Ctrl key and click multiple users to select them When you have selected all the users to add to the group click OK and click OK again to close the Select Users dialog box Click Create to close the New Group dialog box and create the group or click OK to close the existing group s Properties dialog box and accept the changes User Guide 247 C Setting Up Users and Groups Password Security 21 CFR 11 300 b requires that passwords be periodically checked recalled or revised Password policies are therefore recommended although the password duration and rules are up to the system administrator and the organization For instance the exact duration between password changes is flexible To set password policies on a local computer 1 2 and then select Password Policy You see the password policies listed in the right pane of the window Open the Control Panel and select Administrative Tools Local Security Policy In the left pane of the Local Security Policy window expand Account Policies 2 Local Security Policy Sta File Action View Help ensi m Security Settings 4 T Account Policies T Password Policy E Account Lockout Policy T Local Policies E Windows Firewall with Advan Network List Manager Policies E Public Key Policies E Software Restriction Policies E Application Control Policies amp IP Security Polic
9. Close Close All Export E b Export for Publication Image Info Ctrl I Export for Analysis E Page Setup Export for PulseNet Print Ctrl P Lane and Band Table To Excel lx Lane and Band Table To File Exporting Gel Images for Publication Use this format only to export visual information to presentation or word processing software such as PowerPoint or Word To export a displayed image to a file gt Select File gt Export gt Export for Publication Note You can select from bmp png jpg and tif formats The gel displays with any lanes bands and annotations that appear on the screen 198 ChemiDoc Touch Imaging System with Image Lab Touch Software Exporting Gel Images 18 Export for Publication Publishing Source Entire Image Current View Publishing Resolution dpi 300 dpi 600 dpi O Specify Publishing Dimensions cm Width cm 15 02 Height cm 11 31 Publishing Info Width pixels 773 _ Height pixels 1335 Image Size MB 9 25 In this dialog box you can m Select the entire image or the current view m Select the resolution or specify a custom resolution m Specify the publishing dimensions m View the resulting published image size and dimensions User Guide 199 12 Exporting Results You can zoom in on an area in a current view and export only that area or you can export the entire image You can exclude annotations or overlay
10. Safety and Regulatory Compliance Bystanders without protective gear must stand at least 1 5 meters five feet away from the imager and limit their exposure to no more than one hour per day Note There is no exposure to UV radiation with the blue or white trays No protective gear is necessary when excising bands with these trays Warranty The ChemiDoc Touch imaging system is warranted against defects in materials and workmanship for one year If any defect occurs in the instrument during this warranty period Bio Rad Laboratories Inc will repair or replace the defective parts at its discretion without charge The following defects however are specifically excluded m Defects caused by improper operation x Repair or modification done by anyone other than Bio Rad Laboratories Inc or the company s authorized agent m Use of spare parts supplied by anyone other than Bio Rad Laboratories Inc Damage caused by accident or misuse Damage caused by disaster m Corrosion caused by improper solvents or samples General Precautions m Read the user guide carefully m Use the instrument only for the intended purpose of gel and blot image acquisition in research laboratories Connect the instrument to a grounded power source and to a circuit breaker 12 ChemiDoc Touch Imaging System with Image Lab Touch Software Regulatory Notices Do not pour liquids on or inside the instrument x Clean the sample tray afte
11. o amp 6 Lane Labels oV P qV aN OES x aS xS 45396 a e o 1011120135814 15 16 d e b QU UG fo Jas A id f PP a on 2 3 Molecular Weight Labels Band Lane Frame Lane Standard Lane User Guide 137 9 Viewing Images with Image Lab Displaying Gel Images The display toolbar is located above the gel image Each tool is described in the following sections Display Gel Options g This section describes the settings in the Display Gel Options dialog box Fomo a E Annotations V Show Text and Arrow Annotations anes And Bands V Show Lane Frame V Show Lane Labels V Show Lanes V Show Molecular Weight Legend Show Bands 4 Show Band Edges Band Attributes V Show Band Attributes Attribute Band No Selected Lane Only Volumes V Show Volumes V Show Volume Labels Shonen E gt Annotations You can choose whether to show text and arrow annotations that have been drawn on the image Lanes and Bands You can turn on or off any image overlays such as lane frames lanes bands lane labels molecular weight legends and band edges 138 ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Gel Images Band Attributes You can show the following attributes for selected lanes or for all lanes Band number Band label Molecular weight Relative front
12. 65 A Enable Secure Mode User Name dcathey Password Domain amp CC Gere 4 Enter your Image Lab Administrator user name and password 5 If you are set up on a Windows network server type the name of the Windows domain in the Domain field Note The default is the domain on which the current Windows user is located and this name will appear in the field 6 Click OK to save your changes 116 ChemiDoc Touch Imaging System with Image Lab Touch Software T Setting Up Image Lab Security Edition A message appears stating that you must restart Image Lab for the new secure mode enable setting to take effect RUIT You must restart the application for these changes to take effect Image Lab will now exit Click OK The application exits Important For full details on why and how to set your security preferences see Setting Security Preferences on page 119 To disable secure mode 1 2 3 From the Security menu click Security Preferences to display the Security Preferences dialog box JA Security Preferences Enable secure mode Domain to be used in authentication GLOBAL Use local groups for establishing user security levels Clear the Enable secure mode checkbox Click OK User Guide 117 7 Setting Up the Imager with Image Lab Software The Admin Authentication dialog appears
13. Acquiring an Image If you see an exclamation point in place of the camera icon there is a problem that prevents image acquisition The exclamation point will be yellow or red to indicate the severity of the problem Tap the icon to display the error message May 15 2014 12 48Pu s O9 CD m badges Unable to acquire image The door is open MICINNNNNNNKS SO E Cs E Blots Rapid Auto exposure Tap the icon to display the error message Workflow for Acquiring Gel and Blot Images Note For information on acquiring a chemiluminescent image see Workflow for Acquiring a Chemiluminescent Image on page 48 The basic steps to acquiring a gel or blot image are 1 Specify the size of the image 2 Choose the application type 3 Set the exposure time 4 Acquire the image Note You can specify the acquisition settings at any time in your workflow for example before you prepare your sample tray or after the tray is in the 64 ChemiDoc Touch Imaging System with Image Lab Touch Software Workflow for Acquiring Gel and Blot Images transilluminator drawer The imager retains the settings during a session and between sessions until you change them Specifying the Image Size To specify the image size for chemiluminescent images 1 2 In Live View tap IMAGE SIZE To choose a standard size tap Small Medium or Large The preset sizes correspond to these Bio Rad gels Small Mini PROTEAN
14. Gamma Control Other options Zoom in and out displays greater detail about the intensity range Highlight saturated pixels displays areas with saturated signal intensity higher than a measurable range in red Invert image display inverts dark and light areas Clear the box to return dark and light areas to their original display 78 ChemiDoc Touch Imaging System with Image Lab Touch Software Checking Intensity Values Restoring the Default Settings The light intensity range and grayscale settings are adjusted to enhance the contrast in images that have faint bands After making changes to the intensity and contrast you can always return to the default settings To return to the default settings gt Tap Auto to return to the default settings X Log Histogram amp L1 Invert image display 25 LA Auto a E Highlight saturated pixels Auto Checking Intensity Values You can check the intensity values in the acquired image by tapping the area of interest on the screen The location is identified with X and Y coordinates Value is the average intensity of the pixels in a 3 x 3 pixel area If you are zoomed in use this feature to identify where you are in the overall image and to get an approximate idea of the size of the area you are viewing Value gives you accurate information about the intensity values and dynamic range which cannot always be determined by visual inspection
15. Ethidium Bromide SYBR Safe SYBR Gold SYBR Green Fast Blast SYBR Safe SYBR Gold SYBR Green User Guide 47 3 Acquiring an Image To prepare a sample tray 1 Place the gel or blot on the appropriate sample tray 2 Open the main door and pull out the transilluminator drawer for easier access to the imaging bed 3 Place the sample tray on the imaging bed 4 Pushthe transilluminator drawer in and close the main door Workflow for Acquiring a Chemiluminescent Image Note For information on acquiring gels and blots other than chemiluminescent blot images see Workflow for Acquiring Gel and Blot Images on page 64 The basic steps to acquire a chemiluminescent image are 1 Specify the image size 2 Choose the application type 3 Specify the region of interest 4 Setthe exposure time 5 Acquire the image Note You can specify the acquisition settings at any point in the workflow for example before you prepare the sample tray or after the tray is in the transilluminator drawer The imager retains the settings during a session and between sessions until you change them Specifying the Image Size You can select a preset size or specify a custom size for the image To specify the image size for chemiluminescent images 1 InLive View tap IMAGE SIZE 48 ChemiDoc Touch Imaging System with Image Lab Touch Software Workflow for Acquiring a Chemiluminescent Image To choose a standard size tap Small Medium
16. Imager Components Imager Components The illustration identifies the parts of the ChemiDoc Touch imager 2 1 LEGEND 1 USB port 6 Transilluminator drawer 2 Touch screen 7 Front door open position 3 System on off button 8 Imaging bed 4 Sample tray 9 Front door open handle 5 Transilluminator drawer handle User Guide 19 1 Introduction These are the rear panel user components USB ports ncc Ethernet port m AC power receptacle CCD Camera and Lenses The ChemiDoc Touch camera is installed within a lighttight enclosure A motorized zoom stage and motorized zoom lens focus control provide software control of the imaging area and automatic focus A software algorithm controls the zoom mechanism and lens focus See Technical Specifications on page 23 for complete specifications of this system Introduction to Image Lab Touch Software The imager comes with Image Lab Touch software installed The software takes and views images lets you fine tune how images are displayed prints images and lets you export them to a computer with Image Lab software where you can carry out detailed analyses Image Lab is supported on PC and Macintosh systems Emission Filters The ChemiDoc Touch instrument has a motorized emission filter for fluorescent and white light applications When no filter is required to image chemiluminescent samples the filter automa
17. Medium Criterion m Large Wide Mini ReadyAgarose To specify a custom size tap the W width or L length box Enter the width or length of the image in cm using the keypad The valid width values are 9 0 to 21 0 cm The valid length values are 7 2 to 16 8 cm Note When you enter one dimension the other dimension is automatically calculated according to the imager s 5 4 aspect ratio Tap Done to save your changes and close the keypad Choosing the Application Follow this procedure to choose a gel or blot See Supported Tray Types on page 22 for information on the sample trays and applications supported by the ChemiDoc Touch imager To choose a gel or blot T 2 In Live View tap APPLICATION Tap one of the application categories Nucleic Acid Gels Protein Gels or Blots User Guide 65 3 Acquiring an Image 3 Tap one ofthe applications Choose application category Nucleic Acid Gels Choose Application Setting the Exposure Time To set the exposure time for a gel or blot 1 In Live View tap EXPOSURE 2 For stain free gels only If you are imaging a stain free gel pick one of the following gel activation times No Activation choose No Activation if you do not want to activate the gel m 45sec use this setting when you choose western blotting followed by immunodetection 5min use this setting for detecting proteins in low concentrations This duration provides
18. To export the data to Excel or Numbers gt Select File gt Export gt Lane and Band Table to Excel This opens a table directly in the spreadsheet program You can then use the Save As option to produce other formats Exporting Volume Tables to File To export an image as a CSV file gt Select Export gt Volume Table to File Image Lab exports the image as a comma separated values CSV file so the data file can be opened in a database application Screenshot Tool Export Use the Screenshot tool available on the toolbar to capture a displayed image to the clipboard or to save it to a file bmp gif jpg or png Analysis Table Export You can export table analysis data from the File menu or by using the export buttons at the top of the Analysis Table window The Analysis Table window has several buttons to export data to different formats depending on how the data are to be presented User Guide 201 12 Exporting Results Copy Analysis Table to the Clipboard amp Copies the analysis table to the clipboard and then pastes the analysis table into word processing or presentation applications It is best to use the vertical table orientation when copying to an 8 5 x 11 inch page to accommodate the columns Export Analysis Table to a File 2 Exports an analysis table as a CSV file so a data file can be opened in a database application Export Analysis Table to a Spreadsheet 2 Enables you to use sort and for
19. User Guide 249 C Setting Up Users and Groups Password Policy Setting Examples The following examples are only suggestions Your organization needs to establish its own password policy Enforce password history 12 passwords remembered Minimum password age 5 days Maximum password age 30 days Minimum password length 8 characters Password must meet complexity requirements Enabled Store passwords using reverse encryption Enabled Account Lockout Policy Setting Examples Account lockout duration 0 The account is locked out until the administrator unlocks it Account lockout threshold 3 logon attempts Reset account lockout counter after 30 minutes Auditing Windows Event Logs Some global auditing information is stored in the Windows Event logs It is a requirement of 21 CFR Part 11 that these logs be archived However by default Windows systems automatically remove these data without warning Note It is therefore critical that the event log is reconfigured to generate and preserve all necessary log data Regular manual intervention is also required to preserve these data To open the Event Properties Log 1 2 Open Administrative Tools and click Event Viewer Right click on each log and select Properties 250 ChemiDoc Touch Imaging System with Image Lab Touch Software Miscellaneous Security Measures 3 Inthe section When maximum event log size is reached select Do not overwrite events Clea
20. numbers which you have manually added To select multiple annotations gt Press the Ctrl key Command key on a Mao and click each item or drag a selection box around them 182 ChemiDoc Touch Imaging System with Image Lab Touch Software Annotation Tools Text Properties You can change the type size and font of your text annotations m Font click the box you want to change Open the dropdown Font menu to show all fonts installed on your system Select a new font for the text annotation m Size click the box whose font you want to resize Open the dropdown Size list to increase or decrease the size of the text You can set the font size from 6 to 72 points using the dropdown list Color You can change the color of text annotations to make them visible with any color scheme and emphasize them further by adding a color to the annotation s background which is invisible by default To change the color of multiple items gt Press the Ctrl key and click each item m Foreground click a text annotation or arrow This activates the Foreground field so you can select a foreground color from the dropdown list Background click a text annotation This also activates the Background field so you can select a background color from the dropdown list Rotate You can rotate text annotations 90 to the left or right by clicking the Rotate buttons User Guide 183 10 Analyzing Images 7 Volume Tools Vo
21. on Windows based computers Document logs are not viewable on the Mac The document log captures changes from Image tools Lane and bands tools Normalization tools Molecular weight tools Quantity tools Volume tools You can view the document log for any open file This file can be a previously saved file or it can be a newly created protocol or image file that is open on your desktop but which has not yet been saved If the document was previously saved the log is identified with this name If the document has not been saved the log is identified with the time stamp showing when the document was created View Security Window Help Image Overview Operation History View System Log View Protocol1 Log View GS900 Calibrated Blot Log Log file for saved image files View GS900_Calibrated_Blot_LB Log View GS800 63 Log View Theresa Navarro 2013 01 17 13hr 06min Log Log file for open but unsaved image file 206 ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Log Data To open the Document Log Viewer gt From the View menu click the document log that you want to view A typical document log is shown below r AL Protocol2 Log x Date and time User Level Domain Type Description Reason f I Scan coords left 7 3 changed to 7 2 2013 03 07 15 07 10 dcathey Unrestricted GLOBAL Unrestricted Protocol Change
22. s eiecexe eee Gem De ACER we Sa Pee RE S Ue YR age e 72 Selecting and Opening Images from the Gallery llle 73 Adjusting How Images Are Displayed lees 75 Light Intensity Histogram llle 76 Restoring the Default Settings lille 79 Checking Intensity Values 0 0 0 cee re 79 Comparing Mages esie eec ker eee pt BLUE SERE EM E a 80 Searching for Images in the Gallery llle 82 Printing Images vziilesse 9rey IE DSeTbbekeri Ere ur eek utes 83 Renaming Images sex es ewe tee ue ees we eee SI RIEN S 83 Deleting Images adaa tria Eira e E a E Ren 85 Viewing Image Information llis IA 86 Adding Notes about the Image 87 Chapter 5 Excising Bands eere 89 Excising Bands from Samples 0 000 e eee eee 89 Excising Bands on a Chemi UV Stain Free Tray 00 0c eee eee 89 Excising Bands on a White or Blue Tray llle elles 94 Chapter 6 Exporting Images from the Imager 97 Exporting Images to a USB Flash Drive 0 00 eee eee 97 Exporting Images to a Network Drive lessen 98 Chapter7 Setting Up the Imager with Image Lab Software 101 System Requirements llis 101 Image Lab Security Edition l l 101 User Guide v Table of Contents Computer Specifications llle 102 Installing Image Lab Software ille 102 Installing the Drivers on Windows 7
23. 2 Lane 3 Lane 4 Band No Mol Wt KDa Band No Mol Wt KDa Band No Mol Wt KDa Band No Mol Wt KDa 1 250 0 1 203 8 1 207 9 1 210 9 2 150 0 2 118 0 2 119 7 2 121 6 3 100 0 3 99 0 3 100 4 3 102 0 4 75 0 4 70 6 4 716 4 724 5 50 0 5 45 1 5 458 5 463 6 37 0 6 268 6 272 6 27 5 7 25 0 7 17 4 7 17 6 7 17 8 8 20 0 8 12 9 8 13 0 8 13 2 9 15 0 9 10 6 9 10 7 9 10 8 10 10 0 174 ChemiDoc Touch Imaging System with Image Lab Touch Software Quantity Tools Regression Methods There are four regression methods Linear semilog m Point to point semilog Logistic Cubic spline Regression Calculation Methods on page 235 n You can quantify bands in test samples automatically using either the Relative or Absolute tab under Quantity Tools Quantity Tools Relative Quantity Tab To compare the relative quantities of bands 1 Select the Relative tab 44 Quantity Tools Relative Absolute Relative Quantity Select a reference band on the gel 2 Click Select User Guide 175 10 Analyzing Images Click the band you want to use as a reference A small R appears near the band you selected To review the relative quantities of bands gt Go to the Rel Quant column of the Analysis table Lane and Band tab The relative quantity is the ratio of the band volume divided by the reference band volume All other bands now display numerical values that are relative to the reference
24. A Save File dialog box appears 6 Enter a new name for the file and click Save Document Logs Any changes made or actions performed on a protocol or image file generate a document log documenting each change or action This log is created as soon as the protocol or scan file is created Protocols are updated when the protocol is saved or run If you make changes to a file and save it as a new file regardless of whether you are in secure mode the document log is preserved in the new file If you are in secure mode the signature of the previous file is noted as part of the document log Note When a protocol is run its log entries are copied to the resulting image file All major actions and changes are audited generate a document log Examples of auditable actions include Signing a file Changing protocol settings m Changing the image for example by cropping or rotating it Modifying the analysis for example changing the lanes and bands or adding or editing annotation to the images Minor changes that affect only the display are not audited such as m Selecting different columns in the Analysis Table Changing the display options in Lane Profile m Annotating or labeling the image using Annotation Tools Each change you make to a signed protocol or image file must be documented in the Reason for Change dialog box User Guide 225 14 Using the Security Edition Viewing the Document Log The View menu d
25. Acquiring anIlmage 0000c eee eee eee 45 About Sample Trays 00 00 cece ees 46 Workflow for Acquiring a Chemiluminescent Image 0 200 eee 48 Specifying the Image Size 1 knee 48 Choosing the Application 000 ee ee 50 About Exposure Times for Chemiluminescent Images llus 51 The Image Resolution Sensitivity Scale 2 00 eee 51 Specifying the Region of Interest for Auto Exposure sull 57 Setting the Exposure Time for Chemiluminescent Images Ls 59 Setting the Exposure Automatically llelleieleeeees 59 Setting the Exposure Manually llle 60 Signal Accumulation Mode 2 0 0 cece ree 61 Configuring Signal Accumulation Mode llle 62 Acquiring Images esie RIDE h 9RRe wees EE FRe G quse PORES4PeBREFR 63 Workflow for Acquiring Gel and Blot Images 00 e eee eee 64 Specifying the Image Size eee 65 iv ChemiDoc Touch Imaging System with Image Lab Touch Software Table of Contents Choosing the Application s coisi tirader sumiar rapor es 65 Setting the Exposure Time sener sidir raaa eee 66 ACQUIFING IMAGES seie eii aeaea EE E ERG EM EE ERR eee ees 67 Deleting Images raa r d a a n a eee 68 Chapter 4 Viewing Images with the ChemiDoc Touch Imager 69 About Image VIEW ixi RC De ye eed ped ER MO ERI ee wees 71 About the Gallery 53cm er sex One ee wa ed tee ER MEG e 71 Viewing Images
26. Administrator TDS Administrator Supervisor Clinician TDS User TDS Tech Reviewer TDS Guest e ewe 2 Click in any of the four Group Name fields 3 Enter a new name 4 Click OK to save your changes Note The new user group name must comply with standard Windows Local Users and Groups user names rules For more information on setting up security groups see Setting Up Users and Groups on page 237 Using Groups on a Local Domain If you choose not to create or use groups on the network domain set up local groups Add the authorized users to the groups on the local domain In the Security Preferences dialog box select Use local groups for establishing user security levels 122 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Security Edition For information about setting up users and groups for Image Lab Security Edition see Appendix C Setting Up Users and Groups on page 237 Changing Security Preferences Changing the domain that is used to authenticate users is a two step process You first authenticate on the first domain then authenticate on the second domain This change in domains can be performed in either of two ways It can be performed by one individual assigned the Image Lab Administrator role on both domains or it can be performed by two individuals one with the administrator role on the first domain and the other with the a
27. Band Band Attribute and MW Legend This functionality ensures that these elements are visible regardless of the color of the gels View Menu Commands Image Overview displays the gel image with a red rectangle outlining the area visible in the larger main window This is useful when you zoom in to a small section of an image Image Transform displays a histogram that enables you to adjust the light and dark values of a gel image This adjustment does not change your data only the way the data display on your monitor Operations History displays the sequence of actions performed by both the user and the software 134 ChemiDoc Touch Imaging System with Image Lab Touch Software Interface Overview View System Log displays events related to running Image Lab software including enabling or disabling secure mode and the users who log on to or log off of the software View Instrument Log displays events related to the instrument including calibrating the instrument and the success or failure of the calibration This log file is visible only if Image Lab is connected to an instrument View Document Log displays events related to creating and modifying secure protocol and image files This log file is created only when Security Edition is enabled Security Menu Commands Note This menu is only visible in Image Lab Security Edition For more information about Security Edition see Chapter 14 Using the Security Edition Secu
28. Main toolbar May 13 2014 42770 Workspace Image View toolbar Zoom icons The main components of the Image View screen include Main toolbar provides access to the Live View Gallery and Help screens the Settings menu and the Logout icon For more information about each toolbar icon see The Image Lab Touch Main Toolbar on page 34 Workspace displays the acquired image 36 ChemiDoc Touch Imaging System with Image Lab Touch Software About the Image View Screen Image View toolbar optimize images view information about images and delete and save images For more information about each toolbar icon see The Image View Toolbar on page 37 m Zoom icons zoom in and out to focus on an area of the sample The Image View Toolbar The following table describes the Image View toolbar Icon N Description Transform lets you adjust the image brightness and contrast and optimize the image appearance Image Info provides information about the active image including date of acquisition name of the acquisition application and the login name of the user who acquired the image In this dialog box you can also rename the image or add any notes Print prints the displayed image to the Mitsubishi thermal printer Delete deletes the displayed image Send Save saves the displayed image to a USB flash drive or network drive User Guide 37 2 Image Lab Touch Softwa
29. Manual Exposure Time Configure Signal Accumulation Mode ptimal settings amp a k First Image 5 sec Last Image 10 sec Images Higher Resolution Lower Resolution Longer Wait Time Shorter Wait Time Enter the total number of images in the Images text box Tip The recommended total is 3 5 images Tap Done 62 ChemiDoc Touch Imaging System with Image Lab Touch Software Acquiring Images Acquiring Images After you have specified the settings for the image you are ready to acquire the image Be sure the drawer is pushed all the way in and the main door is closed To acquire the chemiluminescent image gt Tap the Camera icon Note If you are taking a series of SAM images the main door must remain closed until all images are acquired If the door is opened during the acquisition process an error message appears and the acquisition is canceled Only images acquired before the door was opened are saved A progress bar shows the progress of the image acquisition Once the image is acquired it is automatically displayed on the screen In this view called Image View you can adjust how the image is displayed and you can print delete rename and delete the image For more information see Chapter 4 Viewing Images with the ChemiDoc Touch Imager May 09 2014 10 40 seo CD ChemiDoc Touch X x Value x o iem eres image Irto Print User Guide 63 3
30. To access a tool gt Click any of the toolbox buttons To return to the Analysis Tool Box menu P Click the green Up arrow to the right of the tool name Image Tools FJ Up arrow User Guide 157 10 Analyzing Images Image Tools EM The image tools enable you to manipulate your images To display the image tools menu gt Click Image Tools PT Image Tools r3 Horizontal m il f Vertical d 90 Left 90 Right x Custom Crop Invert Data Merge m Flip you can flip the gel image horizontally or vertically Rotate you can rotate the gel image 90 using the Left or Right buttons Or you can set a custom rotation using the Custom button m Crop youcan trim the outer edges of your image to any shape or area Invert Data you can toggle the image data from positive to negative m Merge you can merge a chemiluminescent blot image with a colorimetric image of the same blot The sections that follow describe how to use these tools in greater detail 158 ChemiDoc Touch Imaging System with Image Lab Touch Software Image Tools Correcting a Slanted Gel To correct a slanted gel 1 In the Rotate section click Custom Red arrows appear over the gel image Rotate the red arrows to any degree between 0 and 360 by dragging them Right click the gel image and click Rotate to set your gel in the new position Click Cancel if you do not want to set t
31. an Undo Screenshot enables you to take a screen shot of the Lane Profile Window the Standard Curve Window or the default choice Current Image View The screen shot can include the name of the image and it can be placed on the clipboard or saved in a file Default Imager enables users who own two or more imagers to switch between them Report Settings enables you to configure reports This dialog box has three tabs All of the checkboxes are selected by default Clear the boxes to exclude information from reports Your selections apply to all reports until you change them User Guide 133 8 Image Lab Software Overview m The General tab has options for excluding or reporting information about your gel image m The Lane and Band Table tab enables the researcher to choose whether to include all lanes or selected lanes with appropriate identifiers Lane profiles can also be included m The Volume Table tab enables the researcher to choose appropriate identifiers for the volume table and provides the option of excluding the table from reports Preferences enables you to set naming and color preferences for your image files This dialog box has two tabs m The Protocol tab shows presets for naming image files You can choose to include a designated Prefix User Name Date and or Time in the name of your image files m The Colors tab enables you to choose colors for the graphic elements in your gels such as Lane Frame Lane
32. an optimal signal to noise ratio because the gel activation is close to completion at the end of 5 minutes 3 Tap Set Exposure Automatically to have the software automatically determine the exposure time 4 Choose which bands you want optimized in the image and tap Intense Bands or Faint Bands Note To set a specific exposure time tap Set Manual Exposure Time and enter the time in the text box 66 ChemiDoc Touch Imaging System with Image Lab Touch Software Workflow for Acquiring Gel and Blot Images Acquiring Images After you have specified the settings for the image you are ready to acquire the image Be sure the drawer is in and the main door is closed To acquire the gel or blot image P Tap the camera icon A progress bar shows the progress of the image acquisition Once the image is acquired it is automatically displayed on the screen In this view called Image View you can adjust how the image is displayed and you can print rename and delete the image For more information see Chapter 4 Viewing Images with the ChemiDoc Touch Imager v May 09 2014 10 400u Live Ven 2 GEL e eck to Galley Chemi Blot ChemiDoc Touch X Y Value UMP umb UC m ae ee ae a nm Taom Image Into User Guide 67 3 Acquiring an Image If you see an exclamation point in place of the camera icon there is a problem that prevents image acquisition The exclamation point will be yellow or red to ind
33. application Volume Table to Excel exports your volume table data to an Excel or Numbers on a Mac spreadsheet Note Excel or Numbers must be installed on your computer 132 ChemiDoc Touch Imaging System with Image Lab Touch Software Interface Overview Volume Table to File exports as a CSV file so your volume table can be opened in a database application See Exporting Volume Tables to File on page 201 for detailed information about exporting files See Chapter 12 Exporting Results for more information about exporting files Image Info displays information about individual gel and blot images such as acquisition date and data range and image capture detail such as exposure time and illumination source used Click the Image Details Analysis Settings and Notes tabs to display these properties See Image Info on page 144 for more information Page Setup contains print controls such as orientation landscape or portrait margins printer used and paper size Print displays a print preview of the gel and the header information which includes the filename of the image the user s name and the date and time it was printed The usual Windows Print screen is available as well enabling you to select a printer and the number of copies to print Exit closes Image Lab after prompting you to save changes to your protocols or images Edit Menu Commands Undo undoes the last action Redo restores the last action after
34. band If the reference band value is 1 00 values higher than 1 00 indicate that the band quantity is greater than the reference band Values lower than 1 00 indicate the band quantity is less than that of the reference band Absolute Quantity Tab Absolute quantification is used to quantify bands based on known standard bands using a calibration curve To calculate the absolute quantities of the bands 1 Select the Absolute tab Quantity Tools M ee Relative Absolute Absolute Quantity Select Bands to add to calibration curve Standard Bands Ln Bnd Quantity 2 Click Select 176 ChemiDoc Touch Imaging System with Image Lab Touch Software Quantity Tools 3 Select at least two standard known bands and assign quantity values Small A s appear shown below circled in red near the bands you selected User Guide 177 10 Analyzing Images The values display in the Standard Bands table The greater the number of known bands and the wider the range of their values the more accurate the absolute quantity calculation of the unknown bands will be F3 Ln Bnd Quantity 2 2 4 0 4 lt 4 1 0 Note Any standard band selection can be deleted To do so select the entry in the Standard Bands field and then click Delete 4 Select a unit of measure from the Units dropdown list 5 Select a regression method from the dropdown list Consider the following guidelines when making your choice 178 Ch
35. case insensitive You can enter any portion of the date or name As you enter the search text any images that match the text appear in the Gallery Note To see all images in the Gallery clear the search box 3 When you have found the images you want tap Done to close the keyboard Printing Images Note In this release the Mitsubishi P95 is the only supported printer Images are printed from Image View to the Mitusbishi P95 printer You can print an image immediately after you acquire it Or you can go to the Gallery at a later time and print a previously acquired image The printout includes the image name and acquisition date and time Before you begin check that the printer is connected to the imager and it is turned on To print an image 1 Acquire an image or open an image in the Gallery 2 Tap Print Renaming Images When the image is acquired a default name is assigned to it You can change this default name There are two ways to rename an image m Inthe Gallery use the Rename feature m n Image View edit the name in the Image Info dialog box Note Image names are case insensitive To rename an image from the Gallery 1 Select one or more images in the Gallery User Guide 83 4 Viewing Images with the ChemiDoc Touch Imager 2 Tap Rename 3 Inthe dialog box enter the name of the image The image name can consist of 190 alphanumeric characters Spaces are permitted except at the beginning and
36. computer 1 In the New Group dialog box click Add Alternatively double click an existing group in the Groups folder to open its Properties dialog box and click Add You see the Select Users dialog box 242 ChemiDoc Touch Imaging System with Image Lab Touch Software 2 Click Advanced to expand the dialog box Setting Up Image Lab Users and Groups Select Users Eam Selectthis objecttype Users or Builtin security principals From this location LSG07002045 Common Queries Starts with v Starts with v ats Search results Name RDN B Administrator A ANONYMOUS LOG Authenticated Users B BATCH 2 bradmin Bbrguest BA CONSOLE LOGON Bl CREATOR GROUP Bl CREATOR OWNER B DIALUP AI Evervone In Folder LSG07002045 LSG07002045 LSG07002045 Object Types Locations Find Now top FP Cancel n In the expanded dialog box click Find Now to populate the bottom field with all the users on the local computer Click a user name in the list to select it or press the Ctrl key and click multiple users to select them When you have selected all the users to add to the group click OK and click OK again to close the Select Users dialog box Click Create to close the New Group dialog box and create the group Alternatively you can click OK to close the existing group s Properties dialog box and accept the changes User Guide 243
37. extend the drawer further and clear the opening thus making it easier to remove the transilluminator cover The levers are located on both sides of the drawer in the drawer slide release mechanism that slides the drawer in and out Push the lever on the left side down push the lever on the right side up and pull The drawer will extend out another centimeter 4 Loosen the four screws on both sides of the transilluminator cover Tip Leave the loosened screws in the cover to minimize the likelihood of losing them 230 ChemiDoc Touch Imaging System with Image Lab Touch Software Replacing the UV Transilluminator Bulbs Remove the transilluminator cover by sliding it forward and then lifting up Note Do not place the transilluminator cover directly on the bench Place the cover on a nonabrasive surface to avoid scratching or damaging the UV filter glass Important Exercise caution when touching the lamps which may be hot room 7 Rotate a lamp until it becomes loose and the pins are vertical and aligned with the socket 8 Remove the lamp 9 Install the new lamp by setting it in place and rotating it until the pins are seated and horizontal 10 Set the transilluminator cover on the drawer Secure the cover to the drawer with the screws User Guide 231 A Maintaining the Imaging System Replacing the Fuses To replace the fuses 1 Unplug the power cord from the back of the instrument The fuse dra
38. f A Admin Authentication User Name SEAdmin Password m GLOBAL e canca 4 Enter your Image Lab Administrator user name and password 5 If you are set up on a Windows network server type the name of the Windows domain in the Domain field Note The default is the domain on which the current Windows user is located and this name will appear in the field 6 Click OK to save your changes r gt L Enable Secure Mode kisl User Name dcathey Password Domain SLOBA Co Cone 118 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Security Edition A message appears stating that you must restart Image Lab for the new security settings to take effect pO E You must restart the application for these changes to take effect Image Lab will now exit M 7 Click OK The application exits Setting Security Preferences Here are three useful definitions used in these instructions Network domain a remote domain controlling computer or system which ensures that only authorized users with valid credentials can access and run Image Lab Local domain or local computer the computer on which Image Lab is running and which ensures that only authorized users with valid user credentials can access and run Image Lab m Credentials the valid user name and pa
39. field is populated with the 18 digit license code that you entered when you installed Image Lab 110 ChemiDoc Touch Imaging System with Image Lab Touch Software 2 Setting Up Image Lab Security Edition Select Activate Via Create Activation Email Pal security Edition AED a MM Your copy of Image Lab Security Edition is not currently activated You will need the license code that was sent to you with the software License Code Activate Via 2 Internet 9 Create Activation Email Receive Activation Email Click Create Email A Save File window appears with the File name field already filled in Do not change this file name o Save File File name Save as type Text txt Browse Folders Click Browse Folders to choose a location for the file and click Save In your email program create an email addressed to LSG TechServ US Bio Rad com with the subject line Request to Activate Image Lab software Security Edition Attach the ActivationEmail txt file to the email and click Send The Bio Rad Technical Support Department will process your request and reply with an email containing an attachment with your activation code User Guide 111 7 7 8 9 10 11 112 Setting Up the Imager with Image Lab Software When you receive your reply email open it and save the attached UnlockCode txt file to the folder in which you saved the ActivationEma
40. lane User Guide 147 9 Viewing Images with Image Lab Volume Measurement Definitions This section defines the measurements that display in the Volume tab in the Analysis table Use the Display Data Options button to choose the columns to display Volume Number a unique number is assigned to each volume Volume Label software generated labels for different types of volumes U unknown B background S standard Label can be changed in Volume Properties Volume the sum of all the intensities within the band boundaries Adjusted Volume the background adjusted volume Mean Background the mean value of the background Absolute Quantity Volume the quantity of the volume based on the standard volumes and the regression method Relative Quantity Volume the ratio of the adjusted volume and the adjusted volume of the reference volume Pixels number of pixels inside the volume boundary Minimum Value intensity of the pixel with the minimum intensity inside the volume Maximum Value intensity of the pixel with the maximum intensity inside the volume Mean Value mean value of all pixels inside the volume boundary Standard Deviation standard deviation of all pixels inside the volume boundary Area area of the volume in mm 148 ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Data m Lane Profile taneProfie QI Lane Profile Lane 2 ko m
41. message Copying All Lanes appears 4 Select the channel that you want to copy the lanes into 5 From the Edit menu select Paste A channel can contain only one lane frame at a time Therefore if you paste lanes into a channel that already contains a lane frame you are prompted to confirm the deletion of the existing lanes If you click Yes the existing lanes are deleted and replaced with the copied lanes After the lanes are copied into the channel you can manipulate individual lanes using the lane tools so that they are correctly positioned User Guide 165 10 Analyzing Images Detecting Bands Bands are detected for individual images Detect Bands Add Delete e j To detect bands in the image gt Click Detect Bands to open the Band Detection dialog box Select band detection sensitivity and the lanes to which it applies Detection Settings Band Detection Sensitivity Low Better for more prominent bands High Better for faint bands Custom Sensitivity f _ Use advanced settings Apply To All Lanes 5 Lane 1 166 ChemiDoc Touch Imaging System with Image Lab Touch Software Lane and Bands Tools Displaying Advanced Detection Options You can also select Display Advanced Options to set specific parameters for band detection When initially expanded the values in Advanced Options are set in relatio
42. or Large May 15 2014 12 472u s 0 CZD Pick a standard size Specify a custom size To specify a custom size tap the W width or L length box Enter the width or length of the image in cm using the keypad The valid width values are 9 0 to 21 0 cm The valid length values are 7 2 to 16 8 cm Note When you enter one dimension the other dimension is automatically calculated according to the imager s 5 4 aspect ratio Tap Done to save your changes and close the keypad User Guide 49 3 Acquiring an Image Choosing the Application To choose the chemiluminescence application 1 In Live View tap APPLICATION 2 Tap Blots Then tap Chemiluminescence May 15 2014 12 47ru amp S amp wou BIO RAD Choose application category Tap Blots Nucleic Acid Gels Choose applcaon Tap Chemiluminescence 50 ChemiDoc Touch Imaging System with Image Lab Touch Software About Exposure Times for Chemiluminescent Images About Exposure Times for Chemiluminescent Images Image Lab Touch software takes the guesswork out of estimating the shortest exposure time for obtaining high resolution images It uses an Image Resolution Sensitivity scale with different binning settings that you can adjust to acquire the image you need By adjusting the binning settings you can choose higher resolution for publication quality images or higher sensitivity or l
43. page 70 for more information 72 ChemiDoc Touch Imaging System with Image Lab Touch Software Viewing Images Selecting and Opening Images from the Gallery To select images in the Gallery x Tapathumbnail image to select it m To select all images taken on a particular date tap the checkbox for that date Jul31 2014 12 49 PM S om 29 9 Date checkbox 34 Images seectar E 9 selected Bl Thursday may 08 2014 2014 05 08 15hr 08min 35sec Q Wednesday May 07 2014 Q 2014 05 07 10hr 11min 25sec Number of selected images User Guide 73 4 Viewing Images with the ChemiDoc Touch Imager m To select all images in the gallery tap the Select All checkbox at the top of the screen Select All Jul 17 2014 1 05 PM E o ot 31 Images isses E a Bl wednesday May 07 2014 2014 05 07 10hr 11min 25sec Q I Zoom Bl Tuesday may 06 2014 Qt _ 2014 05 06 14hr 34min 14sec v WD Number of selected images Note To change the number of columns of images in view in the Gallery tap zoom 74 ChemiDoc Touch Imaging System with Image Lab Touch Software Adjusting How Images Are Displayed To open an image from the Gallery Double tap a thumbnail to see the full size view of the image m Select between one and four images and tap View x Selected Images x is the number of selected images An example is s
44. page 83 To open an image in the Gallery gt Double tap the thumbnail image The image opens in Image View May 09 2014 10 4000 WeVer Galery oo GRAD K Beck to Galley Chemi Blot ChemiDoc Touch X i Value UMP umb UC We ae c a ae x El ig endum rage This chapter describes the different tasks you can perform on images Some tasks can be performed in either the Gallery or Image View while other tasks can be performed in both places 70 ChemiDoc Touch Imaging System with Image Lab Touch Software About Image View About Image View In Image View you can do the following Focus on a smaller area by zooming in or on a larger area by zooming out Pan across the image from left to right or up and down Restore the image to its original view with a double tap Change how the image is displayed using the Transform feature For more information see Adjusting How Images Are Displayed on page 75 With multiple images copy the transform settings or the zoom and pan settings from one image to the other images Delete the image For more information see Deleting Images on page 85 Save the image to a USB flash drive or network drive For more information see Chapter 6 Exporting Images from the Imager View details about the image For more information see Viewing Image Information on page 86 Note You can perform any of the actions described here on any image that appears in Ima
45. sample tray in the transilluminator drawer Refer to Table 2 for the icons used to represent each type of sample tray When there is no tray in the drawer the image displays NO TRAY Sample tray in the transilluminator APPLICATIO drawer Blots Chemilumines Note You must use the correct tray with the application you select The ChemiDoc Touch imager detects the type of sample tray on the imaging bed If the tray in the transilluminator drawer does not support the selected application an error message appears and you will not be able to acquire the image 46 ChemiDoc Touch Imaging System with Image Lab Touch Software About Sample Trays In some instances you may see an asterisk next to the application name indicating that the associated tray is recommended for that application There are instances where more than one tray can be used with an application Some fluorescent reagents have excitation peaks in both UV and blue wavelengths therefore either excitation source can be used However the resulting images are not identical Using the recommended tray with these fluorescent reagents provides a better signal to noise ratio which translates to increased sensitivity In this situation both tray types are shown and the recommended tray is identified with an asterisk Choose application category Nudeic Acid Gels Acid Gels Protein Protein Gels 5 Choose Application Recommended tray NH NH N NM LJ
46. specify image settings Icons tap an icon to execute a command m Text Boxes tap a text box to display a touch screen keyboard or numeric keypad to enter data User Guide 31 2 Image Lab Touch Software Overview Examples of these interface elements are identified in the Live View screen Gallery icon Live View icon T v Jul 17 2014 1 00 PM tie We 2 0 ELE IMAGE SIZE dialo Choose Image Size x 4 Ten 4 IMAGE size IMAGE SIZE tab APPLICATION tab EXPOSURE tab Text boxes for custom size Acquire image icon Alternatively you can use a USB mouse to click on tabs and icons or click in text boxes and enter data with a USB keyboard Note If you are using a USB mouse replace any instruction to tap with click 32 ChemiDoc Touch Imaging System with Image Lab Touch Software About the Live View Screen About the Live View Screen The Live View screen appears when you start Image Lab Touch On this screen you specify the image size select an application and set the exposure Once these parameters have been set you acquire the image Main toolbar du31 2014 12 50PM imac size Fg WELXTIT exrosune Sample tray _ Bands Tabs for setting acquisition parameters Acquire image Zoom icons The main components of the Live View screen include Main toolbar provides access to the Live View Gallery and Help
47. 143 Image InfO ysis tie cee bab Reta ee Pee ewe AOR oa Re ee a Et 144 Displaying Data s eui lese bk eek E See baer eh ade a WON hea 144 Analysis Table Options lille 145 Lane and Band Table Measurement Definitions 00 147 Volume Measurement Definitions llle 148 vi ChemiDoc Touch Imaging System with Image Lab Touch Software Table of Contents Lane Profiles iti Teres Edere Mee dial dele Dali Wale wa ee Ge fe 149 standard Curve ase ols eee Gee e ae MEE VITE 152 REDOM EEUU 153 Chapter 10 Analyzing Images 2000c eee ence eee 155 Using Auto Analysis a a p E E EEI E nen 155 Analysis Tool BOX Tools ik xd eR UPS E res 157 Image Tools pag Sit ekeesseer eae Eee esu ER cet ies 158 Correcting a Slanted Gel 2 0 eee 159 Cropping a Gel lmage 2 eee eee 159 Inverting Data e ze ene eee ee woven bez deve he ie ere aoe e eg 160 Merging Images cep od cen el duke Ge ee eee KNEES 160 Lane and Bands Tools 00 0c e eee eee eee 161 Detecting Lanes 2 e IEXilsEeSenkCexrxee METdGUecE S as 162 Using the All Lanes and Single Lane Tools llllellsseslesss 162 Copying Lanes eesesseiiwweegx eae eer das Pee eae LEIE RES 165 Detecting Bands 0 2 cee tees 166 Editing the Detected Bands 0 cece eee 169 Molecular Weight MW Analysis Tools 2 00 e eee eee 171 Quantity Tools sonet patet eitat wes A E sates wala area ee eles 175 A
48. 375 provides UV protection However this shield does not guarantee complete protection nor does it provide protection to others in the area around the imager Before performing band excision the user and anyone near the imager must put on protective gear including eyeglasses laboratory glasses provide adequate protection a face shield lab coat and gloves User Guide 25 1 Introduction 26 ChemiDoc Touch Imaging System with Image Lab Touch Software 2 Image Lab Touch Software Overview This chapter describes how you interact with the touch screen interface and gives an overview of the main screens in the software Starting Image Lab Touch To start Image Lab Touch Software 1 Press the power button on the front of the imager to turn it on The instrument starts the Image Lab Touch software and the Welcome screen appears Welcome to the Bio Rad ChemiDoc Touch Imaging System This page is yours to customize Tap the text you want to change You can replace the title with the name of your laboratory or organization You can also replace these text paragraphs with the instructions and cautions specific to your work ChemiDoc Touch Imaging System User Guide 27 2 Image Lab Touch Software Overview You can customize the text on this screen For more information see Editing the Welcome Screen on page 42 Note The First Aid Kit icon is reserved for the use of Bio Rad service technicians 2 Tap Be
49. 4x4 uses 16 pixels compared to a binning of 2x2 which uses four pixels Therefore a binning of 4x4 is four times more sensitive than a binning of 2x2 Resolution resolution decreases at the higher binning settings As pixel binning increases there are fewer pixels in the resulting image Exposure time as binning increases the exposure time is shortened The larger pixel size reduces the time it takes to acquire the image Tip Zooming in on the area to be imaged increases the resolution and may increase the optimal binning The loss in resolution with a higher binning may be offset by the increase in resolution and shorter exposure time 54 ChemiDoc Touch Imaging System with Image Lab Touch Software About Exposure Times for Chemiluminescent Images The binning settings balance sensitivity resolution and exposure time A 2x2 binning level produces images that are relatively higher in resolution and lower in sensitivity with longer exposure times An 8x8 binning level produces images that are relatively lower in resolution with higher sensitivity faint bands are optimized and shorter exposure times Binning Relative resolution and exposure time level High d 2x2 A 3x3 E c E E 5 4x4 o o a 6x6 E 8x8 E Low High LOW Time Fig 6 Relationship between resolution and exposure time User Guide 55 3 Acquiring an Image The two gel lanes to the right of the scale are a
50. 60 CHI Select Exposure Area IMAGE SIZE APPLICATION The imager generates a low resolution image of the blot A rectangle is displayed over the preview image User Guide 57 3 Acquiring an Image 3 Use the rectangle to specify the area you are interested in m Toresize the rectangle touch and drag any of its corners m Toreposition the rectangle touch inside the rectangle and move your finger To adjust the resolution of the preview image use the zoom icons or stretch or pinch your fingers to zoom in or out Tip If you cannot achieve an acceptable image reposition the blot on the sample tray and repeat this procedure 58 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting the Exposure Time for Chemiluminescent Images Setting the Exposure Time for Chemiluminescent Images The exposure time for chemiluminescent images can be set in the following ways Automatically Image Lab Touch determines the optimal exposure time Manually you specify the exposure time Signal Accumulation Mode SAM Image Lab Touch captures a series of images with a range of exposure times For more information on this method see Configuring Signal Accumulation Mode on page 62 Setting the Exposure Automatically To set the exposure for chemiluminescent images automatically 1 In Live View tap EXPOSURE By default the exposure settings on the Auto tab are displayed Review the recommended s
51. Brazil 55 11 3065 7550 Canada 905 364 3435 China 86 21 6169 8500 Czech Republic 420 241 430 532 Denmark 44 52 10 00 Finland 09 804 22 00 France 01 47 95 69 65 Germany 089 31 8840 Greece 30 210 9532 220 Hong Kong 852 2789 3300 Hungary 36 1 459 6100 India 91 124 4029300 Israel 03 963 6050 Italy 39 02 216091 Japan 81 3 6361 7000 Korea 82 2 3473 4460 Mexico 52 555 488 7670 The Netherlands 0318 540666 New Zealand 64 9 415 2280 Norway 23 38 41 30 Poland 48 22 331 99 99 Portugal 351 21 472 7700 Russia 7 495 721 14 04 Singapore 65 6415 3188 South Africa 27 861 246 723 Spain 34 91 590 5200 Sweden 08 555 12700 Switzerland 026674 55 05 Taiwan 886 2 2578 7189 Thailand 1800 88 22 88 United Kingdom 020 8328 2000 14 0506 0514 Sig 1213
52. C Setting Up Users and Groups Configuring Users and Groups on a Network Domain Note The network administrator must know how users and groups are set up using the Windows server software at your site The following example is used to illustrate the choices To locate the users and groups on a Windows server gt Open Administrative Tools and select Active Directory L Console Window Help E Active Directory Users and Computers ol xj Action View e gt m FARIA eH s ve Ge Active Directory Users and Computers genetics bio rad com Builtin E Computers Domain Controllers E ForeignSecurityPrincipals NER Ls BP Clinician 2 ec BP Reviewer a BP_Service BP_Supervisor Tree Users 44 objects Security Group Security Group Global Security Group Global Security Group Global Security Group Global Security Group Bio Plex CFR Administrator Bio Plex CFR Clinician 1 Bio Plex CFR Clinician 2 Bio Plex CFR Reviewer Bio Plex CFR Field Service Bio Plex CFR Supervisor X a a Note that in the Active Directory window the Users folder lists groups as well To create a new user on a Windows server 1 With the Users folder open select Action gt New User Alternatively use the right click context menu You see the New User dialog box New User ET User name Full name Description Password Confirm password
53. Disk Size specifies the size of a hypothetical rolling disk between 0 5 and 99 5 mm in 0 5 mm increments that removes background levels along the length of the lane The size of the disk determines how closely the background level follows the intensity profile A large disk follows the profile trace less closely touching fewer points along the trace and removing less background A smaller disk more closely follows the profile trace removing more background ChemiDoc Touch Imaging System with Image Lab Touch Software Lane and Bands Tools A disk radius that is too large will result in poor background removal A disk radius that is too small might subtract actual data For most samples a size of 10 mm is usually appropriate You can perform this task several times until you are satisfied with the amount of background removed Use the Lane Profile tool to evaluate the appropriate disk size for background subtraction Apply to selected Lane applies the specified level of background subtraction only to the selected lane This option enables you to set different background subtraction levels for each lane Copying Lanes You can copy the lanes from one image into any other image The entire frame and all the lanes are copied Individual lanes cannot be copied To copy lanes between channels 1 Open the Lane and Bands tool 2 Select the channel that contains the lanes you want to copy 3 From the Edit menu select Copy The
54. ERS U ChemiDoc Touch Imaging System with Image Lab Touch Software User Guide Version 1 0 ChemiDoc Touch Imaging System with Image Lab Touch Software User Guide Version 1 0 Bio Rad Technical Support Department The Bio Rad Technical Support department in the U S is open Monday through Friday 5 00 AM to 5 00 PM Pacific Standard Time Worldwide technical support is available on the Web at www consult bio rad com Phone 1 800 424 6723 option 2 Fax 1 510 741 5802 Email LSG TechServ USGBio Rad com U S LSG TechServ IntIi Bio Rad com International Web www consult bio rad com Notice No part of this publication may be reproduced or transmitted in any form or by any means electronic or mechanical including photocopy recording or any information storage or retrieval system without permission in writing from Bio Rad Bio Rad reserves the right to modify its products and services at any time This user guide is subject to change without notice Although prepared to ensure accuracy Bio Rad assumes no liability for errors or omissions or for any damage resulting from the application or use of this information Alexa Fluor Coomassie Fluor Qdot and SYPRO are trademarks of Life Technologies Corporation Coomassie is a trademark of BASF Aktiengesellschaft Cy2 is a trademark of GE Healthcare DyLight and Krypton are trademarks of Thermo Fisher Scientific Inc
55. Excel PowerPoint and Windows are trademarks of Microsoft Corporation Mac and Numbers are trademarks of Apple Inc GelGreen and GelRed are trademarks of Biotium Inc Mitsubishi is a trademark of Mitsubishi Companies PulseNet International is a trademark of Centers for Disease Control and Prevention SYBR is a trademark of Life Technologies Corporation Bio Rad Laboratories Inc is licensed by Life Technologies Corporation to sell reagents containing SYBR Green I for use in real time PCR for research purposes only Precision Plus Protein standards are sold under license from Life Technologies Corporation Carlsbad CA for use only by the buyer of the product The buyer is not authorized to sell or resell this product or its components Copyright 2014 by Bio Rad Laboratories All rights reserved Table of Contents Safety and Regulatory Compliance esse 11 Important Safety Information 0 000 cee eee 11 Warranty PIC 12 General Precautions 000 cee ee 12 Regulatory Notices 0 0 cece tees 13 Instrument Safety Warnings lille 13 Mou 14 Power Safety Information 00 0 0 cece ee 15 Voltage Setting Information l l 15 FUSCS s ce e RS ERE e e rer usa E Ee TOR ie Rae DTP e a us 15 Chapter 1 Introduction 2 2 cl illl ll eR Rr ck 17 Product Features 6s oudse oc aie alah tested v ER o ie E tatit a 17 Imager ComponentS 000 cece ee enn 19 CCD Camer
56. Fit Graph checkbox to display the entire range of possible intensity values in the graph Doing so allows valid comparisons between different lanes Include Background When the Include Background checkbox is selected the Lane Profile window shows the subtracted background under the blue line The area used for band quantification appears in green under the red line When you clear the Include Background checkbox the area of the lane profile that represents the background of the image does not display Identify Bands by You can change how the bands are labeled by choosing from the options in the Identify Bands by dropdown list By default the bands are labeled by band number You can display one of the following attributes Band Number Band No Band Label Molecular Weight Mol Wt m Relative Front Volume ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Data Absolute Quantity Abs Quant Relative Quantity Rel Quant Band Lane Adjusting Band Boundaries Below the profile of each lane there is a strip that displays the bands Each band is surrounded by a pair of vertical lines delimiting its boundaries You can move the vertical lines and change these boundaries To change the boundaries of a band 1 Hold your cursor over one of the boundary lines until a double arrow appears 2 Click and drag the cursor to the new position Note Boundary lines cannot overlap one
57. Lane and Band analysis can be viewed in the Lane and Band Table tab If volume analysis was performed these data can be viewed in the Volume Table tab The buttons above the table provide options for displaying and exporting analysis table data To change the size of the Analysis Table window gt Move your cursor to the top of the window until it changes into a double headed arrow Click and drag the edge of the window until you can see all of the data Note Resizing the Analysis Table window is restricted when a protocol window is open Display Data Options E The Display Data Options dialog box has three tabs Measurements enables you to choose the measurements to display in the table Use the arrows to move the columns between the Not Displayed pane and the Displayed pane By default all measurements are displayed in the Analysis table Note For a description of each Lane and Band measurement type see Lane and Band Table Measurement Definitions on page 147 For a description of each Volume measurement type see Volume Measurement Definitions on page 148 Display enables you to set the display for the analysis table The following settings appear on the Display tab m Default display settings The Move selected lane to top checkbox is selected by default When you click a lane on the image the Analysis table scrolls so that the data for the selected lane appears first in either the vertical or horizontal vie
58. Optimal Auto exposure Rapid Auto exposure e i a a a Higher Resolution Longer Wait Time Lower Resolution Shorter Wait Time malt Wl EXPOSURE nid Auto exposure xL 12 4 em Chemiluminescence 4x4 Recommended binning setting Selected binning setting The selected binning level appears here Fig 4 Binning settings on the Image Resolution Sensitivity scale 52 ChemiDoc Touch Imaging System with Image Lab Touch Software About Exposure Times for Chemiluminescent Images Pixel binning refers to the process of combining data from adjacent CCD pixels to form a single larger pixel with increased sensitivity A binning of 2x2 means that 4 adjacent pixels are combined into one larger pixel A binning of 3x3 means that 9 pixels are combined into one 4x4 means that 16 are combined into one and so on Binning option Combined pixels on the CCD chip None 2x2 4 pixels 1 3x3 9 pixels 1 4x4 16 pixels 1 6x6 36 pixels 1 Fig 5 Combined pixels on the CCD chip for different binning settings User Guide 53 3 Acquiring an Image Pixel binning lets you balance sensitivity resolution and time to produce an image best suited for your purposes m Sensitivity as binning increases sensitivity to light increases and this improves the ability to detect faint bands A binning of
59. a and LenseS 00 eee ete tees 20 Introduction to Image Lab Touch Software 000 e eee eee 20 Emission FilterS 2 0 0 0 000 eee 20 Optional Accessories 0000 cc eee 21 Printer o he ie Sapte egies Shae ee eee oe SMS ets 21 sample Maya ra eset nd ees Ipae EVE Suga aus 21 Supported Tray Types esse Per DR Eee neta LER eee 22 Technical Specifications sers mis weds ree ea E e ra ee 23 Environmental Requirements 00000 eee ees 24 User Guide iii Table of Contents Chapter 2 Image Lab Touch Software Overview 27 Starting Image Lab Touch 0 0 ccc rns 27 Setting the System Date and Time 0 0 00 es 29 Touch Screen Actions a senii aiaee AE E enne 31 The Application Interface lille rre 31 About the Live View Screen 0 00 cee eee 33 The Image Lab Touch Main Toolbar elseleleeereene 34 Using the Tabs 5i wxkexce epee ed erre oS UAE Ee DDR eed d 35 About the Image View Screen 2 0 0 ccc ree 36 The Image View Toolbar 0 0 00 tee eee 37 THE Gallery merde EE Ret ngage ied ede Eg etel ea reli m 38 Getting Help 2222s ete Ie eS ee bee eis 39 Entering Onscreen Text l lllielllseeeeeeleeeee ees 39 Using the Keypad voee Ra wie vem esha aaa a 40 Using the Keyboard see RE ER eek ul Hnc Re IR Rn id a 41 Editing the Welcome Screen 00 tees 42 Setting the Sound Volume sss si ruranata i a EE eens 43 Chapter 3
60. about to deactivate your version of Image Lab Security Edition License Code 111111 222222 333333 Deactivate Via Internet Create Deactivation Email Deactivate Cancel 3 Click Deactivate 114 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Security Edition A Save File window appears File name DeactivationEmail Save as type Tea txt x Browse Folders 4 Navigate to the folder in which you want to save the deactivation email and click Save 5 Create an email addressed to LSG TechServ US Bio Rad com with the subject line Request to Deactivate Image Lab software Security Edition 6 Attach the DeactivationEmail txt file to the email and click Send in your email program The Bio Rad Technical Support Department processes your request and deactivates Image Lab Security Edition Enabling and Disabling Image Lab Secure Mode You must have Image Lab Administrator role privileges to switch between Image Lab secure mode and standard mode User Guide 115 7 Setting Up the Imager with Image Lab Software To enable secure mode 1 From the Security menu click Security Preferences to display the Security Preferences dialog box 6 Aw Security Preferences s Enable secure mode to be used in authen caton 2 Select Enable secure mode 3 Click OK to display the Enable Secure Mode authentication dialog box
61. age Lab 5 0 InstallShield Wizai mem Welcome to the InstallShield Wizard for Image Lab 5 0 The InstallShield R Wizard will install Image Lab 5 0 on your computer To continue click Next WARNING This program is protected by copyright law and international treaties Image Lab Software On the Welcome screen click Next Accept the license agreement and click Next On the Edition Selection screen choose the edition to install d Image Lab 5 0 InstallShield Wizard Edition Selection Image Lab Make selection for desired Image Lab edition E oftware Install Standard Edition The Standard Edition does not require an Activation Code Install Security Edition Requires an Activation Code The security edition contains features to support regulated environments InstallShield User Guide 103 7 104 Setting Up the Imager with Image Lab Software 5 Note the following If you are licensed to install the Security Edition but choose to install the Standard Edition you will need to uninstall the Standard Edition and install the Security Edition before you can use it If you are licensed to install the Security Edition and choose to install it only a user assigned the Image Lab Administrator role or group privileges can enable and disable secure mode Note A user assigned the Image Lab Administrator role will not necessarily also be the ne
62. age Lab Touch Software D Ordering Information Catalog Description 170 8370 ChemiDoc Touch Imager ChemiDoc Touch Trays 170 8374 Chemi UV Stain Free Tray 170 8372 White Tray 170 8373 Blue Tray Optional Accessories 170 8375 ChemiDoc Touch UV Shield 170 8377 Holder for Sample Trays and UV Shield 170 8185 XcitaBlue Viewing Goggles 170 9690 Image Lab Software Windows Mac 170 8376 Gel Alignment Template Kit 170 8089 Mitsubishi Printer 100 240 V USB 170 3759 Bio Rad Fluorescent Ruler 170 3760 Gel Cutter Ruler Replacement Parts 100 1361 UVB Lamp 302 nm 1 each 100 26840 Fuse 8 A 250 V 5 x 20 mm 1 each 170 8097 302 nm Lamp Kit 6 lamps 170 7581 Mitsubishi Thermal Printer Paper 4 rolls User Guide 253 D Ordering Information Catalog Description Nucleic Acid Standards 170 8351 170 8352 170 8353 EZ Load 20 Base Pair Molecular Ruler EZ Load 100 Base Pair Molecular Ruler EZ Load 100 Base Pair PCR Molecular Ruler Protein Standards 161 0373 161 0363 161 0385 Buffers 161 0732 161 0747 Precision Plus Protein All Blue Standards Precision Plus Protein Unstained Standards Precision Plus Protein WesternC Pack 10x Tris Glycine SDS 4x Laemmli Sample Buffer Electrophoresis Cell 165 6001 165 8004 Criterion Cell includes electrophoresis buffer tank lid with power cables 3 sample loading guides Mini PROTEAN Tetra Cell for Mini Precast Gels 4 gel vertical electrophoresis system in
63. alue is greater than the pixel value inside the volume the background adjusted quantity of the volume could be lt 0 In this case redraw the border for this volume Global global background subtraction calculates a single background intensity for the entire gel This average background intensity is then subtracted from all the volumes in the gel The average intensity of the pixels in the background volume is calculated and subtracted from each pixel in all standard and unknown volumes Therefore it is not necessary for the background volume area to be the same size as your unknown To calculate global background subtraction f Use one of the Volume Tools to create a volume in a representative background region of your image that is a nondata region similar to the background surrounding your data 2 Double click the volume This opens the Volume Properties dialog box 3 Select the Background option button Note m If you select Global in the Volume Tools toolbox but do not define a background volume as described no background subtraction is performed m If you create more than one background volume all the pixels in those background volumes are used to calculate the average background Your background volume s will have default names B1 B2 and so on based on the sequence in which they were created m If the region you defined as background has a higher average intensity value than your data object you obtain a negati
64. alue of most of the pixels is that of the background Often there are too few pixels at the intensity levels of the data peaks of interest to make those peaks readily visible in a linear histogram The linear histogram can be useful if the intensity values are more evenly distributed Used in combination with the logarithmic histogram the linear histogram also gives you a better idea of the relative amounts of pixels at each intensity value To change the light intensity range displayed in the image gt Tap the Low or the High slider and drag it where you want it Use the Low and High sliders to narrow the grayscale range that is displayed Dragging the Low slider to the right reduces the background and low intensity bands and makes it easier to visualize high intensity bands Dragging the High slider to the left makes it easier to visualize the background nonspecific binding and low intensity bands However it will further darken the intense bands so they appear overexposed User Guide 77 4 Viewing Images with the ChemiDoc Touch Imager To adjust the grayscale curve gt Tap and drag the gamma slider control or touch anywhere in the slider bar Reducing gamma highlights the background nonspecific binding and faint bands Increasing gamma reduces the background and nonspecific binding and highlights the intense bands X i Log Histogram Q inert image display LAL c Auto a BD ght saturated pixels d
65. ane and Bands view Std appears below the lanes identifying them as standard lanes In the Molecular Weight Analysis view these lanes are indicated with a check mark below the lane 172 ChemiDoc Touch Imaging System with Image Lab Touch Software Molecular Weight MW Analysis Tools There are three standard lanes in the screen shot below lanes 1 16 and 17 Standard lanes are identified with a check mark in the boxes below the lane The molecular weights of the bands in the standard lanes appear on either side of the lane frame The red lines running from one end of the lane frame to the other identify the location of the bands in the standard lanes You can use these lines to see where the bands in the other lanes fall relative to the bands in the standard lanes Note You can use the lane labels to identify your standard lanes e e e qv QS rd ge S e A e s 28 2 e ey e ej TERES EENSENTINMSNO S 10 1 12 13 14 15 16 17 250 250 150 150 100 100 75 e 75 50 50 37 37 User Guide 173 10 Analyzing Images The values for the molecular weight in any standard lane appear in bold In this example the values for the first lane are in bold Lanes 16 and 17 are not included in the screen shot but their values would also be in bold The molecular weight of the bands in the remaining lanes is calculated relative to these standards Lane 1 Precision Plus Lane
66. another Therefore you will not be able to move any boundary line beyond the next boundary line User Guide 151 9 152 Viewing Images with Image Lab Standard Curve E Standard Curve Lane 1 DEK Show Labels Log Y Axis Regression 4 Standards E 3 2 a fi 0 4 0 6 Relative Front Regression Method Linear semi log Formula y 1 45 x 2 4 R Squared Value 0 995342 Mol weight Standard Curve X Abs Quantity Standard Curve V WolumeStandardCurve J The Standard Curve dialog box displays the best curve fit for the defined standards and the bands relative to this curve for the lane selected in the image The tabs at the bottom of the dialog box display the standard curves for three different analyses Standards appear in green Unknown bands appear in red You can toggle the molecular weight display on the y axis between linear and log scale by clicking the Log y axis box at the upper left The regression method you chose in Molecular Weight Analysis Tools appears as well as the formula if applicable and the R value of the regression method Tabs in this window enable you to view the molecular weight standard curve the absolute quantity standard curve or the volume standard curve ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Data l4 Report eet See Generating Reports on page 191 for information about repor
67. are Overview 4 Tap Settings Then tap Set Date and Time to set the current time Set Date To June 05 2014 Set Time To 2 32 PM x lt June 2014 gt Sat Sun 1 30 2 3 4 6 7 8 1 31 AM 9 10 11 12 13 14 15 2 32 PM 16 17 18 19 20 21 22 3 33 23 24 25 26 27 28 29 4 34 30 5 Tap the angle brackets lt and gt in the calendar to navigate to the correct month 6 Tap the day of the month 7 Scroll through the Hour and the Minutes lists until the current time appears in the blue band 8 Scroll the AM PM list until the correct setting appears in the blue band 9 TapOK The new date and time appear at the top of the screen 30 ChemiDoc Touch Imaging System with Image Lab Touch Software Touch Screen Actions Touch Screen Actions The following terms describe touch screen actions Action Tap Double tap Pan Scroll Stretch Pinch Definition Briefly touch the screen surface Tap twice quickly Touch and then move your finger left or right Touch and hold and then move your finger up or down Place a thumb and one or two fingers together on the Screen and then move them apart This is equivalent to zooming in Place a thumb and one or two fingers slightly apart on the Screen and then move them together This is equivalent to zooming out The Application Interface You interact with the application in the following ways m Tabs tapatab to open a dialog box in which you
68. b Touch Software l l 227 Reinstalling Image Lab Touch 1 6 0 cee eren 228 About the UV Transilluminator Bulbs 00 0000 ee eee 228 When Transilluminator Bulbs Fail 0 0 2 0 0 00 cece eee eee 229 Replacing the UV Transilluminator Bulbs llle 229 Replacing the Fuses s aesae ramte aa nh 232 Appendix B Regression Calculation Methods 235 Appendix C Setting Up Users and Groups 237 Setting Up Image Lab Users and GroupS 0 000 e eee eee 237 User ACCOUNTS a cse ssp ERR ret ei ean gun Me oad eee eed 237 User Authentication and Group Membership 00000000 238 Finding the Name of Your Authentication Domain 0 239 Configuring Users and Groups on a Local Computer 240 Configuring Users and Groups on a Network Domain 244 Password Security cri ea GU Rr ege repa Reka ERES 248 Password Policy Setting Examples 0 00 eee eee 250 Account Lockout Policy Setting Examples llle 250 Auditing Windows Event Logs cece ee 250 Miscellaneous Security Measures l l 251 Appendix D Ordering Information 253 User Guide ix Table of Contents x ChemiDoc Touch Imaging System with Image Lab Touch Software Safety and Regulatory Compliance Important Safety Information A Please read these instructions before operating the ChemiDoc To
69. b Touch Software Lane and Bands Tools Shoulder band detection tries to distinguish shoulders as separate bands When looking at a lane trace these bands appear as flat or gently sloping abutments to darker better defined bands that is there is no dip on the trace between the two bands Increasing the shoulder sensitivity results in more shoulders being detected as bands Changing this setting to zero results in no shoulders being recognized as separate bands If band detection calls a doublet a single band check the lane trace to see if there is a dip between the peaks of the two bands If there is no dip increasing the shoulder sensitivity value will help resolve the two bands Normalize Sensitivity compensates for differences in intensity between lanes The intensity of each lane is determined by the darkest band in that lane For example suppose that in all but one of the lanes the darkest band has an intensity of 50 000 counts In the light lane the darkest band is only 25 000 counts With normalization band detection will be twice as sensitive when processing the light lane improving the detection of faint bands Note It does not normalize for band quantitation Band Limit enables you to limit the number of bands that will be detected in each lane thus reducing the need for later editing Editing the Detected Bands You can optimize the bands in your images using these tools Add manually add a band t
70. be saved on your system User Guide 195 11 Generating Reports Adjust the Printer Settings The Printer Settings button accesses options for paper size orientation and page margins 196 ChemiDoc Touch Imaging System with Image Lab Touch Software 12 Exporting Results The most convenient way to archive complete information about experiments is to produce reports However it is possible to export only gel images or analysis table data for analysis in different programs such as Quantity One FPQuest or InfoQuest FP software It is also possible to export only files for presentation or publication Exporting Gel Images Image Lab software includes features for exporting gel images several ways You can export displayed image data to a publication choose Export for Publication You can export raw image data as a 16 bit tif file choose Export for Analysis You can export image data to PulseNet Doing so reduces the image to an 8 bit tif file limits its resolution and restricts its file size to 300 Kb You can export lane and band tables as well as volume tables to a spreadsheet program or to a file User Guide 197 12 Exporting Results The options to export gel images are available using the Export option in the File Menu File Edit View Window Prot New Protocol Ctri N Bi Open Ctrl o Recent Images gt Recent Protocols save Ctrles Save As
71. bles you to normalize volume data in multichannel images so you can correct for sample loading errors in your gels For more information on multichannel images see the ChemiDoc MP Imaging System with Image Lab Software User Guide MW Analysis Tools Molecular Weight Analysis enables you to choose standard samples assign standard lanes and choose a regression method Quantity Tools enables you to automatically quantify bands using either relative or absolute values Annotation Tools enables you to add formatted text and arrows to any area of a gel Volume Tools enables you to manually quantify an object inside a boundary that you define These tools are described in Analysis Tool Box Tools on page 157 Status Bar The status bar at the bottom of the main window shows the imager in use and the X and Y values for the cursor position on the image file Menu Commands The following section describes all menu commands in the File Edit View Window and Help menus Many commands are also available on the toolbar or the Start Page File Menu Commands New Protocol enables you to create a new protocol that contains the necessary steps and choices Protocols can also be altered and stored for reuse Open browses the file system to retrieve a previously saved protocol file or image file Recent Images enables you to open a recent image file User Guide 131 8 Image Lab Software Overview Recent Protocols enables you t
72. ckbox is selected only users and groups that are defined on the local computer on which Image Lab is installed are recognized When this checkbox is not selected only users and groups that are defined on the network domain are recognized Finding the Name of Your Authentication Domain Your authentication domain can be hosted on your local computer a local domain or on a network server a network domain To find the name of your local domain 1 From your Start menu open the Control Panel 2 Click System The System window appears In the Computer name domain and workgroup settings section the name of your local computer is shown as Computer name Computer name domain and workgroup settings Full computer name LSG07002297 Global Bio Rad Com Computer description Image 1 2 Domain Global Bio Rad com User Guide 239 C Setting Up Users and Groups To find the name of your network domain 1 From your Start menu open the Control Panel 2 Click System The System window appears In the Computer name domain and workgroup settings section the name of your network domain is shown as Domain Computer name domain and workgroup settings Computer name LSG07002297 BW Change settings Full computer name LSG07002297 Global Bio Rad Com Computer description Image12 Configuring Users and Groups on a Local Computer To set up users and groups on a local computer 1 In the Windows Control Panel select Adminis
73. click Print log 212 ChemiDoc Touch Imaging System with Image Lab Touch Software Printing Logs The Log Print Preview window displays the contents of the log file GS 900 Log Generated by Dennis Cathey Printed 3 4 2013 2 31 49 PM Date and time User Level Domain Type Description Unrestricted GLOBAL Unrestricted Calibration Successful calibration for flat field image correction Unrestricted GLOBAL Unrestricted Calibration Successful standards location calibration From the Log Print Preview window you can m Click Print log to print the log to a printer m Click Print log to PDF to save the log to a PDF file Click Adjust printer settings to prepare the file for printing User Guide 213 13 Software Logs 214 ChemiDoc Touch Imaging System with Image Lab Touch Software 14 Using the Security Edition 21 CFR Part 11 Image Lab Security Edition is a module within the Bio Rad s Image Lab software that assists users in meeting the U S Food and Drug Administration s regulations on good lab practices in the pharmaceutical and biotechnology industries The Security Edition enables system administrators to ensure that Image Lab operates in compliance with Title 21 of the Code of Federal Regulations CFR Part 11 within a closed system A closed system is defined as an environment in which system access is controlled by
74. cludes electrode assembly companion running module tank lid with power cables mini cell buffer dam Blotting System 170 4155 170 4156 170 4157 170 4158 170 4159 170 4270 170 4271 170 4272 Trans Blot Turbo Starter System blotting instrument includes base 2 cassettes to hold 1 2 midi or up to 4 mini blotting sandwiches blot roller and starter consumable kit Trans Blot Turbo Transfer Pack mini PVDF pkg of 10 Trans Blot Turbo Transfer Pack midi PVDF pkg of 10 Trans Blot Turbo Transfer Pack mini nitrocellulose pkg of 10 Trans Blot Turbo Transfer Pack midi nitrocellulose pkg of 10 Trans Blot Turbo RTA Transfer Pack mini nitrocellulose Trans Blot Turbo RTA Transfer Pack midi nitrocellulose Trans Blot Turbo RTA Transfer Pack mini PVDF 254 ChemiDoc Touch Imaging System with Image Lab Touch Software Catalog Description 170 4273 Trans Blot Turbo RTA Transfer Pack midi PVDF 170 4274 Trans Blot Turbo RTA Transfer Pack mini LF PVDF 170 4275 Trans Blot Turbo RTA Transfer Pack midi LF PVDF Detection Reagents 170 5060 Clarity Western ECL Substrate 200 ml 170 5061 Clarity Western ECL Substrate 500 ml User Guide 255 D Ordering Information 256 ChemiDoc Touch Imaging System with Image Lab Touch Software Life Science Group 10042202 Rev B US EG Bio Rad Laboratories Inc Web site www bio rad com USA 800 424 6723 Australia 61 2 9914 2800 Austria 01 877 89 01 Belgium 09 385 55 11
75. d File 2013 03 04 15 43 Type dcathey Unrestricted GLOBAL Unrestricted File 2013 03 04 14 29 15 dcathey Unrestricted GLOBAL Unrestricted File 2013 03 04 13 43 09 dcathey Unrestricted GLOBAL Unrestricted File 2013 03 04 13 42 38 dcathey Unrestricted GLOBAL Unrestricted File 2013 03 04 13 41 59 dcathey Unrestricted GLOBAL Unrestricted File 2013 03 04 10 37 33 dcathey Unrestricted GLOBAL Unrestricted File 2013 03 04 10 12 07 dcathey Unrestricted GLOBAL Unrestricted Action 2013 03 04 10 11 56 dcathey Unrestricted GLOBAL Unrestricted Action 2013 03 04 10 07 28 dcathey Unrestricted GLOBAL Unrestricted File 2013 03 04 10 07 28 dcathey Unrestricted GLOBAL Unrestricted File 4 Lum ProtocolS beginning run result dcathey 2013 03 04 14hr 29min Created protocol Protocol Protocol4 beginning run result dcathey 2013 03 04 13hr 43min Created protocol Protocol4 Protocol3 beginning run result dcathey 2013 03 04 13hr 41min Created protocol Protocol3 Default protocol saved Default protocol saved dcathey 2013 03 04 10hr 07min created Protocol2 beginning run result dcathey 2013 03 04 10hr 07min User Guide 205 13 Software Logs Viewing the Document Log The View menu displays a list of logs for each open document The document log captures information about creating and editing the Image Lab protocol and image files Note Document logs are viewable only in Image Lab Security Edition and only
76. d are in place If the lights do not turn on verify that the UV shield is installed correctly 3 Raise the UV shield no more than is necessary to work with the sample Caution Keep the UV shield open for as little time as possible User Guide 93 5 Excising Bands 4 Reach around the sides of the shield to excise the bands Caution Sharp cutting tools can easily damage the surface of the trays To avoid this place a sheet of clear glass or plastic on the tray before you add the gel sample Use a chopping motion rather than a sawing motion 5 When you have finished excising the bands tap Turn Transilluminator Off to turn off the UV lamps 6 Close the UV shield 7 Remove the UV shield remove the sample tray slide in the transilluminator drawer and close the main door Excising Bands on a White or Blue Tray Working with white and blue trays does not require using the UV shield or wearing protective gear However you must wear yellow XcitaBlue goggles to see bands on a blue tray 94 ChemiDoc Touch Imaging System with Image Lab Touch Software Excising Bands from Samples Caution Sharp cutting tools can easily damage the surface of the trays To avoid this place a sheet of clear glass or plastic on the tray before you add the gel sample Use a chopping motion rather than a sawing motion To excise bands on a white or blue tray 1 Place a gel sample in the center of the tray 2 With Live View onsc
77. d image if available and unannotated images are printed in the report The unannotated image precedes the annotated image in the report Note If you disable the other checkboxes in the Include Gel Image group the Include Unannotated Image checkbox is automatically disabled Image Info specify what information is included in the report oO oO Oo oO Acquisition Information Analysis Settings Image Information Notes Signature History details on when and why a secure document was signed If a secure document has been signed the user name the date and time of the signature and the reason for signing are all included in the Signature History section If a document has not been signed this section is omitted from the image report User Guide 193 11 Generating Reports Lane and Band Table Tab F3 Report Settings mc General Lane And Band Table Volume Table v Include Lane And Band Table Lanes to show All lanes Lanes v Show Lane Profile v Print one lane per page Not Displayed Displayed Band No Channel Band Label lt Mol Wt KDa Relative Front Volume Int Abs Quant Rel Quant lt Band Lane gt Norm Factor Norm Vol Int a m d The Lane and Band Table tab includes the following settings m Include Lane and Band Table specify whether to include the Lane and Band table in the report Lanes to show specify which lane
78. d with previous versions of Image Lab are unsigned unsecure documents Unsecure documents remain unsecure When you open these files in secure mode you can make changes to these files and save them without restrictions A document log is generated for changes to these files but the log is not viewable in standard mode You must log in to secure mode to see the log User Guide 221 14 Using the Security Edition You can also open unsecure documents in secure mode and sign them You can make changes to these files and save them as secure documents The original unsecure document remains unsigned and unsecure The new document is saved as read only with an incremental revision number and Image Lab generates an audit log Image Lab will not be able to overwrite the secure file but it can overwrite the original unsecure file Secure Documents Protocol and image files created in secure mode are known as secure documents and generate a log However until they are signed such documents save as standard files Only after they are signed are they saved with the secure extension Image files generated from signed protocols automatically open the signing dialog box when the scan completes If you create a default protocol based on an existing signed protocol the resulting new default protocol cannot be edited Note A secure document can be saved unsigned Likewise a signed document can be saved as a new unsigned file In this case the sav
79. dministrator role on the second domain See User Authentication and Group Membership on page 238 for more information about using this dialog box User Guide 123 7 Setting Up the Imager with Image Lab Software 124 ChemiDoc Touch Imaging System with Image Lab Touch Software 8 Image Lab Software Overview Note Any references to protocols creating protocols or protocol files do not apply to the ChemiDoc Touch imaging system Image Lab image acquisition and analysis software works with the to create a reproducible automated and time saving workflow for imaging and analyzing gels In Image Lab a protocol is any combination of imaging analysis and report settings that has been saved to run as a single workflow Researchers can run one protocol repeatedly or easily design a wide range of protocols With Image Lab you can view analyzed data edit the analysis and produce customized reports that show precisely the settings applied in order to ensure repeatable results Image Lab generates two types of files m Protocol files describe the parameters for imaging and analyzing your gel images Image files contain the imaged gel annotations and analysis performed on the gel An imaged gel run according to a protocol file generates an image file User Guide 125 8 Image Lab Software Overview Table 1 lists the extensions and icons for the type of files that Image Lab generates Table 1 Image Lab file exte
80. e are highlighted in red Linear or logarithmic histogram this adjustment changes the y axis on the histogram to display the number of pixels at each intensity value using either a linear or a logarithmic scale User Guide 141 9 Viewing Images with Image Lab Image Colors Image Colors Colormap O Gray O EtBr Coomassie O Stain Free SYBR Green SYPRO Ruby O Flamingo O Silver O False Color O Spectrum O Gold Silver O Pseudo You can choose a color map for your image results file Viewing the image with a different color scheme can make it easier to see all of the elements in the image but it does not change your data The first eight color choices imitate the colors of stained gels The remaining choices supply enough color variation to highlight small differences in the image data The available colors include Gray m EtBr ethidium bromide Coomassie Stain free SYBR Green m SYPRO Ruby m Flamingo m Silver 142 ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Gel Images m False color m Spectrum m Gold Silver m Pseudo 3 D Projection S The 3 D view transforms the gel image into a solid three dimensional model spinning in space with x y and z dimensions Accentuate or diminish the relative heights of data points by pulling the slider at the bottom of the window to the right or left To view the intensity of various bands 1 Se
81. e default names S1 S2 and so on based on the sequence of their creation To review the regression curve gt Open the Standard Curve window and select the Volume Standard Curve tab 188 ChemiDoc Touch Imaging System with Image Lab Touch Software Volume Tools Regression Methods Three regression methods are available to generate the volume quantification curve used for absolute quantity linear point to point and cubic spline To display the standard curve click the Standard Curve button on the toolbar and select the Volume Standard Curve tab in the Standard Curve dialog box Regression Calculation Methods on page 235 The data for volume standards are found in the Absolute Quantity column of the Volume Table Note Selecting the Force Through Origin checkbox always starts the standard curve graph at 0 0 regardless of the best curve fit Alignment Align volumes by using the appropriate alignment button To select several volumes Ctrl click each one then select one of the alignment buttons Hover over any of the six alignment buttons to display its function Align Left Align Right etc Copy and paste selected volumes by pressing Ctrl C to copy Press Ctrl V to paste When you click the Standard Curve button on the toolbar a chart displays all unknown and standard quantities User Guide 189 10 Analyzing Images 190 ChemiDoc Touch Imaging System with Image Lab Touch Software 11 Generating Reports Afte
82. e information and close the keyboard 5 Tap X to close the window User Guide 87 4 Viewing Images with the ChemiDoc Touch Imager 88 ChemiDoc Touch Imaging System with Image Lab Touch Software 5 Excising Bands This chapter describes the steps to excise bands of interest for analysis Excising Bands from Samples With the ChemiDoc Touch imager you can excise bands of interest from agarose or acrylamide gels for applications such as mass spectrometry or DNA cloning The procedure for excising bands varies depending on the type of sample tray you use To excise bands on a white or blue tray see Excising Bands on a White or Blue Tray on page 94 Excising Bands on a Chemi UV Stain Free Tray cause serious damage to unprotected eyes and skin The accessory UV shield catalog 170 8375 provides some UV protection However this shield does not protect others standing in the area around the imager Before performing band excision the user and other lab personnel in proximity to the imager must put on protective gear including UV protective safety glasses a face shield lab coat and gloves to ensure that no skin is exposed A typical and reasonable expectation of use is three operations per user a day for three minutes each Bystanders without protective gear must stand at least 1 5 meters five feet away from the imager and limit their exposure to no longer than one hour per day j WARNING Transilluminators are powerful so
83. ed file is still a secure document All changes to the document are captured in the document log Documents created in secure mode can be signed at any time When a secure document is signed it is saved as read only Image Lab cannot overwrite the document You can open signed documents and sign them again The newly signed file is saved as a second revision and the new signatures are captured in the document log Note Image Lab can never overwrite any signed file You can open secure documents in standard mode of Image Lab Selecting Save As from the File menu creates an unsecure file The original file is preserved No log is generated for the new unsecure document However an entry is added to the original log that the file has been reverted to unsecure 222 ChemiDoc Touch Imaging System with Image Lab Touch Software Electronic Records Secure Documents in SAM mode Images saved in signal accumulation mode SAM follow the same rules as the main image The rules apply when the image is saved from within a protocol If you create an image from a signed protocol all resultant images must also be signed If you try to save a file more than once a warning message appears asking you to confirm the re save And if you confirm this re save and click OK Image Lab creates a new file with an incremental revision number Modifying Secure Documents You can open and change a signed document in Image Lab The original document is read on
84. ee eee 205 Viewing the Document Log 0 eee eee 206 Displaying Log Data 0 e E EEE tees 207 Displaying Data Columns in Logs 00 e eee eee 207 Filt ring Dataiin Logs i 82 rere ERR Pages Mag eglae gad eee res dee 208 Collapsing or Expanding Data Rows 000 eee eee 210 ExportingiLogs uL es Bea Ween ba ee ie ae ed 211 Printing LOGS 2 ooncxsidie REIR LIAECEubeee xe ES 212 Chapter 14 Using the Security Edition 215 2l GER Part ipen o ia a inetd Sate tals Waele ate heath ere eee eas 215 Standard Mode versus Secure Mode 00 e ee eee eee 216 User Names Groups and RolesS nnana 0c eee eee eee eee 217 Role Restrictions 3s aid eke Wed E wi is see ee ee RE dE 219 Starting Image Lab Security Edition l l 220 Saving Documents to Write Once Folders 0000 e eee eee 220 Electronic Records scissa ese Leake nd eee weg bebo pe ted ed edged est 221 Unsecured Documients o eere 0 pes 3e ca Re Ere ee Ege ORS EE ERE 221 Secure Documents sorsa aee taer AER EATE EE eee 222 Modifying Secure Documents llle 223 Signing Documierits x iex sew ea wk x E RE ee x 224 Document Logs luce baec rie ck wy Ede Re PUR E E E uns 225 vii ChemiDoc Touch Imaging System with Image Lab Touch Software Table of Contents Viewing the Document Log s cssesserarse desgi ters e 226 Appendix A Maintaining the Imaging System 227 Updating Image La
85. eight of the bands on the gel image by opening the Display Gel Options window and selecting Mol Wt from the dropdown list in the Band Attributes section See Displaying Gel Images on page 138 for information about displaying band attributes Molecular Weight Standard You can change the standards to ones that are relevant to your samples 44 MW Analysis Tools r3 pee Standards Bio Rad Precision Plus Standard Lanes first last Select standard lanes by checking the box below the lanes Regression Method Linear semi log v User Guide 171 10 Analyzing Images To change standards P Click Change to access the Manage Standards dialog box Choose another standard or add your own standards n Manage Standards Name Type Bio Rad 100 bp Molecular Ruler DNA Edit Bio Rad 100 bp PCR Molecular Ruler DNA Bio Rad 500 bp Molecular Ruler DNA Bio Rad 1 kb Molecular Ruler DNA Bio Rad 2 5 kb Molecular Ruler DNA Bio Rad AmpliSize Molecular Ruler DNA Bio Rad Precision Molecular Mass Ruler DNA Delete Rename Show DNA v Th Standards in red are built in defaults q New standards can be created by copying a default Standard Lanes Standard samples are placed in the first and last lanes by default You can specify other standard lanes by selecting the box below each lane or by entering the standard lane numbers separated by commas in the MW Analysis Tools dialog box In the L
86. emiDoc Touch Imaging System with Image Lab Touch Software Quantity Tools Linear generates a straight line that is the best fit of the values you provided and is preferred in most cases Point to point generates a curve in which each data point is connected directly to the next regardless of the shape of the resulting curve Cubic spline generates a smooth curve that connects each data point At least four standard points are required to use this method of least squares polynomial fits Table 2 Regression Methods Regression Minimum Number Minimum Number with Force Method of Standard Bands Through Origin Option Linear 2 1 Point to point 2 1 Cubic spline 5 4 6 Click Standard Curve on the toolbar and select the Absolute Quantity Standard Curve tab User Guide 179 10 180 Analyzing Images The calibration curve displays Standards are represented by green triangles Unknown values are represented by red triangles Note Selecting the Force Through Origin checkbox always starts the standard curve graph at 0 0 regardless of the best curve fit E Standard Curve Lane 1 DEK v Show Labels Log Y Axis Regression 4 Unknowns Band A Standards Lane Band onu o NM 3 2 E 2 2 E oN FO 0o LI 1 500 2 000 o4 1 000 Band Volume x 1000 Regression Method Linear Formula y 0 00665 x 1 54 R Squared Value 0 933908 Mol Weight Standard Cur
87. en it in a database application ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Data Export Analysis Table to Excel Exports the table data to a spreadsheet so you can use the sorting and formula functions to manipulate your data If you have Excel PC or Mac or Numbers Mac installed on your computer the program opens with your spreadsheet displayed Lane and Band Table Measurement Definitions This section defines the measurements that display in the Lane and Band tab in the Analysis table Use the Data display options button to choose the columns to display Band Number each band in a lane has a unique number sorted from top to bottom Band Label you can assign a custom label to each band by clicking the Band Label field of the Lane and Band table Molecular Weight the molecular weight of the band is calculated based on the user defined standard and regression method Italic values indicate extrapolated values When using nucleic acid gels the size of the band is displayed in base pairs Relative Front values between 0 1 indicate the relative movement of the band from top to bottom Abs Quant absolute quantification of the band Rel Quant relative quantification of the band compared to the reference band Band percentage of the band s volume compared to all band volumes in the lane Lane percentage of the band s volume compared to the entire volume of the
88. end The following characters cannot be used M Note If you select more than one image each image will have the same name followed by a number for example ChemiBlot 1 ChemiBlot 2 and so on 4 Tap OK To rename an image in Image View 1 InLive View tap Image Info 2 In the Image Info window tap in the Name box A keyboard appears on the screen 3 Triple tap to select the text Then type the new name The image name can consist of 190 alphanumeric characters Spaces are permitted except at the beginning and end The following characters cannot be used M i 4 Tap OK to save the image name and close the keyboard 5 Tap X to close the window 84 ChemiDoc Touch Imaging System with Image Lab Touch Software Deleting Images Deleting Images Images can be deleted in the following ways In the Gallery multiple images can be deleted at one time Any open image in Image View can be deleted The procedures that follow describe each method From the Gallery you can manage the number of images stored on the ChemiDoc Touch imager and delete images that you no longer need To delete an image from the Gallery 1 3 In the Gallery select the images to delete in one of the following ways m Tapone or more thumbnails m Tap the checkbox for one or more days to select all thumbnails for those days m Tap Select All to select all thumbnails in the Gallery Tap Delete The Delete Image promp
89. enter a custom name to replace the default label Volume Type Unknown Standard Background Quantity Custom Label C Reference volume Unknown volumes are volumes you want to quantify Standard volumes are used for absolute quantities See Absolute Volume Quantity on page 188 Background volumes are used to remove the background from the calculation The result of volume background subtraction appears in the Adjusted Volume column of the analysis table Volume Table tab Note This volume type needs to be assigned only when using Global Background subtraction Volume Background Subtraction When you draw a volume some nondata background pixels might be included inside the volume These background pixels usually have an intensity value that you do not want to include in your volume quantification There are two methods of calculating this background intensity for your volumes local and global Local local background subtraction calculates a separate background intensity for each unknown and standard volume you create For each 186 ChemiDoc Touch Imaging System with Image Lab Touch Software Volume Tools volume the intensities of the pixels in a 1 pixel border around the volume are added together and divided by the total number of border pixels This gives an average intensity for the background around each which is then subtracted from the intensity of each pixel inside the volume If the background v
90. etting on the Image Resolution Sensitivity scale and change the setting if necessary Tap a binning setting Auto Manual oOx e Optimal Auto exposure Q Rapid Auto exposure u a a BE Higher Resolution Lower Resolution Longer Wait Time Shorter Wait Time ESIZE APPLICATION EXPOSURE v Recommended binning setting Selected binning setting The selected binning level appears here For more information on the Image Resolution Sensitivity scale see The Image Resolution Sensitivity Scale on page 51 User Guide 59 3 60 Acquiring an Image 3 Tap a dynamic range Tap Optimal Auto exposure for an image that uses the full dynamic range but which does not exceed saturation ChemiDoc Touch optimizes the image for the brightest region within the selected area Tap Rapid Auto exposure for an image that is usable but which may not detect fainter bands The exposure time is shorter than for Optimal Auto exposure Use this option if you are less interested in detecting faint bands Or use Rapid Auto exposure to get an initial image that you can use to estimate the time for a manual exposure setting Tap Image Info to get the exposure time For more information on manual exposure settings see Setting the Exposure Manually on page 60 Setting the Exposure Manually To set the exposure for chemiluminescent images manually 1 2 In Live View tap EXPOSURE Tap Manual Review the
91. f the data are not very linear Point to point semilog No single equation is available for the point to point method The slope of each segment of the curve between data points is calculated independently Note The log of the molecular weight values is used to calculate the slope for each segment of the curve Logistic The x equation is ys2d 1 j User Guide 235 B Regression Calculation Methods where x mobility y molecular weight a estimated molecular weight at infinity b slope of the tangent at midpoint c midpoint d estimated molecular weight at zero mobility Since the curve generated by the logistic 4PL regression method represents a perfectly shaped S it might not fit the data very well in all cases Cubic spline Cubic spline curves are smooth curves that go through every data point The model is a cubic polynomial on each interval between data points In some cases a spline curve can work well as a standard curve for interpolation However because the curve is calculated individually for every pair of points it does not correspond to any single equation 236 ChemiDoc Touch Imaging System with Image Lab Touch Software C Setting Up Users and Groups Setting Up Image Lab Users and Groups This appendix explains how to set up users and groups to run Image Lab Security Edition software in secure mode Note This task requires System Administrator privileges on the client co
92. g requires authentication a login dialog box appears Enter your username and password Tap OK Tip The username must include the domain to which the network drive belongs as in domain_name username where domain name is the name of the domain and username is your user name on the domain A progress bar provides feedback on the image export 6 When the export is completed tap OK The images are exported to a folder at the top level of the specified drive with the name Chemidoc Touch Images followed by a time stamp of the image export for example Chemidoc Touch Images 2014 04 29 19 08 51 User Guide 99 6 Exporting Images from the Imager 100 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up the Imager with Image Lab Software System Requirements Image Lab software runs on Microsoft Windows and Mac OS X Images scanned at high resolution can be quite large The amount of memory required for using the program is determined by the size of the images you scan and analyze For this reason we recommend that you archive images on a network file server or on removable storage media Bio Rad can also provide an appropriate computer to use with this system Contact your local Bio Rad representative for more details Image Lab Security Edition Note Image Lab Security Edition must be installed on a computer running Windows to take advantage of the secure mode features Image Lab Security Edition is
93. ge View If there are multiple images tap the desired image then perform the task You can see thumbnails of all the images acquired to date in the Gallery For more information see About the Gallery on page 71 About the Gallery From the Gallery you can do the following Open a single image in Image View For more information see To open an image from the Gallery on page 75 Open up to four images in Image View For more information see To open an image from the Gallery on page 75 User Guide 71 4 Viewing Images with the ChemiDoc Touch Imager m Rename the image For more information see Renaming Images on page 83 Manage the acquired images and delete images you no longer need For more information see Deleting Images on page 85 m Exportthe images to a USB flash drive or to a network drive For more information see Chapter 6 Exporting Images from the Imager Viewing Images Images are viewed in Image View There are two ways that an image appears in Image View m After a gel or blot image is acquired the image is automatically displayed in Image View An example of a single image in Image View is shown here A gm May 09 2014 1040 5 amp 0 GIO lt Sack to Galley Chemi Blot ChemiDoc Touch X ve Value UMP umb UM ae eue I ae PE Toom image irto igh m From the Gallery you can select and open one or multiple images at a time See To open an image in the Gallery on
94. ge exports in progress Important The Image Lab Touch software must be running before you insert the USB flash drive into the USB port To update Image Lab Touch 1 Login to Image Lab Touch 2 Insert the USB flash drive into the USB port above the main door on the front of the imager A dialog box displays the current software version and the software update version 3 Optional If the dialog box does not appear tap Settings Then tap Update Installation 4 Tap OK The installer updates the imager with the latest version of Image Lab Touch When the installation is complete Image Lab Touch restarts and the login screen appears User Guide 227 A Maintaining the Imaging System Reinstalling Image Lab Touch Reinstall Image Lab Touch if you are experiencing software problems that appear to be due to a flawed installation or corrupted files Complete any image acquisitions or image exports before you start the installation To reinstall Image Lab Touch 1 Insert the USB flash drive into the USB port above the main door at the front of the imager 2 Login to Image Lab Touch 3 Tap Settings e in the main toolbar 4 Tap Update Installation A dialog box displays the current software version and the software update version 5 TapOK When the installation is complete Image Lab Touch restarts and the login screen appears About the UV Transilluminator Bulbs Use the 302 nm standard bulb transillumi
95. ged in ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Security Edition m Select the Use local groups for establishing user security levels checkbox Cus Securty preferences M n V Enable secure mode Domain to be used in authentication GLOBAL 7 Use local groups for establishing user security levels 3 To set preferences so that only local users can run Image Lab Inthe Domain used in authentication field enter your local computer name See To find the name of your local domain on page 239 for instructions on how to determine this name Note The default domain name that will appear in this field is the domain on which the current user is logged in m The Use local groups for establishing user security levels checkbox is grayed out not accessible 4 x 7 Enable secure mode Domain to be used in authentication LocalComputerName Use local groups for establishing user security levels e ems User Guide 121 7 Setting Up the Imager with Image Lab Software Renaming Security Groups To rename any of the four default Security Groups 1 From the main menu select Security Rename Security Groups Note This menu option is visible only if the person logged on to the local computer is logged on as a member of the Windows Administrators group A Rename Security Groups Security groups Access Level Group Name
96. gin The Live View screen appears Jul 17 2014 12 58PM To begin 1 Pull out the transilluminator drawer 2 Place a tray on the transilluminator 3 Close the drawer APPLICATION EXPOSURE 4x4 28 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting the System Date and Time Setting the System Date and Time Before you begin using the imager check that the date and time settings are correct for your locale If you are connected to a network date and time are synchronized to the network setting The date and time are used in the default name assigned to acquired images The system date and time are determined by a combination of the time zone and the current time settings To set the system date and time 1 Tap Settings 1 Then tap Set Time Zone Set Time Zone To x UTC 08 00 Pacific Time US amp Canada Select New Time Zone UTC 12 00 International Date Line West UTC 11 00 Coordinated Universal Time 11 UTC 10 00 Hawaii UTC 09 00 Alaska UTC 08 00 Pacific Time US amp Canada UTC 08 00 Baja California UTC 07 00 Chihuahua La Paz Mazatlan UTC 07 00 Arizona UTC 07 00 Mountain Time US amp Canada UTC 06 00 Guadalajara Mexico City Monterrey UTC 06 00 Saskatchewan 2 Scroll through the list until the time zone for your locale appears Tap the time zone to select it 3 TapOK User Guide 29 2 Image Lab Touch Softw
97. hat you install the software on only one desktop computer and one laptop To load the Image Lab Security Edition on a second computer the software must be deactivated on the first computer before it can be activated on another You can deactivate the Security Edition automatically via the Internet or you can deactivate it manually by sending a deactivation email To deactivate the Security Edition automatically via the Internet 1 Onthe Security menu click Deactivate Security Edition to display the Deactivate Security Edition dialog box 2 Select Deactivate Via Internet ra Deactivate Security Edition You are about to deactivate your version of Image Lab Security Edition License Code 324100 000064 XXXXXX Deactivate Via Q9 Internet Create Deactivation Email Deactivate Cancel 3 Click Deactivate User Guide 113 7 Setting Up the Imager with Image Lab Software The system sends a message to the Bio Rad Technical Support Department a window stating that your deactivation was successful appears and Image Lab Security Edition is immediately deactivated A Image Lab i Deactivation was successful To deactivate the Security Edition via email 1 From the Security menu click Deactivate Security Edition to display the Deactivate Security Edition dialog box 2 Select Deactivate Via Create Deactivation Email c5 Lu Deactivate Security Edition m You are
98. he rotation Cropping a Gel Image You can save crop settings and use them to crop other images This feature is useful when you want to crop the same area in several images To crop a gel image 1 2 3 Click Crop A red box outlines the image area Drag the red box to surround the image area you want to keep Optional Right click the image to open the Crop menu and click Save Crop Settings The Save Crop Settings dialog box appears Optional Type a name for the crop settings and click OK Right click and select Crop or Cancel Selecting Crop crops the image to the area inside the red box To crop an image using saved crop settings 1 2 3 Click Crop A red box outlines the image area Right click the image to open the Crop menu and click Load Crop Settings Select the saved crop settings that you want to use and click Load The red box resizes and the crop specifications appear on the image Right click and select Crop The image is cropped to the area specified in the crop settings you selected User Guide 159 10 Analyzing Images To delete crop settings 1 With an image open click Crop 2 Right click the image inside the red box to open the Crop menu and click Delete Crop Settings 3 Select the crop settings in the dialog box that appears and click Delete Inverting Data Use this button to change the image data from positive to negative Invert Data is used for negative stains and zymog
99. hown here tt B May 15 2014 3 448 amp m GU Gite ChemiDoc Touch X Y Value Chemi Blot 30sec Chemi Blot 5sec Chemi Blot 15sec 2 g Image Info Chemi Blot_60sec e m Adjusting How Images Are Displayed Image Lab Touch optimizes images based on the range of intensity levels in the image and the known behavior of the applications Use this optimized image as a starting point Use the histogram scale and the grayscale curve settings in the Transform dialog box to adjust the image brightness and contrast as necessary Important The transform settings change only the appearance of the image the underlying data are not altered Note Chemiluminescent images taken in SAM mode are displayed with a fixed transform because this allows them to be compared with each other The intensity is set to the bottom third of the full range and the gamma is set to 75 By using a fixed transform you can see the differences between the images within one SAM acquisition and select the best one User Guide 75 4 Viewing Images with the ChemiDoc Touch Imager Light Intensity Histogram Transform adjusts image brightness and contrast optimizing the image display so faint details can be seen The minimum to maximum range varies depending on the light and dark values present in the image Adjustments to brightness and contrast do not change the data They change only the way the data are displayed The frequency dis
100. icate the severity of the problem Tap the icon to display the error message May 15 2014 124000 2 D am Unable to acquire image The door is open Tap the icon to display the error message Deleting Images As you acquire images you can immediately discard any unnecessary images To delete an image in Image View 1 In Image View tap Delete A prompt appears asking you to confirm the deletion 2 Tap OK to delete the image 68 ChemiDoc Touch Imaging System with Image Lab Touch Software 4 Miewing Images with the ChemiDoc Touch Imager The Gallery is the collection of all images acquired on the ChemiDoc Touch imager The images are displayed as thumbnails and are organized by the date they were acquired with the most recent acquisition date shown first To navigate to the Gallery gt Tap the Gallery icon in the main toolbar In the example six images were acquired on Wednesday April 16 2014 Gallery m sc 60 CZD 61mages Setect as Qa Date images acquired M wesnesday Apri 18 2014 nui I Image name ssr cx 7 Safe tt rw User Guide 69 4 Viewing Images with the ChemiDoc Touch Imager The image name appears below each thumbnail image The default name consists of the date and time of the acquisition An example is 2014 02 18 18hr 30min 51sec scn You can change the default name in Image Info For more information see Renaming Images on
101. ies on Local Ci Advanced Audit Policy Config rm D Policy Security Setting 38 Enforce password history 1 passwords reme Z Maximum password age 181 days J Minimum password length 6 characters Si Password must meet complexity requirements Disabled Store passwords using reversible encryption Disabled 248 ChemiDoc Touch Imaging System with Image Lab Touch Software 4 Password Security To change password policy settings a Right click the policy and select Properties to open its properties dialog box Minimum password age Properties EM Local Security Setting Explain PI Minimum password age Password can be changed after b Modify the default setting to meet your company policy c Click Apply d Click OK to close the Properties dialog box Close the Local Security Policy window To set password policies in Active Directory 1 Open the Control Panel and select Administrative Tools Domain Controller Security Policy In the left pane of the Domain Controller Security Policy window expand Security Settings Account Policies and select Password Policy To change password policy settings a Right click the policy and select Properties to open its properties dialog box b Modify the default setting to meet your company policy c Click Apply d Click OK to close the Properties dialog box Close the Domain Controller Security Policy window
102. il txt file On the Security menu click Activate Security Edition to display the Security Edition Activation dialog box Select Activate Via Receive Activation Email f A Security Edition Activation a not currently activated you with the software License Code Activate Via Internet Create Activation Email Receive Activation Email Receive Email Your copy of Image Lab Security Edition is You will need the license code that was sent to 111111 222222 333333 Click Receive Email An Open File window appears Navigate to the location where you saved the UnlockCode txt file select the file and click Open at the bottom of the window Open ENT Look in ActivateDeactivate Process Name ActivationEmail My Recent Documents _ DeactivationEmail Desktop l l l File name My Network Places Files of type Text Files Date 3 5 2013 3 45 PM 2 28 2013 12 01 PM ala x ci EB ves Type Text Document Text Document Size ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Security Edition The Security Edition activation complete window appears A Image Lab o Activation was successful 12 Click OK to close the window Deactivate Image Lab Security Edition Image Lab can be installed on more than one computer Bio Rad Laboratories recommends t
103. is restricted 218 ChemiDoc Touch Imaging System with Image Lab Touch Software User Names Groups and Roles Role Restrictions Your role determines which features of the security edition you have permission to use If you attempt to perform an action that is not permitted for a user in your role you will see an error message In some instances the user s role determines which Security Edition features are visible and or enabled Therefore you might not see all of the features described in this chapter Table 4 lists the Image Lab Security Edition functions that each role has permission to perform Table 4 User access to features by role Function Administrator Supervisor Clinician Reviewer Enable disable secure mode X View log files X X X X Enable disable Write Once X Support Set up and recalibrate the X instrument Create new protocols Open existing protocols Run protocols Edit protocols Create new images Open existing images Edit images Analyze images xX XxX KK KK KK X x X XxX X X Sign documents User Guide 219 14 Using the Security Edition Starting Image Lab Security Edition When secure mode is enabled you are prompted to log on when you start the Image Lab application To start Image Lab in secure mode 1 Click the Image Lab icon to start the application 2 Inthe Log on to Image Lab dialog box enter your user name and password En EE x UserName dcathey Password Do
104. isplays a list of logs for each open document The document log captures information about creating and editing Image Lab protocol and image files You can view the document log for any open file This file can be a previously saved file or it can be a newly created protocol or image file that is open on your desktop but which has not yet been saved If the document was previously saved the log is identified with this name If the document has not been saved the log is identified with the time stamp of when the document was created View Security Window Help Image Overview Operation History View System Log View Protocol1 Log View GS900_Calibrated_Blot Log View GS900_Calibrated_Blot_LB Log View GS800 63 Log View Theresa Navarro 2013 01 17 13hr 06min Log Log file for saved image file Log file for open but unsaved image file The document log includes Date and time m User m Level the security role of the user Type the type of event Description the actual event captured m Reason the reason for signing a document For more information about logs see Chapter 13 Software Logs on page 203 226 ChemiDoc Touch Imaging System with Image Lab Touch Software A Maintaining the Imaging System Updating Image Lab Touch Software Updates of Image Lab Touch software are delivered on a USB flash drive Before you start the update complete any image acquisitions or ima
105. k server For details on how to find this name see Finding the Name of Your Authentication Domain on page 239 f AL Security Preferences O v Enable secure mode Enter the name of your local computer or the name of the network server used for your authentication domain Domain to be used in authentication GLOBAL 1 Use local groups for establishing user security levels In the Security Preferences dialog box if you or your network administrator choose a local domain to be used for authentication you are considered a local user If you or your network administrator choose a network domain you are considered a domain user Group Membership Evaluation In the group membership evaluation process Image Lab verifies that a user is a member of one or more of the four default Image Lab user groups TDS Administrator TDS User TDS Tech or TDS Guest The valid members for each of these groups can be specified in one of two places as defined by the Use local groups for establishing user security levels checkbox on the Security Preferences dialog box ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Users and Groups E AW Security Preferences Enable secure mode VBAL This checkbox specifies whether TER EE DEXVOENS valid users and groups are defined on the local Image Lab computer Cx or on the network domain L When this che
106. keyboard to increase the lane width and the minus key to decrease the width You can also change the lane width by specifying the size of the lanes Click Width enter a number in mm in the box and click Apply Note You might see that the number in the box changes after you click Apply For example you enter 5 75 and the number changes to 5 71 The image is made up of pixels and the Image Lab software can only draw a boundary for the lane between pixels If the number you specify would cause the boundary to fall anywhere on the pixels Image Lab moves the boundary so that it falls between two pixels and updates the number accordingly Note The All Lanes Width tool makes the width of all lanes uniform Therefore if you used the Single Lane tool to change the width of an individual lane this change is overridden by the All Lanes Width tool Single Lane Tools Specific information about how to use each lane tool is described in the following section You can modify an individual lane in your image using these tools Add adds a lane to a gel image Click Add then click within the lane frame where you want to place the new lane The lanes are automatically renumbered Note To add a lane outside the frame add a lane inside the frame and click Move to expand the lane outside the frame s boundaries Delete deletes a lane Click Delete then click either the lane or its lane number The lanes are automatically renumbered
107. lat fielding patent pending Autoexposure Length 63 cm 24 Width 50 cm 20 m Height 53 cm 21 32 kg 78 Ib 100 240 VAC 50 60 Hz 10 28 C 10 80 relative humidity noncondensing Application driven tray based imaging Precalibrated focus for any zoom setting Dynamic precalibrated and optimized per application 2 user defined modes rapid or optimal for chemiluminescent applications 2 user defined modes intense or faint bands for fluorescent and visible applications Using the optional Blue Tray cat 170 8373 is highly recommended if performing SYBR Safe DNA applications because the conversion to blue light lets you visualize DNA samples while protecting them from UV damage Environmental Requirements The ChemiDoc Touch imager requires a space 52 x 56 x 62 cm W x Hx D anda clearance of at least 8 cm from the back for instrument ventilation and for connecting or disconnecting the AC power cord Place the imager on a sturdy and level laboratory bench or table away from excessive heat and moisture The imager s operating temperature range is 10 28 C The imager contains a universal power supply that supports a voltage range of 100 240 VAC 24 ChemiDoc Touch Imaging System with Image Lab Touch Software Environmental Requirements Warning Transilluminators are powerful sources of UV radiation which can cause serious damage to unprotected eyes and skin The accessory UV shield cat 170 8
108. lect the 3 D button in the display toolbar 2 Click and drag the model to rotate it into your preferred view 3 Bring the window into focus by clicking the image 4 Press C to display an inverted green cone which can be dragged around to evaluate the intensity of various bands 5 Press C again to hide the tool User Guide 143 9 Viewing Images with Image Lab Image Info is The Image Info dialog box provides information about the active image The dialog box has the following tabs Image Details acquisition and image information appear in this tab Analysis Settings settings that were used when the gel was analyzed are displayed here For example Band Detection and Molecular Weight Analysis will appear if they were performed Notes on this tab you can add notes point out the types of samples used and add any other information about the results You can create custom labels for the lanes in your image Displaying Data You can view results from analyzed data associated with a gel image using an analysis table a lane profile a standard curve or a report The buttons in the main toolbar turn these views on or off You can view your data with all views simultaneously 144 ChemiDoc Touch Imaging System with Image Lab Touch Software Analysis Table Options i Displaying Data Numerical data associated with an analysis can be viewed in an analysis table Data from the
109. lipboard enabling you to paste them into a word processing or presentation application Tip You can also open a log in the log viewer and press Ctrl C to copy the log entries to the clipboard Export log entries to a file exports the log entries as a CSV file that can be opened in a database application Export log entries to Excel exports the log entries to an Excel file where you can use Excel s sorting and formula functions to manipulate your data If Excel is not installed on your computer this feature is disabled User Guide 211 18 Software Logs To export a log file 1 From the View menu click the log you want to view and export 2 Click one of the icons to export the data in one of the supported formats Copy log entries to clipboard Export log entries to File Export log entries to Excel J amp Protocol2 Log s Date and time User Level Domain Type Description Reason Pitna Eun EI unease icathey Unrestricted GLOBAL Unrestricted Protocol Changes Scan coords right 22 8 changed to 22 7 2013 03 07 15 07 2013 03 07 15 07 10 dcathey Unrestricted GLOBAL Unrestricted Protocol Run Beginning protocol run 2013 03 07 15 06 57 dcathey Unrestricted GLOBAL Unrestricted File Protocol created Printing Logs A Log data can be sent to a printer or saved to a PDF file To print a log 1 From the View menu click the log you want to view and print 2 Inthe log viewer
110. lization Quantities Volumes Artinn Xj C Ji ew jJ Select a value and click OK Tip You can select multiple values to filter User Guide 209 13 Software Logs Removing filters in logs The Remove all filters icon is enabled only after you set a filter on a column This icon clears all filters on all columns A System Log Filtered a User Level Domain dcathey Unrestricted GLOBAL Unrestrict Description as Secure Mode Enabled user DCATHEY not a member of an Image Lab security group does not have permission in GLOBAL ii dcathey Unrestricted GLOBAL Unrestrict Secure Mode Enabled user DCATHEY not a member of an Image Lab security group does not have permission in GLOBAL dcathey Unrestricted GLOBALUnrestrict dcathey Admin GLOBAL Admin Secure Mode Enabled user DCATHEY not a member of an Image Lab security group does not have permission in GLOBAL Secure Mode Disabled security mode has been disabled dcathey Admin GLOBAL Admin User GLOBAL dcathey logged into Image Lab dcathey Admin GLOBAL Admin Secure Mode Enabled security mode has been enabled dcathey Admin Local Security Enabled local group authentication has been enabled dcathey Admin Domain Redefinition domain for authentication has been redefined to GLOBAL dcathey Admin Secure Mode Enabled security mode has been enabled dcathey Unrestricted Secure Mode Enabled user DCATHEY no
111. lume tools enable you to manually quantify features on a sample image when automated lane and band analysis is not appropriate or possible such as in dot blots You can use Volume tools to quantify the signal intensity of bands spots arrays and other image data Define an area of interest by surrounding it with a shape You can choose a rectangle circle freehand or lane shape by clicking the appropriate button under the Volumes field 184 ChemiDoc Touch Imaging System with Image Lab Touch Software Volume Tools A default label appears within the shape drawn The volume label is assigned a sequential number and can be one of three types U unknown m Std standard m B background ae uim EE a Btd3l _ UU e Each new volume you create initially has a red border which indicates that the volume is selected When you click elsewhere on the image the border changes to blue indicating that the volume is no longer selected Note Double click a volume area to change its properties To review data for the volumes gt Open the analysis table and select the Volume tab Volumes are listed based on their number and or the associated information per volume See Volume Measurement Definitions on page 148 User Guide 185 10 Analyzing Images Volume Types You can define the volume type unknown standard or background the quantity of standard volumes or
112. ly and cannot be overwritten Saving the revisions opens the Save As dialog box The changes are saved into a new revision with an incremental revision number Each time a secure document is modified you must provide a reason for each change before you can sign the document The modifications are logged in the document log The new signed document takes with it the entire history of the original document in its log User Guide 223 14 Using the Security Edition Signing Documents To sign a document 1 Select the protocol or results file 2 From the Security menu click Sign Document The Signing Document dialog box appears e t Signing Document Protocol1 i e Enter the user name and password for an authorized user on the domain User name Password Reason for signing document Caa c 3 Enter the user name and password of a user authorized to sign documents Note The user name and password can be for a user other than the current user 4 Enter a reason for signing the document Typical reasons include review approval responsibility or authorship Note You must provide a reason in order to sign the document The user name date and time of the signature and reason for signing are always included in the Signature History section of the image report see page 193 224 ChemiDoc Touch Imaging System with Image Lab Touch Software Document Logs 5 Click OK
113. main global Wi Cox Coma 3 Click OK Note If you have any questions or problems logging on see your system administrator Saving Documents to Write Once Folders If users in your organization have set up Write Once folders an Image Lab Administrator must enable Write Once Support so that Image Lab software works with those folders Users can create documents such as protocols and images in Image Lab and save them to a Write Once folder however they cannot modify or delete them 220 ChemiDoc Touch Imaging System with Image Lab Touch Software Electronic Records To enable Write Once Support 1 Login to the Security Edition as an Image Lab Administrator 2 From the Security menu select Write Once Support 3 Acheckmark appears to indicate that Write Once Support is enabled r Tid Image Lab 5 2 Secunty Edition Bio Rad Intemal Use File Edit View Security Window Prototype 3 Security Preferences New Protocol Rename Security Groups v Write Once Support Sign Document l Deactivate Security Edition Electronic Records Image Lab Security Edition enables you to create secure electronic records as defined by 21 CFR Part 11 In Image Lab the following are electronic records m Protocol files m Image files Document log files x Instrument log files x System log files Unsecured Documents Protocol and image files created in standard mode or create
114. ment operating the software or changing the documents Secure Mode in this mode in addition to the features available in standard mode extensive security features are enabled including document signing the use of Write Once folders and log creation When Image Lab is in secure mode a padlock symbol appears in the left corner of the status bar If no padlock is present the software is running in standard mode E Lock indicates secure No lock indicates standard mode is enabled mode is enabled When Image Lab is installed by default it is set to run in standard mode It continues to run in this mode until a user with Image Lab Administrator privileges enables secure mode This chapter assumes you are running the application in secure mode unless otherwise noted 216 ChemiDoc Touch Imaging System with Image Lab Touch Software User Names Groups and Roles User Names Groups and Roles When Image Lab Security Edition is run in secure mode you must log in with a user name and password in order to run the application The Microsoft Windows system administrator generally creates the user names and passwords The Image Lab administrator defines the groups to which the Security Edition roles will be associated Note See Setting Up Image Lab Users and Groups on page 237 for additional information about setting up groups user names and passwords There are four default roles in Image Lab Security Edition Each
115. mputers and possibly their domain on which Image Lab is installed User Accounts To give users access to Image Lab Security Edition you can create new Windows user accounts add existing user accounts to the four default user groups specified in Table 3 on page 218 or rename any of the four default user groups A user account can have any name but must have a password defined for the account See the section on Password Security on page 248 for information about setting passwords for maximum security m Each user can belong to the Image Lab Administrator group and one other Image Lab user group For example a user can belong to the Administrator group and the Supervisor group but a user cannot belong to both the Clinician group and the Supervisor group User Guide 237 C 238 Setting Up Users and Groups User Authentication and Group Membership Authentication in Image Lab is made up of two processes user authentication and group membership evaluation User Authentication In the user authentication process Image Lab matches authenticates a user name with permissions assigned to that user name on the authentication domain That domain can reside on your local computer a local domain or on a network server a network domain You set the location of this domain in the Domain to be used for authentication field of the Security Preferences dialog box This name must be the exact name of your local computer or networ
116. mula functions of a spreadsheet program with data If you have Excel or Numbers on a Mac installed on your computer the data open in the spreadsheet program 202 ChemiDoc Touch Imaging System with Image Lab Touch Software 13 Software Logs Image Lab software provides three types of logs Instrument log records events related to the instrument including calibrating the instrument and the success or failure of the calibration This log file is visible only if the computer running Image Lab is connected to an instrument System log records events related to running Image Lab including enabling or disabling of secure mode and the users who log on to or log off of Image Lab Documentlog Security Edition only records events related to the creating and modifying of secure protocol and image files User Guide 203 13 Software Logs Viewing the Instrument Log Instrument operations that you perform with Image Lab are recorded in the instrument log To open the Instrument Log Viewer gt From the View menu click the log for your instrument Image Overview Operation History View System Log View GS 900 Log View Protocoll Log View dcathey 2013 03 07 13hr 36min Log View SimulatedMultichannel Log View Protocol2 Log View dcathey 2013 03 07 15hr 07min Log The menu displays the specific instrument to which you are connected The GS 900 de
117. n example of what an image would look like given the selected resolution setting As you tap on the different binning settings the example changes to show the relationship between resolution and sensitivity It shows more intense bands with higher resolution at the lower binning settings At the higher binning settings the faint bands are more prominent however with lower resolution igher Resolution Longer Wait Time 2x2 Fig 7 2x2 binning setting example Optimal settings 5 Higher Resolution Longer Wait Time Fig 8 8x8 binning setting example 56 ChemiDoc Touch Imaging System with Image Lab Touch Software Lower Resolution Shorter Wait Time Example Lower Resol fion Shorter Wait Time 8x8 Example About Exposure Times for Chemiluminescent Images Specifying the Region of Interest for Auto Exposure With chemiluminescent images you can specify the area of the blot you are interested in Image Lab Touch determines the optimal auto exposure time for this specified area in the final image By focusing on a particular area you can shorten the exposure time To specify the region of interest in chemiluminescent images 1 2 In Live View tap EXPOSURE Tap Show Preview Note The main door must be closed to see a preview image Opening the door at any time during this process returns the image to Live View Close the door and repeat this procedure to return to a preview of the image
118. n to the band detection sensitivity that you select in Detection Settings You can set specific parameters for the sensitivity level and apply the parameters to all lanes or to a specific lane If later you change the band detection sensitivity in Detection Settings the values in Advanced Options change in relation to the new sensitivity levels You might need to reset these parameters to the original values Detection Settings Band Detection Sensitivity Low Better for more prominent bands gt High Better for faint bands Custom Sensitivity V Use advanced settings Advanced Options Sensitivity Size Scale Noise Filter Shoulder E Normalize Sensitivity Band Limit 0 Apply To All Lanes Lane 1 User Guide 167 10 168 Analyzing Images Advanced Detection Options Sensitivity determines the minimum optical density that will be defined as a band The higher the sensitivity value the lower the minimum signal intensity therefore the more bands will be detected If the sensitivity is set too high background staining might be detected as bands If the setting is too low bands of interest might not be detected The default sensitivity setting is 10 0 If the gel has faint bands for example if the optical density is less than 0 05 and counts are less than 2 000 you may want to increase this value to 20 0 Size Scale distinguishes between trends in signal in
119. nator bulbs with the imager See Appendix D Ordering Information for the catalog number Depending on the amount of use they get the UV bulbs can last for many years An error message displays when one or more of the bulbs needs to be replaced 228 ChemiDoc Touch Imaging System with Image Lab Touch Software Replacing the UV Transilluminator Bulbs When Transilluminator Bulbs Fail The six bulbs are organized into three groups of two bulbs and are identified as Bank 1 Bank 2 and Bank 3 When a transilluminator bulb fails an error message appears informing you which bank of bulbs has a failure T i i 1 L Replacing the UV Transilluminator Bulbs At any time one or more transilluminator bulbs may fail When this occurs Bio Rad recommends that you replace all six bulbs including those that are still functioning This ensures consistent quality over the imaging area To replace the transilluminator bulbs you need a 2 5 mm hex wrench Important The transilluminator bulbs contain heavy metals including mercury Do not throw used bulbs in the general trash Dispose of them in accordance with local recycling and disposal guidelines User Guide 229 A Maintaining the Imaging System To replace the bulbs 1 Turn off the power to the imager 2 Disconnect the AC power cord from the imager 3 Open the main door and pull the transilluminator drawer out completely Tip Use the drawer slide release levers to
120. ncy distribution histogram shows the total data range in the image and the amount of data at each point in the range Auto Scale determines an optimal setting for the image automatically The lightest part of the image is set to the minimum intensity and the darkest is set to the maximum m The High progress indicator determines which intensity value is shown at the maximum gray scale or other color in the gel image 140 ChemiDoc Touch Imaging System with Image Lab Touch Software Displaying Gel Images The Low progress indicator determines which intensity value is shown at the minimum gray scale or other color in the gel image The Gamma progress indicator changes the gray scale curve A value of 1 is linear A value 1 redistributes a greater proportion of the gray scale to the first half of the intensity values A value gt 1 redistributes a greater proportion of the gray scale to the second half of the intensity values You can also type numerical values in the boxes next to the progress indicators Clicking anywhere on the progress indicator bars moves the progress indicator incrementally Options Invert image display inverts dark bands on a light background to light bands on a dark background Light bands on a dark background are inverted to dark bands on a light background Highlight saturated pixels when this checkbox is selected areas of the image with saturated signal intensity higher than a measurable rang
121. nnotation Tools e 2 sno Rete Rs qum xs ee dy eee noes 181 Add Annotations sse Re ere a n RR RE REO eo A eren d 182 AligniTient omesssttigReeU E Eexgeuree iru ee Re Lua DS AME 182 Text Propertles 1 peter ees a Sea dea eive ei eed 183 Color th St E a ot MILO i s ete tue 183 nori 183 Voume Tools du exem gie UU goby ety nb UR nme ub esee dus 184 Chapter 11 Generating Reports 00c eee eee eens 191 RepOTFt oo am cite pea Datus Peele eid oa Me aod tomen erret a e deed 191 Report Settings Jerrie ertr noga me es Reg Rc m me Rye Xe d Roe en 192 Pint Repor onto E nthe aati UA eru athe E edat 195 Print Report to a PDF File 000 ee 195 Adjust the Printer Settings lllelsleeeeereee 196 User Guide vii Table of Contents Chapter 12 Exporting Results 000c eee eee eee eee 197 Exporting Gel Images ss scssi inama aTa e a eee 197 Exporting Gel Images for Publication llle 198 Exporting Gel Images for Analysis 0 00 cee eee eee 200 Exporting Gel Images to PulseNet International 0 00 200 Exporting Lane and Band Tables to Excel 000 ee eee eee eee 201 Exporting Volume Tables to File 2 2 ee ee 201 Screenshot Tool Export 0 000 eee 201 Analysis Table Export 20 0 c ce eee 201 Chapter 13 Software Logs 22220ce cece eee e eens 203 Viewing the Instrument Log 0 0 eee 204 Viewing the System Log 0 0c e
122. not supported on the Mac User Guide 101 7 Setting Up the Imager with Image Lab Software Computer Specifications Specifications Minimum Specifications Operating system Microsoft Windows 7 32 and 64 bit Microsoft Windows 8 1 64 bit Mac OS X 10 8 or 10 9 Processor Intel Core i3 or equivalent Hard disk space 60 GB Memory RAM 4 GB Ports for connecting instrument 1 USB 2 0 port Installing Image Lab Software The process of installing Image Lab differs depending on your operating system This section explains how to install Image Lab software on a Windows PC and on a Mac Note During the Windows installation process you are prompted to install Image Lab Standard Edition or Security Edition In order to enable secure mode you must have Image Lab Administrator role privileges Bio Rad recommends that you create the required groups and assign the Image Lab roles to users within those groups before installing Image Lab software See User Names Groups and Roles on page 217 for additional information about the required Image Lab roles groups and users See Setting Up Users and Groups on page 237 for information about setting up groups user names and passwords To install Image Lab on a Windows PC 1 Insert the Image Lab software CD in your CD ROM drive 102 ChemiDoc Touch Imaging System with Image Lab Touch Software Installing Image Lab Software The Image Lab installer automatically launches lt JE Im
123. nsions and icons File type File Extension Icon Unsigned Signed Unsigned Protocols ptl sptl Images scn Sscn M anl 126 ChemiDoc Touch Imaging System with Image Lab Touch Software Interface Overview Interface Overview The following illustration shows the Image Lab main window This section explains the main software elements Menu Items Toolbar sole mnn none Start Page Analysis 9 Tool Box CV aus shon onstatup Desktop Status Bar Main Window Image Lab displays a single main window All image and protocol dialog boxes that present choices open in the workspace which is the gray area of the main window If many screens are open in the workspace you can make one active by clicking the title bar at the top of the selected screen A list of open protocols and image files also appears in the main window menu Select one to make it active You can view complete analyses for images or protocols one at a time or compare image results by arranging screens in the workspace User Guide 127 8 128 Image Lab Software Overview Main Toolbar Many Image Lab tools can be selected by clicking toolbar buttons The Screenshot tool enables you to send a screen capture of your image to the clipboard or to save it as a file You can view demonstrations of various functions by clicking Tutorials The unlimited Undo and Redo buttons enable you to correct missteps easily Results Da
124. nsitometer is shown as an example above Note You can view an instrument log only if Image Lab is connected to the specified instrument The instrument log includes the following information date and time of the action m the user name of the user logged into the computer at the time of the action m the user s security level m the domain where the current user is logged in m the type of action performed m theresult of the action taken including complete records of the calibration m the user s reason for the action if provided 204 ChemiDoc Touch Imaging System with Image Lab Touch Software Viewing the System Log User Level Domain Type Description Reason dcathey Unrestricted GLOBAL Unrestricted Calibration Successful calibration for flat field image correction z i GS 900 SCAWBO0006 Log 2013 03 04 11 04 37 dcathey Unrestricted GLOBAL Unrestricted Calibration Successful standards location calibration Viewing the System Log Events related to running Image Lab including enabling or disabling of secure mode and users logging on to or logging off from Image Lab are recorded in the system log To open the System Log Viewer gt From the View menu click View System Log AL System Log Description CJDC WIP GS 900 ImageLab Dennis Cathey 2013 02 07 14hr 19min scn opened User Level Domain Date and time dcathey Unrestricted GLOBAL Unrestricte
125. o a lane Click Add then click at the desired location in a lane Image Lab then locates a faint band close to where you clicked Tip You can darken your entire image to view faint bands more easily using the sliders in the Image Transform dialog box For instructions see Image Transform on page 140 User Guide 169 10 Analyzing Images Delete deletes a band from a lane Use this feature to remove bands that are not relevant to your analysis Click Delete and then click on the band you want to remove m Adjust adjusts the height of a band Click Adjust Boundary lines appear on either side of each band Move the cursor over a boundary line until you see a double headed arrow Move the boundary line up or down The center is recalculated and the band appears there Note You can also adjust band boundaries in the Lane Profile view 170 ChemiDoc Touch Imaging System with Image Lab Touch Software Molecular Weight MW Analysis Tools kDa Molecular Weight MW Analysis Tools lem Molecular Weight Analysis tools enable you to determine molecular weight or base pairs if using nucleic acid gels by comparing a test sample with known standards Note Before you can use the Molecular Weight Analysis tools you must detect the lanes and bands in your image You can view each band s molecular weight in the molecular weight column of the Lane and Band tab in the Analysis Table You can also display the molecular w
126. o open a recent protocol Save enables you to save a protocol or image file after it is named Save As enables you to name and store a protocol or image Protocols are stored with a ptl or sptl extension Image files are stored with an scn or sscn extension Close closes the active window Close All closes all the windows Export enables you to export gel images or analysis tables with the following options Export for Publication exports a displayed image to a file You can select from bmp png jpg and tif formats The gel displays with any lanes bands and annotations that appear on the screen See Exporting Gel Images for Publication on page 198 for more information m Exportfor Analysis creates a tif file that retains all gel image data Analysis data are not included Use this option to analyze the image in other software such as Quantity One FPQuest or InfoQuest FP See Exporting Gel Images for Publication on page 198 for more information Export for PulseNet reduces the image to an 8 bit tif file Resolution is limited and file size is restricted to 300 dots per inch dpi Lane and Band Table to Excel exports your lane and band table data to an Excel or Numbers on a Mac spreadsheet Note Excel or Numbers must be installed on your computer Lane and Band Table to File exports as a comma separated values CSV file so that your lane and band table can be opened in a database
127. og reports This is a requirement of 21 CFR 11 50a Description this field must also be filled out Bio Rad recommends entering the user s title as the description Password enter and confirm a password for the user Tip Select the User must change password at next logon checkbox This prevents the Windows system administrator from knowing the passwords of the users Note If you select the User must change password at next logon checkbox the user must actually log on to Windows and change the User Guide 241 C Setting Up Users and Groups password before using Image Lab Security Edition Otherwise Security Edition will not recognize the user To create a new group on a local computer 1 Inthe Computer Management window click on the Groups folder to open it and select Action New Group Alternatively use the right click context menu The New Group dialog box appears New Group 9 msan Group name Description Members Add Help eate Close i 2 Inthe Group name field enter the name of one of the groups specified in Table 3 on page 218 TDS Administrator TDS User TDS Tech TDS Guest You can also enter a description in the Description field The group does not need any special operating system level privileges 3 Click Create to create and save the new group 4 Repeat this task for the remaining groups specified in Table 3 on page 218 To add a user to a group on a local
128. onger exposure times when the bands are faint Image Lab Touch automatically determines the optimal setting required to achieve publication quality images Images acquired at this setting have a resolution of 175 microns per pixel You can choose a different setting with the following results Selecting a setting to the left of this default setting increases the resolution however the imaging time may be longer Selecting a setting to the right of the default setting may reduce the resolution below that required for publication however the exposure time is shortened Bio Rad recommends that you start with the optimal binning setting examine the result and then make any adjustments to subsequent images The Image Resolution Sensitivity Scale The Image Resolution Sensitivity scale has five pixel binning settings 2x2 3x3 4x4 6x6 and 8x8 indicated with the B icon xX Show Preview 7 Show Previev Q Optimal Auto exposure e Rapid Auto exposure Set Exposure Area E a a a Higher Resolution Wait Time 2x2 3x3 4x4 6x6 8x8 Fig 3 Binning settings on the Image Resolution Sensitivity scale User Guide 51 3 Acquiring an Image Image Lab Touch automatically determines the optimal binning setting required to achieve publication quality images and indicates this on the Image Resolution Sensitivity scale with the i icon Images acquired at this setting have a resolution of 175 microns per pixel Ox O
129. or opening an image in the Gallery m Select one or more images from the Gallery to export Tap Send Save User Guide 97 6 Exporting Images from the Imager 3 Tap Send to USB Drive A progress bar provides feedback on the image export 4 When the export is completed tap OK The images are exported to a folder at the top level of the specified drive with the name Chemidoc Touch Images followed by a time stamp of the image export for example Chemidoc Touch Images 2014 04 29 19 08 51 Exporting Images to a Network Drive To export images to a network drive 1 Do one of the following Navigate to Image View by acquiring an image or opening an image in the Gallery Select one or more images from the Gallery to export Tap Send Save Tap Save to Network In the dialog box enter the location of the network drive or select from the Recent Locations list Recent Locations displays the ten most recent network locations where images have been saved The list is in reverse chronological order with the most recent location listed first You can delete network locations you no longer need by tapping a location and tapping Remove 98 ChemiDoc Touch Imaging System with Image Lab Touch Software Exporting Images to a Network Drive 5 Tap Save m If the network drive requires no authentication then a progress bar shows the progress of the image export m If the network drive to which you are connectin
130. ple on a sample tray choose the image acquisition presets then acquire a sample image by tapping a single button Note Image Lab Touch software does not support image analysis Use Image Lab software version 5 2 or greater running on a separate Windows based computer to analyze images acquired with the ChemiDoc Touch instrument Product Features The ChemiDoc Touch instrument is a scientific imaging instrument that supports the acquisition of images from a wide range of laboratory gels and blots It uses a supersensitive camera with a charge coupled device CCD and a large maximum aperture lens that provides high chemiluminescent sensitivity The imager has a built in UV transilluminator and white LEDs for epi reflective illumination and it works with blue and white trays that are used with gels and blots stained with a wide range of dyes and fluorophores Additional features include Support for chemiluminescent imaging colorimetric western blotting applications and DNA protein gel visualization Dynamic flat fielding specific to each application User Guide 17 1 Introduction Smart tray based imaging that identifies the correct applications and presents appropriate filter and illumination sources for each Support for imaging applications that require high sensitivity chemiluminescent western blots m Dynamic range of gt 4 orders of magnitude 18 ChemiDoc Touch Imaging System with Image Lab Touch Software
131. r in the Type column to File and Image Lab will display only the rows where Type is equal to File 208 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting filters in logs To filter the entries of a column 1 3 Displaying Log Data In the log click the heading of the column that you want to filter The Display Filter options icon in the Actions tool bar is enabled By default the log opens with all event types displayed Note The Display Filter options icon is enabled only when you click on a column that can be filtered The Display Filter options icon remains disabled if you click a column that cannot be filtered Click the Display Filter options icon to display the Select filter values dialog box Tip Alternatively right click the heading of a filterable column to display the Select filter values dialog box J System Log User Date and time Level Type 2013 02 07 11 48 53 theresan supervisor Reviewer File 2013 02 07 11 48 49 theresan supervisor Reviewer 2013 02 07 11 48 36 tnavarr 2013 02 07 11 48 31 theresan admin 2013 02 07 11 48 31 theresan admin 2013 02 07 11 47 53 tnavarr 2013 02 06 13 40 21 tnavarr 2013 02 06 13 40 10 tnavarr lt LU Secure Mode Status Admin Secure Mode Admin Secure Mode Status Unrestricted File Unrestricted File j Select filter values Secure Mode File Calibration Alert Image Tools Lane and Band Molecular Weight Annotation Norma
132. r logs manually 4 Increase the maximum size of the event log to cover any possible messages The smaller the maximum size of the event log the more often the system administrator must manually view archive and clear the system log Auditing information generated by the operating system is recorded in the Security Log Logon failures in Image Lab Security Edition are recorded in this log During the review process the log should be examined for attempted breaches of security such as a series of failed logon attempts To avoid the risk of losing data the size should be very large and this inspection archive process should occur daily The Audit Policy should be set as follows x Audit account logon events Failure should be checked at a minimum x Audit account management both Success and Failure should be checked Audit logon events Failure should be checked at a minimum Audit policy change both Success and Failure should be checked Miscellaneous Security Measures Bio Rad recommends that you use the built in protections that Windows Server offers in order to protect the computer while the user is absent Note Microsoft is continually updating its operating systems in response to security issues It is critical to keep all components of the Windows operating system especially any domain controllers up to date User Guide 251 C Setting Up Users and Groups 252 ChemiDoc Touch Imaging System with Im
133. r use Regulatory Notices A The ChemiDoc Touch imaging system is designed and certified to meet EN 61010 the internationally accepted electrical safety standard EMC regulations and TUV requirements Certified products are safe to use when operated in accordance with this user guide Do not modify or alter this instrument in any way Modification or alteration of this instrument will Void the manufacturer s warranty m Void the regulatory certifications m Create a potential safety hazard WARNING Bio Rad Laboratories Inc is not responsible for any injury or damage caused by use of this instrument for purposes other than those for which it is intended or by modifications of the instrument not performed by Bio Rad Laboratories Inc or an authorized agent Instrument Safety Warnings Icon A Notes cautions and warnings are used to highlight certain operating procedures and recommendations The table below describes how each is used in this document in addition to general instrument precautions Meaning Caution A caution precedes an operational step that could damage the instrument or destroy data unless the operator takes certain precautions Cautions located in the main text are preceded by the word Caution and are accompanied by the caution symbol in the left margin User Guide 13 Safety and Regulatory Compliance Meaning Warning A warning precedes an operating procedure that could cause injury to the ope
134. r viewing results you can generate a report that displays the analyzed gel images all of the settings used in the protocol and as much information about the data as you want to include You can choose print settings within the Report Settings dialog box in the Edit menu or by clicking Report in the main toolbar A Report i To produce a preview of the report gt Click Report on the toolbar Report Print Preview Lysates Use the following dialog boxes to customize the content in reports Doing so does not modify the data from the analysis User Guide 191 11 Generating Reports Report Settings Use this dialog box to customize the content of the report General Tab 2 iB Report Settings el General Lane And Band Table Volume Table v Include Gel Image v Show Lanes and Bands v Show Annotations v Show Volumes Include Unannotated Image Image Info v Acquisition Information v Image Information v Analysis Settings v Notes AN The General tab includes the following settings Include Gel Image specify whether the image is included in the report If the image is included the following options determine which overlays are displayed on the gel image o Show Lanes and Bands o Show Volumes o Show Annotations o Include Unannotated Image 192 ChemiDoc Touch Imaging System with Image Lab Touch Software Report When you select this checkbox both the annotate
135. rams Intensity values of bands must be greater than background to perform analysis on the gel View the gel as a 3 D projection to determine if the data must be inverted Merging Images Use this button to merge a chemiluminescent blot image with a colorimetric image of the same blot If you have used colorimetric prestained standards for a chemiluminescent blot you can acquire an epi white light image of the blot to show the standards and a chemiluminescent image to show immunodetection These two images can then be merged into a combined image with both signals Note Merging images can have an adverse effect on quantification If accurate quantification is required perform analysis on the original separate images Only images of the same size can be merged 160 ChemiDoc Touch Imaging System with Image Lab Touch Software Lane and Bands Tools nun Lane and Bands Tools The Lane and Bands tools enable you to identify the lanes and bands in your images To open the Lane and Bands tool gt Inthe Analysis Tool Box click Lane and Bands then select the tab for the Lanes or the Bands tool User Guide 161 10 Analyzing Images Detecting Lanes To detect the lanes in the image do one of the following m Click Automatic if the gel image is fairly typical Click Manual to detect a specific number of lanes or if automatic lane detection did not find all the lanes Using the All Lanes and Single Lane Tools To use
136. rator if not followed correctly Warnings located in the main text are preceded by the word Warning and are accompanied by the warning symbol in the left margin Caution With the exception of cleaning or replacing light bulbs refer all servicing to qualified Bio Rad personnel or their agents If you experience technical difficulties with the instrument contact Bio Rad to schedule service The instrument should not be modified or altered in any way Alteration voids the manufacturer s warranty and might create a potential safety hazard for the user Caution If the tray interlock is defeated there is a possibility of UV B radiation hazard due to UV B light exposure Exercise caution when servicing the instrument Caution Bio Rad is not responsible for any injury or damage caused by the use of this instrument for purposes other than that for which it is intended or by the modification of this instrument when not performed by qualified Bio Rad personnel or their agents Warning This instrument must be connected to an appropriate AC voltage outlet that is properly grounded PPP gt RP Notice The ChemiDoc Touch instrument is intended for laboratory use only This device is meant for use by specialized personnel who know the health risks associated with reagents used in electrophoresis The UV light source is computer controlled and proper interlocks are implemented to avoid users accidental exposure to UV radiation Bio Rad Labo
137. ratories Inc is not responsible for any injury or damage caused by use of this instrument for purposes other than those for which it is intended or for instrument modifications not performed by Bio Rad Laboratories Inc or an authorized agent 14 ChemiDoc Touch Imaging System with Image Lab Touch Software Power Safety Information Power Safety Information Voltage Setting Information The ChemiDoc Touch imager has a universal power supply that automatically chooses the correct voltage for your country or region Fuses The imager has two user serviceable fuses F1 and F2 which are located on the rear panel and are a part of the power entry module See Replacing the Fuses on page 232 for information about replacing the fuses User Guide 15 Safety and Regulatory Compliance 16 ChemiDoc Touch Imaging System with Image Lab Touch Software 1 Introduction The ChemiDoc Touch system is a compact full featured chemiluminescent capable gel blot imaging instrument This instrument removes the guesswork traditionally associated with selecting blot detection parameters and acquires high quality and high sensitivity gel and western blot images with the push of a button The ChemiDoc Touch system uses Bio Rad s Image Lab Touch software to control image capture and optimization for selected applications The instrument is controlled with an integrated touch screen and a simplified user interface Position the gel or blot sam
138. rd is ready to begin installation S oftwa re Click Install to begin the installation Tf you want to review or change any of your installation settings click Back Click Cancel to exit the wizard InstallShield The wizard installs Image Lab JE Image Lab 50 InstallShield Wizard Installing Image Lab 5 0 Image Lab The program features you selected are being installed Software Please wait while the InstallShield Wizard installs Image Lab 5 0 This may take 19 several minutes Status Installing ChemiDoc USB driver InstallShield 106 ChemiDoc Touch Imaging System with Image Lab Touch Software Installing Image Lab Software 11 When the installation is complete you are prompted to display the Release Notes and or the Windows Installer log JE Image Lab 5 0 InstallShield Wizard x InstallShield Wizard Completed The InstallShield Wizard has successfully installed Image Lab 5 0 Click Finish to exit the wizard 7 Show the Release Notes file 7 Show the Windows Installer log Image Lab Software The following screen shot is an example of the Windows Installer log Ime os File Edit Format View Help H Verbose logging started 1 31 2013 11 30 21 Build type SHIP UNICODE 5 00 7601 00 Calling process C WINDOWS SysWOW64 MSIEXEC EXE MSI c B4 48 11 30 22 039 Entering MsiProvideComponentF
139. re Overview The Gallery The Gallery displays thumbnail images of all acquired images In this view you can open an image in Image View delete selected images and save selected images to a USB flash drive or network drive Search Thumbnail images ES EZSCEZ I Sache Ba cm amp Cocenassue Gei Cherri Blot 15sec DNA Gel 0 Selected Images Rename images Delete images Send or save images Zoom icons The main components of the Gallery screen are Main toolbar provides access to the Live View Gallery and Help screens the Settings menu and the Logout icon For more information about each toolbar icon see The Image Lab Touch Main Toolbar on page 34 Thumbnail images thumbnails of all acquired images are organized by the date and time of acquisition with the most recently acquired displayed first 38 ChemiDoc Touch Imaging System with Image Lab Touch Software Getting Help m Search search for selected image by date or name Rename rename selected images Delete delete selected images Send Save save selected images to a USB flash drive or network drive Zoom icons zoom in and out to focus on an area of the sample Getting Help Online help is available from each of the main views and from selected dialog boxes To access help m Tap the Help icon to open the help topic for that screen m Scrollto see longer topics and
140. recommended setting on the Image Resolution Sensitivity scale and change the setting if necessary Tap a binning setting Recommended binning setting Auto Manual Set Manual Exposure Time Configure Signal Accumulation Mode x 0 5 sec Higher Resolution Longer Wait Time Lower Resolution Shorter Wait Time EXPOSURE COC Blots Chimiluminescence Selected binning setting The selected binning level appears here ChemiDoc Touch Imaging System with Image Lab Touch Software Signal Accumulation Mode For more information on the Image Resolution Sensitivity scale see The Image Resolution Sensitivity Scale on page 51 Tap the Manual tab Tap Set Manual Exposure Time Tap the sec seconds text box to display the keypad noo m e Enter the duration of the exposure in seconds Note You can use the exposure time from a Rapid Auto exposure image to estimate this exposure time For more information see Setting the Exposure Automatically on page 59 8 Tap Done Signal Accumulation Mode Signal Accumulation Mode SAM makes it easier to acquire high quality chemiluminescent images Rather than taking a series of independent images with different exposure settings SAM lets you take a series of cumulative images Each successive image includes all of the accumulated signal of the previous images plus additional exposure time To use the SAM exposure set
141. reen tap Turn Transilluminator On The transilluminator turns on illuminating the gel with the appropriate type of light Note The lights turn on only when the sample tray is in place 3 Excise the bands 4 When you have finished excising the bands remove the sample tray and tap Turn Transilluminator Off 5 Slide in the transilluminator drawer and close the main door User Guide 95 5 Excising Bands 96 ChemiDoc Touch Imaging System with Image Lab Touch Software 6 Exporting Images from the Imager On the ChemiDoc Touch imager you use Image Lab Touch software to view images make changes to improve how the images are displayed and generate printouts of images For more detailed analysis of the images use Image Lab software version 4 0 or later on a computer Export the images to a USB flash drive or to a network drive and then transfer them to a PC where Image Lab is installed For more information on analyzing images with Image Lab software see Chapter 10 Analyzing Images You can export images to a USB flash drive or network drive by Displaying an acquired image in Image View and clicking Send Save Displaying an image from the Gallery in Image View and clicking Send Save Selecting one or more images in the Gallery and clicking Send Save Exporting Images to a USB Flash Drive To export images to a USB flash drive i Do one of the following m Navigate to Image View by acquiring an image
142. rity Preferences allows the Image Lab Administrator to enable and disable secure mode In this dialog box the administrator chooses the domain to be used for authentication and whether to use local groups for security levels Rename Security Groups allows a person logged on as a member the Windows Administrators group to change any of the four default Image Lab security group names TDS Administrator TDS User TDS Tech and TDS Guest Note This menu option is visible only if the person logged on to the local computer is logged on as a member of the Windows Administrators group Only users who are logged on as a member of that group maintain the authority to change any of the four default Image Lab security group names Any changes made to these Security Group names must match the names your Windows system administrator has given those groups Sign Document enables users to sign images and protocols Users enter their user name and password and provide a reason for signing When the document is signed the reason is saved in the System Log file Window Menu Commands The Window controls enable you to show and hide multiple open image files in your workspace A list of all currently open images and protocols appears in this menu User Guide 135 8 136 Image Lab Software Overview Tile aligns all open image files so they are visible at the same time Tile Horizontal aligns all open image files from top to bottom Tile Vertical align
143. role is associated with one of the four default Image Lab user groups and each user is assigned a role that provides the user access to specific features in the software Table 3 lists the default Image Lab Security Edition user groups and the corresponding roles It also provides a brief description of the permissions for each role Note System administrators can change the user group names if necessary to meet their local company standards User Guide 217 14 Using the Security Edition Table 3 Image Lab Security Edition groups and roles User Group Image Lab Role Description TDS Administrator Administrator Users with this role can enable or disable secure mode Administrator users can also view log files but they do not have access to any other features TDS User Supervisor Users with this role have full access to all features and functions of the application They can also sign files Supervisors cannot enable or disable secure mode TDS Tech Clinician Users with this role can perform instrument operations run existing protocols and view protocol files results files and log files They can also sign files All other access is restricted For example they cannot create or edit protocols TDS Guest Reviewer Users with this role can open and view protocol files results files and log files They can also sign files Users with this role cannot create new protocols and cannot change protocols All other access
144. romDescriptor Descriptor JgAVn f ZXfeAR6 jiHandWritingFiles gt RMn1s Rh9 lqc3L JQB PathBuf 8COSC pcchPathBuf 8C058 pcchArgsOffset 8BFB8 MSI c B4 48 11 30 22 041 MsiProvideComponentFromDescriptor is returning O MSI c B4 48 11 30 22 041 Entering MsiProvideComponentFromDescriptor Descriptor gAVn f ZXfeAR6 jiHandWritingFiles Wz B plK LZgdoVXdYG PathBuf 8CO5C pcchPathBuf 8C058 pcchArgsOffset 8BFB8 MSI c B4 48 11 30 22 042 MsiProvideComponentFromDescriptor is returning O MSI c B4 48 11 30 22 045 Font created Charset Req 0 Ret 0 Font Req MS Shell Dig Ret MS Shell Dig MSI c B4 48 11 30 22 045 Font created Charset Req 0 Ret 0 Font Req MS Shell Dig Ret MS Shell Dig MSI c B4 94 11 30 22 052 Resetting cached policy values MSI c B4 94 11 30 22 052 Machine policy value Debug is O MSI c B4 94 11 30 22 052 RunEngine 12 Select or clear the checkboxes in the Install Wizard Completed dialog 13 Click Finish to exit the wizard User Guide 107 7 Setting Up the Imager with Image Lab Software The Image Lab icon appears on your desktop Follow the instructions in the next section to connect your system To install Image Lab on a Mac 1 Insert the Image Lab software CD in your CD ROM drive 2 Double click the CD icon on your desktop to see the folder contents 3 Double click the file Image Lab dmg 4 Drag the Image Lab applica
145. s English aed Numbers and symbols Western European characters Fig 2 Touch screen keyboard displaying English alphabet You can switch among three keyboards each of which displays different characters and symbols Tap on the keys indicated in Figure 2 to display the different keyboards and enter English alphabetic characters numbers and symbols and Western European characters User Guide 41 2 Image Lab Touch Software Overview Editing the Welcome Screen After you log on to the ChemiDoc Touch imager the Image Lab Touch software starts and a Welcome screen appears There are two text boxes on the Welcome screen where you can add custom text for your organization For example you can enter the name of your business or laboratory in the upper box and add a warning message or other helpful information in the lower box Welcome to the Bio Rad ChemiDoc Touch Imaging System This page is yours to customize Tap the text you want to change You can replace the title with the name of your laboratory or organization You can also replace these text paragraphs with the instructions and cautions specific to your work ChemiDoc Touch Imaging System To edit the Welcome screen 1 Tap in a box The touch screen keyboard appears For more information see Entering Onscreen Text on page 39 2 Triple tap to select the text 3 Enter the new text Note You can enter one line of text in the upper bo
146. s Scan coords right 22 8 changed to 22 7 2013 03 07 15 07 10 dcathey Unrestricted GLOBAL Unrestricted Protocol Run Beginning protocol run 2013 03 07 15 06 57 dcathey Unrestricted GLOBAL Unrestricted File Protocol created Displaying Log Data The display toolbar is located above the log Displaying Data Columns in Logs Lr By default the logs display the following columns Date and time m User m Level the security role of the user Domain domain where the current user is logged in m Type the type of event Description the actual event captured Reason For Secure Mode only the reason for signing a document You can change your view of any log by displaying or hiding data columns User Guide 207 13 Software Logs To display or hide columns 1 From the View menu open the log file 2 Click the Display log viewer options icon 3 Inthe Display Column Options dialog box use the arrow keys to move columns between the Not Displayed and Displayed lists gt A Display Column Options System Log Viewer e Not Displayed Displayed Date and time lt User Level Domain M Type Description lt Reason j I f L Wu Le ee 4 Click OK Filtering Data in Logs Wi X For all Image Lab logs you can filter the entries in the following columns Date and time m User Type For example you can set the filte
147. s all open image files from left to right Cascade stacks all open image files and protocols with overlapping title bars so each one can be easily chosen for viewing Imitate Zoom changes the zoom setting of all open images to the same zoom setting as the current image file Imitate Transform changes the brightness and contrast of all open images to the same transform settings as the current image file Next cycles through all open image files from oldest to newest Previous cycles through all open image files from newest to oldest Help Menu Commands Default User Guide displays the user guide for the active imager User Guides displays a list of user guides you can choose from Register Image Lab displays the Image Lab Registration Form About displays Image Lab software version and release date ChemiDoc Touch Imaging System with Image Lab Touch Software 9 Viewing Images with Image Lab After a gel is imaged the image appears in the Image Lab software workspace Many controls are available to optimize viewing and to analyze the image The following screen shot shows a gel image with band and lane detection as well as annotations The labels are overlays that you can display or hide There are many ways to view the data associated with the results You can view data as an analysis table a standard curve and a report Broad Range Dilution Read Only Broad Range Standards Dilution starting with 1ug Band Annotation
148. s by clicking Display Gel Options on the toolbar to access the appropriate settings Ga Display Gel Options M S Annotations Show Text and Arrow Annotations Lanes And Bands v Show Lane Frame V Show Lane Labels V Show Lanes V Show Molecular Weight Legend V Show Bands V Show Band Edges Band Attributes V Show Band Attributes Attribute Band No x Selected Lane Only All Lanes Volumes V Show Volumes V Show Volume Labels E Cc Cee Exporting Gel Images for Analysis To export an image for analysis Select File Export Export for Analysis This exports the raw data only as a 16 bit tif file Note 16 bit tif images are not compatible with all image viewers The image might require contrast adjustment when it is imported into analysis software This option creates a file that can be analyzed in other programs such as Quantity One FPQuest or InfoQuestFP software Exporting Gel Images to PulseNet International To export an image to PulseNet International gt Select File gt Export gt Export for PulseNet 200 ChemiDoc Touch Imaging System with Image Lab Touch Software Exporting Gel Images Image Lab reduces the image to an 8 bit tif image file Resolution is limited and file size is restricted to 300 Kb Exporting Lane and Band Tables to Excel If you have Excel or Numbers on a Mac installed on your computer you can export the data to the spreadsheet application
149. s to display in the report Show Lane Profile specify whether to display the Lane Profile view Print one lane per page specify whether all lanes are printed on one page or whether each lane is printed on a separate page adds a page break after each lane Show Lane Profile include the lane profile for each lane Not Displayed Displayed remove columns that you do not want to display in the report By default the report displays all columns from the Lane and Bands table 194 ChemiDoc Touch Imaging System with Image Lab Touch Software Report Volume Table Tab B Report Settings General Lane And Band Table Volume Table v Include Volume Table Not Displayed Displayed No Label Volume Int lt Type Abs Quant Adj Vol Int Mean Bkgd Int Rel Quant of Pixels gt Min Value Int Max Value Int Mean Value Int Std Dev Area mm2 o jJ ewe _ J The Volume Table tab includes the following settings Include Volume Table clear to exclude this information from a report NotDisplayed Displayed remove columns that you do not want to display in the report By default the report displays all columns from the Volume table Print Report amp Click the Print Report button to print the report Print Report to a PDF File ea The Print Report to pdf File button opens a Save dialog box so the PDF file can
150. screens the Settings menu and the Logout icon For more information about each icon in the toolbar see The Image Lab Touch Main Toolbar on page 34 Workspace displays a live view of the sample on the sample tray Sample tray displays a thumbnail image of the type of sample tray on the imaging bed User Guide 33 2 34 Image Lab Touch Software Overview m Tabs tap tabs to open dialog boxes where you specify the image acquisition settings Acquire Image tap the camera icon to take an image of the sample Zoomicons zoom in and out to focus on an area of the sample The Image Lab Touch Main Toolbar The following table describes the Image Lab Touch main toolbar Icon or Text KC Date and time Logout Description Live View display the sample in the sample tray in real time specify image settings and acquire images Gallery displays thumbnails of all acquired images On this screen you can view browse delete print or export images Date and Time displays the current date and time of the imaging system Go to Settings Set Date and Time to change this setting Settings displays system settings and provides access to software updates Help displays information about Image Lab Touch Screens Logout logs out of Image Lab Touch and returns to the Welcome screen ChemiDoc Touch Imaging System with Image Lab Touch Software About the Live Vie
151. ssword that allows or prohibits specific user actions There are three possible combinations of settings in the Security Preferences dialog box Here are explanations of how to choose the settings and why you will want to choose any of the three 1 To set preferences so that only users who are set up on a network domain can use Image Lab User Guide 119 7 Setting Up the Imager with Image Lab Software 2 120 In the Domain to be used in authentication field enter the name of your network domain See To find the name of your network domain on page 240 for instructions on how to determine this name Note The default domain name that will appear in this field is the domain on which the current user is logged in Do not select the Use local groups for establishing user security levels checkbox 2 gt Aw Security Preferences o V Enable secure mode Domain to be used in authentication GLOBAL Use local groups for establishing user security levels Cancel To set preferences so that only users who are domain users and who are also valid members of specific local groups can run Image Lab In the Domain to be used in authentication field enter the name of your network domain See To find the name of your network domain on page 240 for instructions on how to determine this name Note The default domain name that will appear in this field is the domain on which the current user is log
152. t a member of an Image Lab security group does not have permission in GLOBAL dcathey Admin User GLOBAL dcathey logged into Image Lab m Each filterable column has a Remove filters icon as well This icon removes the filter for that column only v Select filter values Secure Mode File Calibration Alert Image Tools Lane and Band Molecular Weight Annntatinn C e Remove filtering by this column n X Collapsing or Expanding Data Rows A You can expand the size of rows in any log to display the full content of the row or you can collapse the row size to display more rows in the table The icon toggles between collapse and expand 210 ChemiDoc Touch Imaging System with Image Lab Touch Software Exporting Logs To display the full content of a row Click the Collapse or expand rows icon to expand the row height The row adjusts to fit the text of the longest entry This action expands all rows in the log where an entry is longer than the width of the column Rows that do not need to wrap are not affected To display more rows in the table Click the Collapse or expand rows icon to collapse the row height to the default height setting This action collapses all rows in the log to display data on a single line Exporting Logs AGA From the log viewer you can Copy log entries to the clipboard copies the log entries to the c
153. t appears Tap OK to delete the selected images To delete an image in Image View 1 Do one of the following m f one image is open in Image View tap Delete m fmore than one image appears in Image View select the image you want to delete and tap Delete A prompt appears asking you to confirm the deletion Tap OK User Guide 85 4 Viewing Images with the ChemiDoc Touch Imager Viewing Image Information 86 The Image Info window provides information such as the image name the acquisition s exposure duration and date and the application type You can add other information about the image and change the name Name 2014 05 16 10hr 12min 47sec x Notes Acquisition Information Imager ChemiDoc Touch Exposure Time sec A Serial Number Software Version 9 0 Application Chemiluminescence Excitation Source No Illumination Emission Filter No Filter Binning 4x4 Image Information Acquisition Date Image Area mm Pixel Size um Data Range int To view information about the image gt In Image View tap Image Info The Image Info box appears ChemiDoc Touch Imaging System with Image Lab Touch Software Adding Notes about the Image Adding Notes about the Image To add information about the image 1 In Image View tap Image Info 2 Inthe Image Info window tap in the Notes box A keyboard appears 3 Type your information using the keyboard 4 Tap OK to save th
154. ta Results data associated with gel images can be viewed as an analysis table a lane profile a standard curve or in a report Different tools for viewing the results data are easily accessible from the main toolbar These tools are described in Chapter 9 Viewing Images with Image Lab The views display the analysis for the selected image All of the views can be displayed at the same time See Displaying Data on page 144 for details Display Toolbox The display toolbox at the top of every image enables you to display images in the most useful ways See Chapter 9 Viewing Images with Image Lab for a description of each option as E o 2 FE 2 E E t 2 ERI ao S S Os T N o 0 od o Gc 2 E ChemiDoc Touch Imaging System with Image Lab Touch Software Interface Overview Start Page The Start Page guides you through creating opening and viewing protocols and images Analysis Tool Box The Auto Analysis button quickly analyzes images The remaining tools customize the analyzed data User Guide 129 8 Image Lab Software Overview An image file must be selected to make analysis tools available Image Tools enables you to flip rotate and crop images and to transform the image files Lane and Bands enables you to resize adjust and bend lanes and to detect adjust add or delete bands 130 ChemiDoc Touch Imaging System with Image Lab Touch Software Interface Overview Normalization ena
155. tensity and random intensity fluctuations It is the number of pixels in a vertical column that are taken together to determine whether a band is present The Size Scale parameter uses the size of objects in the image to determine the nature of those objects If a gel image has high levels of background noise a larger size scale is appropriate At low noise levels a smaller value is preferable You can also increase the size scale if the gel has only a small number of thick bands scanned at high resolution Noise Filter minimizes the number of small fluctuations or noise in the image that are called bands while still recognizing larger features the real bands This filter becomes especially important at higher sensitivity levels The noise filter value refers to the size of the filter in pixels for example a value of 2 50 equals a filter size of 2 50 x 2 50 pixels Features smaller than the filter size will not be recognized as bands Entering a noise filter size of zero turns it off completely If band detection identifies doublets as single bands decrease the noise filter setting and or increase the sensitivity level Tip You can also decrease the Size Scale parameter instead of the noise filter to improve the detection of closely spaced bands However if you decrease both the noise filter and the size scale the fuzziness around bands might be mistakenly detected as separate bands ChemiDoc Touch Imaging System with Image La
156. the All Lanes and Single Lane tools gt Click the lane tool first then click the lane to which you want to apply the change All Lanes Tools You can modify all the lanes in your image using these tools Resize resizes the lanes in your image Click Resize and then drag the handles of the red squares to resize all lanes Adjust adjusts the orientation of all lanes Click Adjust and then drag a single corner of the lane frame The Adjust All Lanes tool does not resize lane width You can add anchor points to the top or bottom borders of the rectangle by clicking the lane frame Remove any unneeded anchor point by right clicking it By dragging these additional anchor points you can adjust for smiling gels Note You can move the entire lane frame when resizing or adjusting the lanes Click Resize or Adjust and make the changes to your lanes Then click anywhere in the frame and move it to the desired location Tip On the PC you can press the Shift key or the Ctrl key and use the arrow keys on your keypad to move the lane frame On a Mac press the Shift or the Command key and use the arrow keys Delete deletes all lanes 162 ChemiDoc Touch Imaging System with Image Lab Touch Software Lane and Bands Tools Width changes the width of all lanes at the same time Click Width and then drag one of the anchor points on any lane to change the width of all lanes Tip You can use the plus key on your
157. the persons who are responsible for the content of electronic records that are on the system Section 11 3 b 4 Note Image Lab Security Edition is not supported on the Mac x The ChemiDoc Touch imaging system does not support the acquisition of images in secure mode and any reference to the creation of secure documents does not apply However an image acquired on ChemiDoc Touch and exported to Image Lab can be opened in secure mode and signed For more information on this feature see Unsecured Documents on page 221 and Signing Documents on page 224 For information about the logs that document these actions see Document Logs on page 225 m The security controls built into Image Lab Security Edition must be properly configured and administered by the system administrator s in your organization in order to be secure and in compliance with 21 CFR Part 11 Bio Rad makes no claim that Image Lab Security Edition software is CFR compliant in and of itself nor does the company guarantee User Guide 215 14 Using the Security Edition compliance for the user Your organization must establish policies and standard operating procedures that work in conjunction with the tools provided by Bio Rad to ensure compliance with 21 CFR Part 11 Standard Mode versus Secure Mode Image Lab Security Edition can be run in either of the following modes Standard Mode in this mode there are no restrictions on controlling the instru
158. tically moves out of its position in front of the camera lens 20 ChemiDoc Touch Imaging System with Image Lab Touch Software Optional Accessories Optional Accessories See Appendix D Ordering Information for a list of optional accessories and replacement parts Printer An optional USB printer the Mitsubishi thermal printer cat 14170 8089 is available from Bio Rad for use with the ChemiDoc Touch imaging system Sample Trays White Tray The optional White Tray cat 1170 8372 is a phosphor screen that produces white light transillumination Blue Tray The optional Blue Tray cat 170 8373 is a UV to blue light conversion screen that lets you visualize DNA samples while protecting them from UV damage User Guide 21 1 Supported Tray Types 22 Introduction The ChemiDoc Touch imager can be used with the Chemi UV Stain Free white and blue trays Table 1 shows which applications are supported with each tray type Table 1 Supported applications with each tray type Chemi UV Stain Free cat 4170 8374 White cat 4170 8372 Blue cat 41170 8373 Supported Applications Alexa Fluor 488 a Chemiluminescence Colorimetric Blots LI Coomassie Fluor Orange Cy2 DyLight 488 Ethidium bromide EtBr Flamingo Fluorescent Gel Stain Fluorescein GelGreen GelRed Coomassie Blue stain Cooper stain Fast Blast DNA Stain Alexa Fluor 488 Cy2 DyLight 488 Ethidium bromide
159. ting estimate the shortest and the longest exposure times you think will achieve the optimal image Decide on the total number of images to be taken within this time range For example assume you want to take four images You specify the minimum exposure time as 60 seconds the maximum as 240 seconds The first image is taken at 60 seconds the last image is taken at 240 seconds and the remaining two images are taken at even intervals in between at 120 and 180 seconds SAM is useful for determining the optimal imaging time for a chemiluminescent sample However SAM produces data that are not as accurate as data from a single image Signal near the intensity of background noise becomes increasingly masked with each successive image After you have used SAM and determined the optimal exposure time acquire the image again as a single image using this optimal exposure to identify very faint signals in the image User Guide 61 3 Acquiring an Image Configuring Signal Accumulation Mode To configure signal accumulation mode 1 InLive View tap EXPOSURE 2 Tap Manual Then tap Configure Signal Accumulation Mode 3 Enter the exposure times in seconds in the First Image and Last Image text boxes Tip Allow a minimum of 60 seconds to acquire each image Therefore if you specify three images to be acquired see step 4 then specify a minimum of 60 seconds exposure time for First Image and a minimum of 180 seconds for Last Image set
160. tion icon into the Applications folder Follow the instructions in the next section to connect your system Installing the Drivers on Windows 7 If you are running Windows 7 the device driver is installed during the Image Lab installation process After successful installation you see a message similar to the following a GS900 NX Device driver software installed successfully Note During the installation process you might see a warning similar to the following You can ignore this warning because it appears even when the driver has been installed correctly Device driver software was not successfully installed Generic USB Hub of Ready to use USB Input Device of Ready to use Unidentified Device Device unplugged USB 2 0 Camera Ready to use What can I do if my device did not install properly 108 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Security Edition Setting Up Image Lab Security Edition Activating and Deactivating Security Edition m Before you activate or deactivate Image Lab Security Edition close any open document files m After you change the active status of the Security Edition you must restart Image Lab Activate the Image Lab Security Edition 1 Double click the Image Lab icon on your desktop to open Image Lab The License Code field is populated with the 18 digit license code that you entered when you installed Image Lab The Securi
161. tivity options are as follows Low Band Detection Sensitivity sets detection at a low level for images with prominent bands Faint bands are not detected with this setting High Band Detection Sensitivity sets detection at a higher level for images that are faint Extraneous bands can be removed using the Band Tools in the Analysis Tool Box See Lane and Bands Tools on page 161 Custom enables you to set a value between 1 and 100 to select the best detection sensitivity for your sample You can also drag the sliding bar left or right to set the value When Low Band Detection Sensitivity is used the numerical value is set at 25 when High Band Detection Sensitivity is used the value is set at 75 Molecular Weight Analysis Settings Molecular Weight Standard choose any of the many Bio Rad standards or another standard you added to your standards list Standard Lanes choose or change the lanes in which the standards are placed 156 ChemiDoc Touch Imaging System with Image Lab Touch Software Analysis Tool Box Tools Regression Method four regression methods are available Regression Calculation Methods on page 235 Analysis Tool Box Tools All Analysis Tool Box tools customize the analyzed data in image files These tools are available only when an image file is open Click a specific image to select among the many windows that might be open in your workspace Note Some tools delete the existing analysis
162. to access links to related topics Tap the X in the upper right corner to close the help screen Access additional help topics by tapping Help Topics at the bottom of the screen Entering Onscreen Text Text boxes let you enter or edit text with a touch screen keyboard or keypad Tap in the box and the appropriate input device appears Alternatively you can use a USB keyboard User Guide 39 2 Image Lab Touch Software Overview Using the Keypad Fig 1 Touch screen keypad Tips for using the keypad m Tapthe text box to display the range of valid values below the box m The software does not allow you to enter an invalid number Therefore if you tap a number and it does not appear on the screen verify that the number you are attempting to enter falls within the range of valid values If you tap Done and the box turns red then the number is invalid m Some properties are set by entering data in multiple text boxes Tap the next text box when you are done with the first All edits in the first text box are preserved You do not have to tap Done to move to the next box Tap Done or tap anywhere on the screen to close the keypad 40 ChemiDoc Touch Imaging System with Image Lab Touch Software Using the Keyboard Tap in a text box to display the CEL Entering Onscreen Text keyboard oaaoaaag fis Pe Re JE Es te PEE Ue EI Epp goo ly e
163. trative Tools 2 Select Computer Management 3 Inthe Computer Management window expand the System Tools folder and then expand the Local Users and Groups folder Computer Management l lok File Action View Help 9 46 os 8h Computer Management Name Full Name Description Actions 4d System Tools Administr Built in account for admini Users a Task Scheduler b i S bradmin 8j Event Viewer More Actions gt f brguest Built in account for guest a 8 Shared Folders 4 Local Users and G Users E Groups Performance amp Device Manager 4 amp Storage f Disk Management 5 Services and Applicat 4 rr D 240 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Users and Groups To create a new user on a local computer 1 Click on the Users folder to open it and select Action New User Alternatively use the right click context menu The New User dialog box appears New User 9 ie User name Full name Description Password Confirm password v User must change password at next logon s d never expires Accountis disabled Help t Close 2 Fill out all the fields User name the user name must be unique Full name the full name must be unique Bio Rad recommends using the user s actual full name as this name will be shown in the document log and all the l
164. tribution histogram shows the total data range in the image and the amount of data at each point in the range Tap Auto to return to the default setting The lightest part of the image is set to the minimum intensity and the darkest is set to the maximum m The High indicator determines which intensity value is shown at the maximum value of the gray scale in the gel image The Low indicator determines which intensity value is shown at the minimum value of the gray scale in the gel image m The Gamma indicator changes the grayscale curve A value of 1 is linear A value 1 redistributes a greater proportion of the gray scale to the first half of the intensity values A value 1 redistributes a greater proportion of the gray scale to the second half of the intensity values 76 ChemiDoc Touch Imaging System with Image Lab Touch Software Adjusting How Images Are Displayed To change the histogram scale m Clear the Log Histogram box to choose the linear scale m Tapthe box to choose the logarithmic scale Linear L 2123 50057 a histogram os Histogram Q FJ invert image display 5 gc a A Bl Highiight saturated pixels a Low High Logarithmic x histogram iios istosram a invert image display k a i Le Bill Highlight saturated pixels Tip The logarithmic histogram can reveal the presence of intensity values that are otherwise obscured In images with a large background area the intensity v
165. ts User Guide 153 9 Viewing Images with Image Lab 154 ChemiDoc Touch Imaging System with Image Lab Touch Software 10 Analyzing Images Analysis Tool Box tools are enabled when an image file is opened and in focus An active or in focus window has a darker blue menu bar on a Windows PC On a Macintosh the window control icons display more brightly when a window is active This distinction helps you to identify the active window among many open image files in your workspace Using Auto Analysis Auto analysis detects the lanes and bands and optionally calculates the molecular weight of the bands in your image Click Auto Analysis in the Analysis Tool Box to do the following Analyze images obtained with protocols that did not include steps for auto detection and analysis Change your analysis parameters to reanalyze your images Note If you change any settings for an analyzed gel the initial analysis is overwritten To preserve both analyses save each image file with a different name User Guide 155 10 Analyzing Images Auto Detection Settings 1 Auto Analysis Broad Range Dilution Read Only Detection Settings Band Detection Sensitivity Low Better for more prominent bands High Better for Faint bands Custom Sensitivity C Molecular Weight Analysis Settings Mol Wt Standard Bio Rad Precision Plus Change Standard Lanes First last The band detection sensi
166. twork or IT administrator You must be assigned the correct role within Image Lab to enable or disable secure mode For more information see Setting Up Image Lab Security Edition on page 109 If you are not licensed to install the Security Edition but choose to install it you will be prompted for a license key when you start Image Lab Click Next ChemiDoc Touch Imaging System with Image Lab Touch Software Installing Image Lab Software A screen appears requesting your license code Note Your 18 digit license code can be found in the Image Lab product folder pocket P J Image Lab 5 0 InstallShield Wizard s Database Folder Image Lab Security Edition requires a License Code Software Enter your Security Edition License Code to continue InstallShield eee Joe ee Enter the 18 digit code in the three text boxes The software verifies the code Tip If you do not know or do not have access to the code contact your Bio Rad customer service representative Note Until you provide a license code Image Lab will function only in standard mode Click Next On the Install Location screen accept the default location or click Change and browse to another folder Click Next User Guide 105 7 Setting Up the Imager with Image Lab Software 10 On the Ready to Install the Program screen click Install Image Lab 5 0 InstallShie Image Lab The wiza
167. ty Edition Activation dialog box appears r gt LL Security Edition Activation m Your copy of Image Lab Security Edition is not currently activated You will need the license code that was sent to you with the software License Code 324100 000064 111111 Activate Via 9 Internet Create Activation Email Receive Activation Email eae Gm E You can activate the Security Edition automatically via the Internet or you can activate it manually by creating an activation email User Guide 109 7 Setting Up the Imager with Image Lab Software To activate the Security Edition via the Internet 1 Select Activate Via Internet E n i Security Edition Activation Your copy of Image Lab Security Edition is not currently activated You will need the license code that was sent to you with the software License Code 324100 000064 111111 Activate Via Q9 Internet Create Activation Email Receive Activation Email Activate Cancel 2 Click Activate Within about 30 seconds you will receive a confirmation that your Image Lab Security Edition has been activated 4 Image Lab i Activation was successful To activate the Security Edition via email 1 Double click the Image Lab icon on your desktop to open Image Lab The Security Edition Activation dialog box appears The License Code
168. uch imager This instrument is suitable for research use only Therefore it must be used only by specialized personnel who know the health risks associated with the reagents that are normally used with this instrument WARNING The imaging of some applications involves UV illumination This instrument should be used only by trained personnel who know the health risks associated with the UV radiation normally associated with this instrument Users should be trained on the appropriate personal protection gear for working with UV light to minimize UV exposure To perform band excision using the Chemi UV Stain Free tray the transilluminator drawer is pulled out with the UV source enabled This exposes the user to UV radiation which can cause permanent damage to the eyes and skin In its lowered position the instrument s acrylic shield provides UV protection However in its raised position it does not provide complete protection to the user and it does not protect others who are standing in the area around the imager To protect users and bystanders these procedures must be followed m Protect all skin surfaces including the neck ears and hands Before performing band excision the user and anyone near the imager must put on protective gear including UV protective safety glasses a face shield lab coat and gloves A typical and reasonable expectation of use is three operations per user a day for three minutes each User Guide 11
169. urces of UV radiation which can Important Before you excise bands on a Chemi UV Stain Free tray you must always install the UV shield User Guide 89 5 Excising Bands To install the UV shield 1 Place a UV tray on the transilluminator drawer 2 Hold the UV shield by diagonal corners so you can guide it accurately 90 ChemiDoc Touch Imaging System with Image Lab Touch Software 3 Excising Bands from Samples Insert the two locking tabs that extend from the front of the UV shield into the two transilluminator drawer slots UV shield locking tabs Transilluminator drawer slots User Guide 91 5 Excising Bands 4 Ensure that the two wedges on the front of the UV shield snap into position on the transilluminator handle UV shield wedge 92 ChemiDoc Touch Imaging System with Image Lab Touch Software Excising Bands from Samples To excise bands on a Chemi UV Stain Free tray The UV lights turn off after 15 minutes of continuous use To turn the UV lights back on tap Turn Transilluminator On Important Before you begin put on the required protective gear and be sure that the UV shield is installed 1 Place a gel sample in the center of the tray 2 With Live View onscreen tap Turn Transilluminator On Turn Transilluminator On changes from green to blue and the UV lights turn on illuminating the gel Note The UV lights turn on only when both the sample tray and the UV shiel
170. v User must change password at next logon Use Passwo annot change password never expires Accountis disabled Help Create Close 244 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting Up Image Lab Users and Groups Fill out all the fields User name The user name must be unique Full name The full name must be unique Bio Rad recommends using the user s actual full name as this name will be shown in the document log and all the log reports This is a requirement of 21 CFR 11 50a Description This field must also be filled out Bio Rad recommends that you enter the user s title as the description Password Enter and confirm a password for the user Tip Select the User must change password at next logon checkbox This prevents the Windows system administrator from knowing the users passwords Note If you select the User must change password at next logon checkbox the user must actually log on to Windows and change their password before using Image Lab Security Edition Otherwise Security Edition will not recognize the user User Guide 245 C Setting Up Users and Groups To create a new group on a Windows server 1 With the Users folder open select Action New Group Alternatively you can use the right click menu You see the New Object Group dialog box e Create in genetics bio 1ad com Users Group name Group name pre Windo
171. ve A Abs Quantity Standard Curve Volume St gt Jj Note Clicking the Standard Curve table generates a crosshair tool that displays the numerical values associated with the placement of the cursor in the graph ChemiDoc Touch Imaging System with Image Lab Touch Software Annotation Tools Annotation Tools EJ You can annotate results with text and arrows to emphasize areas of interest Transparent v 90 Left r 90 Right User Guide 181 10 Analyzing Images Add Annotations m Text enables you to add text annotations to images to emphasize important details Click Text then click an area on the image where you want to insert your comment A box appears with a dotted line border Type your comment in the box Tip To add a new line to the box place your cursor where you want the break and press Shift Enter To move the box gt Click and drag the box to change its position Arrow enables you to add arrows to images to emphasize important details Click where you want the arrow to start and drag to stretch the arrow point to the location you want to emphasize To move the arrow on the image click the middle of the arrow and drag it to the new position To change where the arrow points gt Click either end of the arrow Square boxes appear Drag a box to change the length or orientation of the arrow Alignment The alignment buttons enable you to align multiple annotations such as lane
172. ve value for your adjusted volume in the analysis table If this happens select a new background region with less intensity than your data object User Guide 187 10 Analyzing Images Relative Volume Quantity You can choose any one volume as a reference volume by selecting the Reference Volume checkbox in the Volume Properties dialog box The reference volume is indicated by an asterisk on the volume label for example U1 Relative quantities are displayed in the Relative Quantity column in the analysis table Volume Table tab The relative quantity is the ratio of the background adjusted volume divided by the background adjusted reference volume All other volumes now display numerical values relative to your reference volume Values higher than 1 00 indicate that the volume is greater than the reference volume Values lower than 1 00 indicate the volume is less than the reference volume Absolute Volume Quantity If you have drawn your volume around an object of known quantity you can use it to calculate the quantity of your unknown volumes The quantities of your unknown volumes are calculated based on the standard volumes and the selected regression method To classify a particular volume as a standard 1 Double click the volume This opens the Volume Properties dialog box 2 Select the Standard option button and enter the quantity in the Quantity box 3 Click OK to close the dialog box Standard volumes will have th
173. w Screen Using the Tabs IMAGE SIZE APPLICATION and EXPOSURE tabs are used to specify the image settings Tapping a tab opens a dialog box For example when you tap the IMAGE SIZE tab this dialog box appears Close Choose image size Blue border indicates current selection LIT EE Small Blots 4 Images from 5 W 9 5xL7 6cm EXPOSURE Chemiluminescent Selection is indicated on the tab Note the following m A blue border indicates the current selection m Tabs always display the current settings In the example screen the image size Small and image dimensions W 9 5 x L 7 6 cm appear below the tab Similarly the selected application and exposure settings appear below the APPLICATION and EXPOSURE tabs m Forinformation on entering text using the on screen keypad or keyboard see Entering Onscreen Text on page 39 m To close the dialog box tap the X in the dialog box or tap anywhere on the screen User Guide 35 2 Image Lab Touch Software Overview About the Image View Screen Image View displays acquired images in the following situations m When you acquire an image in Live View the image appears in Image View Inthe Gallery when you double tap a thumbnail of an acquired image the full size image appears in Image View You can fine tune the image display view information about the image delete the image or save it to a USB flash drive or network drive
174. w of the table User Guide 145 9 146 Viewing Images with Image Lab Hu Per Measurement Precision set the precision decimal places for the measurements in the Lane and Band table and the Volume table o Example shows an example of how measurements will display with the selected measurement and precision settings m Export enables you to choose how to export the analysis data The following settings appear on the Export tab o Export formatting select checkboxes to include lane headers Lane and Band table tab only and or column headers in the exported file o Export delimiter select a delimiter option for the exported file Comma delimited Tab delimited Use other delimiter user defined Change Analysis Table Orientation This button toggles between two table orientations Horizontal displays the lanes volumes beside each other so you can scroll through the table from left to right Vertical displays the lanes volumes on top of each other so you can scroll through the table from top to bottom Copy Analysis Table to the Clipboard i Copies the table data to the clipboard so that you can paste the data into word processing or presentation applications Tip It is best to use the vertical table orientation when copying to an8 5 x 11 inch page to give the columns enough room to display Export Analysis Table to a File i Exports the table data as a CSV file so you can op
175. wer sits above the power plug Fuse drawer im 232 ChemiDoc Touch Imaging System with Image Lab Touch Software Replacing the Fuses 2 Insert the tip of a screwdriver as far as it will go under the center of the fuse drawer im 3 Using the screwdriver tug hard to open the fuse drawer User Guide 233 A Maintaining the Imaging System 4 Remove the drawer from the power module 5 Remove the fuses from the drawer and inspect them to determine if they need to be replaced 6 Snapthe new fuses in place 7 Pushthe fuse drawer in until it snaps into place 234 ChemiDoc Touch Imaging System with Image Lab Touch Software B Regression Calculation Methods Each regression method calculates a standard curve Some of the methods provide the formula for the standard curve In this case the molecular weight can be calculated by x relative front of the band of interest y molecular weight of the band of interest Linear semilog The linear equation is y a bx where a is the intercept and b is the slope of the line Note The linear equation is calculated on the log of the molecular weight values The R value can be used to determine the overall quality of the linear fit A linear regression with an R2 value of gt 0 99 is considered a very good fit The primary advantage of this method is that it is extremely simple The primary disadvantage is that it will deliver incorrect results i
176. ws 2000 Group scope Group type C Domain local Security Global C Distribution c Eu pem 2 Inthe Group name field enter one of the group names specified in Table 3 on page 218 TDS Administrator TDS User TDS Tech TDS Guest Type the name exactly as specified You can also enter a description for the group in the Description field Note The group does not need to have any special operating system level privileges To add a user to a group on a Windows server 1 In the New Group dialog box click Add Alternatively double click an existing group in the User Manager folder to open its Properties dialog box and click Add You see the Select Users dialog box 246 ChemiDoc Touch Imaging System with Image Lab Touch Software 2 Click Advanced to expand the dialog box Setting Up Image Lab Users and Groups Search results Name RDN amp Administrator E ANONYMOUS LOG Bl Authenticated Users Bi BATCH 8 bradmin B brguest B CONSOLE LOGON BI CREATOR GROUP BI CREATOR OWNER B DIALUP A Evervane In Folder LSG07002045 LSG07002045 LSG07002045 Ok Cancel Select Users D Lo Selectthis objecttype Users or Built in security principals Object Types From this location LSG07002045 Locations Common Queries Starts with v els Starts wih v Find Now top PF n In the expanded dialog box click Find Now to populate the bottom field with all the users
177. x and up to three lines of text in the lower box Tap OK to save the changes 42 ChemiDoc Touch Imaging System with Image Lab Touch Software Setting the Sound Volume Setting the Sound Volume You can set the volume of the system sound or you can turn the sound off To set the sound volume 1 Tap Settings te Then tap Set Sound Volume 2 Tapa volume level 3 Tap X to close the dialog box User Guide 43 2 Image Lab Touch Software Overview 44 ChemiDoc Touch Imaging System with Image Lab Touch Software 3 Acquiring an Image This chapter describes the steps to acquire an image It is organized around the following workflows m Workflow for Acquiring a Chemiluminescent Image page 48 m Workflow for Acquiring Gel and Blot Images page 64 Note The chapter gives specific attention to chemiluminescent blots It addresses how to specify the area of focus to shorten the exposure time required and how to use the different exposure options to get the result you want User Guide 45 3 Acquiring an Image About Sample Trays Each application must be used with a specific sample tray The ChemiDoc Touch imaging system supports the following sample trays Table 2 Sample Trays Tray Icon Chemi UV Stain Free tray White tray Blue tray L1 For information on the applications to use with these trays see Supported Tray Types on page 22 On the Live View screen the toolbar displays the icon for the

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