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Odyssey Infrared Imaging System Operator`s Manual v 2.1

1. oe andGroup Confirm Intent to Shutdown the e Change Password Instrument Manage Groups e Manage User Accounts L Shutdown Now Instrument Utilities e Instrument Status e Delete Preset Click Shutdown Now to lO Shutdown the Instrument confirm that you want to e Networking Setup shut down the instrument Set System Time e Scan Test Pattern Editing Network Addresses Network connections and cabling for both Odyssey and the system computer are discussed in the Odyssey Installation Manual Before connecting to your local network consult with your network admin istrator on how to fill out the Network Setup page A brief description of how Odyssey uses each field is given below Network Configuration Netscape File Edit View Go Communicator Help Odyssey gy Home Gp Scan Network Setup 4 View Account and Group Utilities e Change Password Manage Groups e Manage User Accounts Instrument Utilities e Instrument Status Delete Preset e Shutdown the Instrument iO Networking Setup Set System Time Scan Test Pattern The Network Setup link e Update Scanner is found on the Utilities Software page Diagnostic Utilities User Diagnostics e Technician Diagnostics View System Log e View Scan Log e Browser Test Note For stand alone non network configurations the IP Address and Net Mask can be entered from the Odyssey front panel as describ
2. Crop Image Select two sets of coordinates to crop the image Set 1 Selected Set 2 Selected Reset Image 3 View Scan Netscape Eile Edit View Go Communicator Help Odyssey gy Home Gp Scan Crop Image Select two sets of coordinates to crop the image Set 1 Selected Set 2 Selected To display the entire image again click the Reset Image button 66 CHAPTER 7 Importing and Editing Scanned Images Changing Image Sensitivity When an image is first opened the bands or dots may appear too strong too weak or may not appear at all The appearance of the image can be changed by clicking Adjust in the toolbar and changing the sensitivity 3 View Scan Netscape iof x Eile Edit View Go Communicator Help te 3 ateaeast amp Back Foward Reload Home Search Netscape Print Security Stop 7 wt Bookmarks amp Location http 195 44 23 174 scanapp imaging nonjava index z EE What s Related j TE SurfSaver amp Instant Message E WebMail Contact E People E Yellow Pages Download Chant Odyssey fa Home D Vi Utilities ep open save zoom crop flip invert info El P amp ta a doo del a e Adjust Sensitivity Sensitivity 700 Sensitivity 800 Adjust The sensitivity settings change how the wide range of data values in the image are mapped to the comparatively small number of color or grayscale values on the displa
3. Change Password Status IO Manage Groups e Manage User Accounts Group Name O AddGroup Instrument Utilities e Instrument Status e Delete Preset jim Permissions Remove Scans Shutdown the public Permission Remove Scans Instrument Panra 3 Use the Permission Level drop down list next to the user name to change access permission of the user Odyssey Control Level Administration Netscape D x File Edit wiew Go Communicator Help Odyssey gy Home QP Scan lt d View Utilities PD Help Account and Group Selected Group MyGroup Utilities e Change Password User Name Permission Level e Manage Groups eae None E e Manage User Accounts jim Instrument Utilities e Instrument Status Delete Preset Shutdown the Change Cancel Instrument mike A permission level of None indicates no access Users with permission level of None will not see the indicated group when selecting a group for new scans or while opening scans Access permission level allows users to open completed scans but not change them Change permission allows users to start new scans and store them in the scan group as well as to edit any scans in the scan group Change permission also allows you to let other users access a scan group by changing their access permission 50 CHAPTER 5 User and Scan Group Administ
4. C4 SutSaver Rinstant Message E WebMail E Contact E People E YellowPages E Download C4 Chan Odyssey gy Home Gp Scan View Utilities C2 Help The View toolbar has Cren asrar buttons for opening and saving scans as well as image editing Group public z a All files stored on the Odyssey Imager are separated into scan groups Each user has their own scan group in which new scans are stored There is also a public scan group available to all users that is most 63 commonly used to store scans started from the Odyssey front panel Each user has the ability to let other users access their scan group Chapter 5 The Group drop down list shows all scan groups that are available to the user who is logged in 2 Use the Scan drop down list to select one of the scans in the designated scan group 3 Click Open to open the image file s View Scan Netscape iof xi Fie Edit View Go Communicator Help 3 3 a A s amp FH Back Foward Reload Home Search Netscape Print Security Stop z wt Bookmarks 4 Location http 7 1 95 44 23 174 scanapp imaging nonjava index z E What s Related ca SurfSaver amp Instant Message E WebMail E Contact People E Yellow Pages Download t Chani O dyssey fal Home Gp Scan lt View Utilities E Help Open a Scan Group public z Scan MEEA Z Open Images are initially displayed in the right side of the window at actual si
5. Scan Layers 700 channel W 800 channel 7 oo View on 71 Displaying Scan Information To display information about the scan click Info in the View toolbar Chapter 6 describes how the Auto Update On Off button Scan Console button and Progress bar are used during scans 35 View Scan Netscape ioj x File Edit View Go Communicator Help Odyssey fal Home 4 View Utilities E Help Scan Information Scan Name fp3016116 Group Name 6116 Dimensions 296x21 File Size 0 01 MB Channel More Information Auto Update Image Off On Off Time Left 00 00 00 Progress 100 oil Jo w SP fal 4 Z The More Information button shows complete information about a completed scan or a scan still in progress All scan parameters are displayed including resolution quality intensity scan size focus point comments and the image channels scanned 700 or 800 72 CHAPTER 7 Importing and Editing Scanned Images Saving Changes to Images After images are open they can be saved to a local storage drive by clicking Save in the View toolbar and clicking the save buttons for the images that you want to save If you also want to save the log file for the scan click Save Scan Log View Scan Netscape Of x Eile Edit View Go Communicator Help gt 3 4a asas E Back Foward Reload Home Search Netscape Print Security Stop 3 wt 7 Bookmarks 4 Location i http 19
6. Confirm request to remove User Account jsmith Remove User Account Cancel Note The last Administrator account cannot be deleted An error message will be displayed if you attempt to delete the last Administrator account 47 Deleting the Original Admin Account If you are concerned about security you may want to create a new Administrator account and delete the account named admin that was shipped with Odyssey This will prevent unauthorized access Creating and Changing Groups Initially users have access to their own scan group and the public scan group Additional scan groups can be created for special purposes For example if several people are all doing scans for a particular research project it might be useful to keep all of the scans for a project in one scan group Important The Odyssey Imager should not be used for permanent file storage When the hard drive is full the oldest scan will be automatically deleted to make room for new scans See Chapter 3 for scan size examples Creating a New Scan Group 1 Click the Manage Groups link on the Utilities page Odyssey Administration Level Selection Page Netscape Eile Edit View Go Communicator Help Odyssey gy Home QP Scan lt 2 View Utilities C2 Help Account and Group Utilities Change Password Manage Groups Manage User Accounts Instrument Utilities Instrument Status Delete Preset 48 CHAPTER 5 User and
7. Instrument Utilities e Instrument Status e Delete Preset Instrument e Networking Setup Conunents Set System Time Email Complete Session e Scan Test Pattern e Update Scanner Download Complete Session Transfer Options odyssey tech licor c 2 P e Shutdown the Reply Back To Your Return Email Address m Download Software Diagnostic Utilities Id User Diagnostics TE Technician Diagnostics View System Log e View Scan Log Browser Test Diagnostic Results Motor Control Card PASSED Signals Board PASSED System Resources PASSED 85 86 CHAPTER 8 Instrument Utilities and Diagnostics At the end of the diagnostic summary results are given at the bottom of the page for the Motor Control Card Signals Board and System Resources All of these results should indicate PASSED If any of these results indicate FAILED contact LI COR Technical Support 1 800 645 4260 or your local LI COR Distributor A variety of tests are performed during the User Diagnostic Most of these tests are meaningful only to LI COR Technical Support staff so only summary results are displayed LI COR or your Distributor may ask for a copy of the complete test results The test results can be transferred to a file by clicking the Download button The file can then be transferred to LI COR via mail or as an e mail attachment If you have a gateway address and DNS server address specifi
8. could differ each time the Odyssey Imager is powered on To use a host name enter the host name assigned by your network administrator in the Host Name field Enter the domain name in the Domain field and enter the IP address of the domain name server s that will be used to resolve the host name in the Domain Name Servers field If there is more than one domain name server enter only one address per line in the field Entering a Gateway Address In the Gateway field enter the address of the router that connects your subnet to the rest of the network A gateway address and Domain Name Server must be specified to enable direct e mail of scan logs and system logs for troubleshooting 79 Setting Date and Time All scan files stored on the Odyssey hard disk have a date time stamp that identifies when the files were created The Set System Time link on the Utilities page is used to set the clock in Odyssey A backup battery maintains the clock when power is disconnected so it is generally only necessary to set the clock when Odyssey is first installed File Edit View Go Communicator Help te 3 4 2 sts amp Back Forward Reload Home Search Netscape Print Security Stop 3 WA Bookmarks 4 Location http argus7 licor com scanapp admin admin time pl g E What s Related C4 SufSaver Instant Message E WebMail E Contact E People E YellowPages El Download C4 Chani Odyssey fal Home ae Scan 42 View Utilities C 2 Help Se
9. Diagnostic Utilities e User Diagnostics Technician Diagnostics View System Log View Scan Log Browser Test 5 Click the Add Account link Odyssey Administration Level Administration Netscape The Manage User Accounts page displays a list of all current accounts Using this page accounts can be added deleted or changed com scanapp admin admin ini geUserccounts Odyssey ey Home Scan 42 View Utilities Account and Group Sheep Utilities e Change Password Add Account Manage Groups Chafige Account Rights ia Manage User Accounts l Password Instrument Utilities previ Password Instrument Status i Password gt Delete Preset e Shutdown the Instrument gt Networking Setup Odyssey Administration Level Administration Netscape A a wy d Stop 195 44 23 174 scanapp admff admin index action Add amp ccount Ea confor E Pepe E 3 G Home Sp Scan 4 amp 2 View Utilities E Help E assword Password Set Account Rights Set User Name and Password None e Manage Groups Browse Manage User Accounts Control Z C Administrator C Technician WARNING For service use only e Netawarkine Sehin 6 Set the Account Rights for the new user according to the following definitions e None When account rights are set to
10. Indoor use only operating temperature 15 35 C and dew point not greater than 20 C non condensing altitude not to exceed 2000m Environmental Conditions Pollution Degree 1 Fuse Ratings Fuses are non user replaceable A 5A fast blow fuse protects the Digital Signal Processor DSP Power Requirements Switched voltage selection between 100 127 VAC and 200 240 VAC voltage fluctuations not to exceed 10 of the nominal voltage 47 63 Hz 1 1 A at 120V typical 2 25A at 120V maximum 270W Insulation Category II Dimensions 37H x 53W x 58D cm 14 5 x 21 x 23 inches Weight 33 kg 72 Ib Data Storage Capacity gt 25 GB Network Protocol TCP IP Network Connection Cat 5 RJ 45 10Base T 100Base TX 2 CHAPTER 9 Appendices Error Messages The following error messages may be encountered when using the Odyssey browser interface Scan Setup Error Message Do not use illegal character for this name It is a reserved character Description Allowable characters are underscores dashes periods and alphanumeric characters including spaces Error Message The scan dimensions must be in cm Description The user entered a dimension that is not an integer Error Message Enter a name for the scan Description The name field for the scan is blank Error Message Select or enter a name for the group the scan belongs to Description The group field is blank Error Message The focus values must be between 0 0 a
11. None the user account becomes inactive and the user cannot access data or start scans 40 CHAPTER 5 User and Scan Group Administration 7 8 9 Browse A user with Browse rights can access data in a read only capacity Browse rights do not permit a user to start new scans but scans can be viewed manipulated or downloaded Control Most users are given Control rights which consist of Browse rights plus the ability to start new scans Administrator Users with Administrator rights have Control rights plus complete access to all Administrator level pages Administrator rights should be restricted to as few qualified individuals as is practical Technician Technician rights are only used by LI COR or LI COR Distributors in order to perform instrument diagnostic functions Technician rights are not needed for any user operation or maintenance functions Improper use of technician functions can render the Odyssey Imager inoperable Enter the new user name case sensitive in the User Name field User names and passwords can be 1 to 32 characters long Alphabetic or numeric characters as well as spaces dashes and underscores are acceptable Avoid all other characters Type the password for the new user in the Password field Type the password again in the Confirm field for verification Click Create User Account 10 Go back to the Manage User Accounts page and verify that the new account is in the account lis
12. Safety Interlocks The Odyssey Infrared Imager has two safety interlocks that prevent access to the laser when the instrument lid is opened during operation Do not attempt to defeat these interlocks The interlocks are located on the front of the instrument bezel as shown below Audible tones sound when the lid is opened and closed Figure 1 3 Chemical Safety LI COR recommends that all biochemicals be handled carefully and that safe laboratory procedures be followed at all times Be aware of the hazards associated with any chemical before you begin work The Odyssey Imager should not be used with any radioactive materials Placement in the Laboratory The Odyssey Infrared Imaging System weighs approximately 31 8 kg 70 Ib The system should be placed on a level laboratory bench that is sufficiently sturdy to bear its weight Ambient Laboratory Conditions Place the Odyssey System away from external heat sources furnaces windows etc Additional heating can cause high temperatures within the enclosure resulting in instrument shut down Place the instrument away from sinks or other sources of water that pose a shock hazard Recommended operating conditions are 15 35 C and a dew point not greater than 20 C Ventilation The instrument enclosure and circuit boards are cooled with two internal fans There are no restrictions regarding placement of the instrument with respect to the fan cover the fan shrouds are not fi
13. Scan Group Administration 2 Enter a name for the group in the Group Name field 3 Odyssey Control Level Administration Netscape Me x File Edit View Go Communicator Help Account and Group Utilities e Change Password iO Manage Groups Status e Manage User Accounts 3 Group Name fnyorour are Instrument Utilities Instrument Status Delete Preset jim Permissions Remove Scans Shutdown the public Permissions Remove Scans Instrument a Matrarlrina Tahin 3 Click Add Group to create the new group The status line will indicate that the group has been successfully created In addition the newly added group should now be listed in the table with the other groups The user who created the group is automatically given permission to access the new group The next section shows how to give others access to the group Changing Access Permission of a Scan Group Any user with Control account rights and Change permission to a scan group can permit other users to access the scan group Users with Administrator rights can change permission for any scan group 1 Click the Manage Group link on the Utilities page 49 2 Click the Permissions link next to the scan group that you want to change t Odyssey Control Level Administration Netscape File Edit View Go Communicator Help Account and Group Utilities
14. Status Please Confirm Removal of MyGroup and all ofits contents Once Group Utilities initiated this operation cannot he undone Change Password j en Confirm Remove Group Cancel Accounts Viewing and Deleting Scans Within a Scan Group Any user with Control rights and Change permission to a scan group can use the Utilities page to display a list of scans in a group and delete any of the listed scans Users with Administrator rights can delete scans in any scan group Important Deleted scans cannot be restored Make sure you want to delete the scan before using this function 1 Click the Manage Groups link on the Utilities page Odyssey Administration Level Selection Page Netscape Odyssey fal Home Scan 42 View Utilities C2 Help e Manage Groups Manage User Accounts ITnetramant Thlitiac 52 CHAPTER 5 User and Scan Group Administration 2 Click the Scans link next to the scan group containing the scans you want to view or delete Status G Manage Groups Manage User Accounts Group Name Instrument Utilities e Instrument Status e Delete Preset ljim Permissions Remove Scans e Shutdown the public Sar eee 3 All scans in the selected group are listed To delete a scan click the Remove Scan link next to the scan name and confirm that the scan should be removed 3 Odyssey C
15. a scan before the entire area has been scanned click Stop To abandon a scan completely click Cancel The difference between Stop and Cancel is that Stop saves the scan files and Cancel does not The Close button simply closes the window Saving and Deleting Preset Parameters Any user with Control rights can save Preset scan parameters using the Scan Setup window used to start scans Presets can be saved by editing the scan parameters and clicking Save Preset at the bottom of the Scan Setup window Delete Preset Netscape Mil x File Edt View Go Communicator Help I 2 3 a a a i Back Forward Reload Home Search Netscape Print Security Stap z wt Bookmarks 4 Location http 195 44 23 arn z e What s Related j SurfSaver amp Instant Message E WebMail E Contact 5 People E Yellow Pages E Download ch Chan Odyssey gy Home GP Scan 4 View Utilities C2 Help Delete Scan Presets To delete Preset param eters open the Utilities page click the Delete Preset link check the Presets you want to delete and click Delete Selected Account and Group Utilities e Change Password e Manage Groups Manage User Accounts Instrument Utilities Instrument Status ISO Delete Preset e Shutdown the Instrument e Networking Setup ene eee eee ae i Chapter 7 Importing and Editing Scanned Images Opening the View Page 1 Open the Odyssey home page using a browser as des
16. fA Home Utilities Cn Rotate Scan 90 Cw 90 CCW 69 Flipping the Image To flip the image horizontally or vertically click Flip in the toolbar The Left to Right button flips the image horizontally and Top to Bottom flips the image vertically i View Scan Netscape ol x File Edit View Go Communicator Help Odyssey aJ Home Utilities Corn Left to Right Top to Bottom Showing and Hiding Image Channels When a scan is opened the images are initially displayed in color with both image channels overlaid The 700 channel image is red and the 800 channel image is green At pixel locations where fluores cence from both channels overlap the image is some shade of yellow Where the fluorescence on both images is equal and strong the color will be bright yellow 70 CHAPTER 7 Importing and Editing Scanned Images To view only one of the two images click Layer in the toolbar Next uncheck the image 700 channel or 800 channel that you don t want to see and click the View button The image that remained checked is displayed in grayscale format 3 View Scan Netscape oj x File Edit View Go Communicator Help Odyssey gy Home Q Scan gt Vi Utilities C2 Help Scan Layers 700 channel M 800 channel M View View Scan Netscape File Edit View Go Communicator Help fal Home A ol Dor aod oe Odyssey S Scan View Utilities OD telp ifo ne
17. number in the static IP address press Start Y to scroll through numbers 0 through 9 When you reach the desired number press Next to move the cursor to the next number Continue to enter each of the numbers in the IP address in this manner 4 When you have finished entering the address press Next again You are prompted to accept the IP address shown Press Start Y to confirm the address Starting Scans From the Front Panel Scan parameters including resolution quality intensity the size and origin of the area to be scanned and the focus offset can be saved in a configuration file called a Preset These Presets are created and stored in the Odyssey Imager using the Scan page of the Odyssey Server Software software Chapter 6 Once stored Presets can be chosen when starting scans from the front panel keypad All the scan parameters are automatically set by the Preset Starting scans from the front panel can save time when you are doing repetitive scans with membranes or gels that are all the same size If you need to ia 28 CHAPTER 3 Operation change any of the scan parameters like scan area use the Odyssey Application Software to start the scan rather than the keypad see Odyssey User Guide Scans are initiated from the keypad by pressing the Start button Presets are chosen by scrolling through the list using the Next button and pressing the Start button when the desired Preset is displayed Scanning will start and wi
18. update CD or have downloaded the update files via FTP the update procedure is as follows 1 Open the Odyssey home page using a browser as described in Chapter 4 81 X Odyssey Netscape Of x File Edit View Go Communicator Help Server Software LICOR Biosciences Scan View Utilities Status r 2 Click Status and make sure the Odyssey Imager is not in operation 3 Return to the home page and click Utilities to open the Utilities page 4 If necessary enter the User Name and Password of a current account with Administrator rights in the password window User Name and Password are case sensitive Username and Password Required xi Enter username for LICOR Odyssey at 195 44 23 174 User Name fismith Cancel 82 CHAPTER 8 Instrument Utilities and Diagnostics 5 Click the Update Scanner Software link on the Utilities page 3 Odyssey Administration Level Selection Page Netscape File Edit View Go Communicator Help Odyssey fey Home Gp Scan lt gt View Utilities DP Heip Account and Group Utilities e Change Password Manage Groups Manage User Accounts Instrument Utilities Instrument Status e Delete Preset e Shutdown the Instrument e Networking Setup e Set System Time e Scan Test Pattern Update Scanner Software Diagnostic Utilities e User Diagnostics Technician Diagnostics View System Log View Scan Log Browser Test S
19. version 4 or above or equivalent can be used to access Odyssey directly to start scans manipulate image files or retrieve files Users with Adminis trator access rights can also use an Internet browser to add or delete user accounts and to perform routine diagnostic functions Not all functions in Odyssey Server Software are available to all users For example users who are assigned Browse or Control access rights cannot perform functions that require Administrator access rights Functions that have restricted access are noted where appro priate throughout the remainder of this manual Note Browser based access to images on Odyssey is possible only for stand alone configurations and networks that permit such access Connecting to the Odyssey Imager Using a Browser Each Odyssey Imager is assigned an Internet Protocol IP address or host name by your network Administrator The IP address distin guishes Odyssey from any other device on your network and the Internet When the IP address or host name is entered into an Internet browser as a URL Odyssey sends HTML pages that can be used to start scans retrieve scan data etc 34 CHAPTER 4 Accessing Odyssey With An Internet Browser Follow the steps below to log on to Odyssey using an Internet browser 1 In the Location URL field of your browser enter http plus the IP address or host name of the Odyssey Imager Use the IP address supplied by your System Administrator not the o
20. 16 Chapter 3 Operation Before YOu Begin cece nain a n 17 Cleaning the Scanning Surface 0 17 Using Membranes sescncccnescnnsseni 18 Using Gelsin renerne a 19 Using Microplates 0c cesses 20 Using the MousePOD Accessory 21 Positioning Membranes and Gels 22 Positioning Microplates cece 24 Scanning Multiple Microplates 25 Front Panel Controls cceeeeeeeeseeeeeees 26 Setting the Network Address From the Front PaMmelosscis eitees isinen a 27 Starting Scans From the Front Panel 27 Downloading Scans 28 File Size and Storage Capacity 29 Scanning Limitations 0 0 eee eee 31 Software Options sssaaa oiana 32 Odyssey Application Software 32 Browser Interface c eceeeeeeeeseeseeeeeees 32 Chapter 4 Accessing Odyssey With an Internet Browser OVE EW pesse Sarker EEEn EE E EAE 33 Connecting to the Odyssey Imager Using T BOWS E essnee sses unire ESE EE E RRE 33 Checking Instrument Status cee 35 Chapter 5 User and Scan Group Adminstration Adding User ACCOUNTS sssr 37 Adding User Accounts in Odyssey Application Software ceeeeeeeeeees 41 Changing User Account Rights 00 42 Changing Your Own Password 000 43 Changing Other User s Passwords 45 Deleting User Account ceeeeeeeeeeee 46 viii Deleting the Original Admin Account 47 Creating and Chan
21. 5 44 23 174 scanapp imaging nonjava index gt Cal What s Related C SutSaver instant Message E WebMail E Contact E People Yellow Pages Download C4 Chant Odyssey fy Home QP Scan View Tie 2 Save Scan Group public Scan fp30 16 1 Channels 700 300 Save 700 Channel Save 800 Channel Save Scan Log 73 Printing Image Files After images are open they can be printed by clicking Print in the View toolbar and clicking the Printable Image button When Printable Image is clicked the image is displayed in a new window that does not contain the buttons related to Odyssey operation The image can then be printed by choosing File gt Print The image s are printed exactly as shown If image channels are overlaid a composite image of both channels is printed If only a single channel is displayed a grayscale image of one channel is printed View Scan Netscape Of x Eile Edit Yiew Go Communicator Help 2 2 2A zaas st B Back Forward Reload Search Netscape Print Security Stop 7 wt Bookmarks 4 m 95 44 23 174 scanapp imaging nonjava index S a What s Related q SurfSaver instant Message WebMail Contact People Yellow Pages Download Chant Odyssey gy Home Gp Scan D gt Vi Utilities ED Hep 7 Chapter 8 Instrument Utilities and Diagnostics Instrument Status Chapter 4 describes opening the Status page for Odyssey by clicking the Status link on
22. IDYSSEY Infrared Imaging System Operator s Manual Version 2 1 LI LO Biosciences E LI COR inc Biotechnology 4308 Progressive Ave P O Box 4000 Lincoln Nebraska 68504 USA SERVING RESEARCHERS IN EE Phone 402 467 0700 BIOLOGICAL SCIENCES FAX 402 467 0819 Information 1 800 645 4267 Toll free U S amp Canada Technical Support 1 800 645 4260 Toll free U S amp Canada E mail biohelp bio licor com Declaration of Conformity Manufacture s Name LI COR Inc Manufacture s Address 4308 Progressive Ave Lincoln Nebraska USA 68504 declares that the product Product Name Odyssey Infrared Imager Model Number s 9120 Product Options All conforms to the following Product Specifications Safety UL 3101 1 1993 CSA 22 2 1010 1 1992 EN61010 1 1993 EN61010 1 Amendment 1 1995 21 CFR Chapter 1 Subchapter J Class 1 Laser Product IEC 825 1 1994 Class 1 Laser Product FCC Title 47 CFR Part 15 Class A EN61326 1998 Class A EN61000 4 2 1995 8kV CD 15kV AD EN61000 4 3 1995 3V m EN61000 3 3 1995 EN61000 3 2 1995 Supplementary Information The product herewith complies with the requirements of the Low Voltage Directive 73 23 EEC and the EMC Directive 89 336 EEC December 1 2000 Dave Dilley Document 53 06639 Director of Engineering Note on Safety LI COR products have been designed to be safe when operated in the manner described in this manual The sa
23. MySroup E Presets Select Preset Resolution 337 7 pm Quality low z poof H Intensity 00 S z iv Channels By M 200 X Y Y Axis cm Width 10 cm i Height 5 em Focus Offset fo non 2nd gel project 3143 2 55 Entering Scan Parameters Scan parameters such as resolution and scan area can all be entered individually or loaded from stored sets called Presets For most scans it is easiest to load Preset parameters and then edit individual param eters like scan area to suit the current scan Loading Preset Parameters 3 Choose a set of scan parameters from the Preset drop down list If you are not using Preset parameters skip to Step 4 Odyssey initially has three sets of Preset parameters one for membranes and two for gels LI COR Presets Membrane DNA Gel Protein Gel Resolution 169 169 169 Quality medium medium medium Intensity 5 0 8 0 5 0 Scan Origin 0 0 0 0 0 0 Scan Size 10 10 10 10 10 10 Focus Offset 0 0 2 0 0 5 The default Presets generally produce good results but you will probably want to save your own Presets that more closely match your needs If you scan microplates you may also want to create a Preset for microplates using the parameters shown above Creating Presets is discussed later in this chapter 56 CHAPTER 6 Starting Scans Using An Internet Browser Editing the Scan Parameters 4 Customi
24. OPERATION THIS PRODUCT COMPLIES WITH CDRH RADIATION PERFORMANCE STANDARD 21 CFR CHAPTER 1 SUB CHAPTER J Model 9120 S N ODY LI COR INC 4421 SUPERIOR ST LINCOLN NE 68504 USA Made in U S A Patents Pending CAUTION Use of controls or adjustments or performance of procedures other than those specified herein may result in hazardous radiation exposure The Odyssey Infrared Imaging System contains two lasers one emitting at 785 nm and one at 685 nm Each has a peak power rating of 30 milliwatts The 685 nm laser emits visible laser radiation direct exposure to either beam may cause eye damage Laser radiation is emitted through apertures at the top of the Odyssey microscope assembly Because the microscope assembly moves in both planes relative to the glass scanning surface laser radiation could be focused at any position on this surface Safety interlocks below automatically turn the lasers off when the Odyssey lid is opened The label shown below is affixed to the inside of the Odyssey instrument case at two locations one near the laser microscope assembly scanning bed and the second on the cover that is used to seal the above mentioned assembly VISIBLE AND INVISIBLE LASER Figure 1 2 DANGER RADIATION WHEN OPEN g A AVOID DIRECT EXPOSURE TO BEAM RAYONNEMENT VISIBLE ET INVISIBLE LASER EN CAS DANGER D OUVERTURE EXPOSITION DANGEREUSE AU FAISCEAU 4 CHAPTER 1 Operational Information
25. SP is located on one of the printed circuit boards PCB shown below This fuse is not user serviceable Figure 1 6 is shown for reference only 8 CHAPTER 1 Operational Information Fuse Location MY EE Figure 1 6 Location of DSP fuse on circuit board Routine Maintenance The Odyssey Imager requires only minimal maintenance However as with any equipment utilizing electrical voltages there is a danger of fire or electrical shock if the equipment is not properly maintained LI COR recommends that you routinely inspect the system and the scanning surface The following are some general maintenance guidelines e Wipe all chemical spills from the case and or scanning surface to prevent damage to the surface coating e Inspect all cables and power cords for evidence of fraying exposed wire or loose connections e Keep the scanning surface free of organic solvents and other combustibles e Clean the exterior case parts with warm water and a damp cloth The exterior case parts are painted with a durable urethane coating that is resistant to chemical spills Do not use scouring compounds solvents such as acetone benzene carbon tetrachlorides lacquer thinner or alcohol to clean the case Chapter 2 Odyssey Overview and Overview General Description The Odyssey Imager is a network server device that is connected to a network and ultimately to a computer via TCP IP This allows access to the Odyssey Imager via th
26. Technician Diagnostics e View System Log View Scan Log IO Browser Test If the test fails download a current copy of Netscape Communicator www netscape com or Internet Explorer www microsoft com from the Internet 88 CHAPTER 8 Instrument Utilities and Diagnostics Technician Diagnostics The Diagnostic Utilities links on the Utilities page includes links for Technician Diagnostics View System Log and View Scan Log These functions all require Technician level access and are only for trouble shooting and factory calibration Do not use these functions unless directed to do so by LI COR or LI COR authorized Distributors Similarly you should not need to use the Scan Test Pattern link unless directed to do so by LI COR The Scan Test Pattern page contains complete instructions for scanning the test pattern included with Odyssey and interpreting the results 89 Chapter 9 Appendices Specifications Laser Microscope Laser Lifetime 60 000 hours typical 700 Channel Laser Source Solid state diode laser at 685 nm 800 Channel Laser Source Solid state diode laser at 785 nm Detectors Silicon avalanche photodiodes Scanning Speed 5 40 cm s Resolution 21 337 um Focusing Scan bed is movable in the Z dimension allowing the fluores cence detection microscope to be aligned to the top surface of the glass to obtain the best signal to noise ratio Operating Specifications Operating Conditions For
27. an into the current project File Size and Storage Capacity The file size for scans from the Odyssey Imager is dependent upon the resolution of the scan and the area of the sample that is scanned Scan resolution can be set at 21 42 84 169 or 337 um The largest 29 30 CHAPTER 3 Operation area that can be scanned is 25 cm x 25 cm At the highest resolution 21 um a 25 x 25 cm scan would require 283 4 Mb of disk space for each of the two image channels Table 3 1 shows typical file sizes for various scan areas at the 5 different resolutions Table 3 1 File sizes for various scan areas and 5 scan resolutions in kilobytes or megabytes per channel Resolution Scan Size 5x5cm 5x10cm 88k 350k 1 4M 5 7M 5x15cm 132k 525k 2 1M 8 5M 5 x 20 cm 176k 700k 2 8M 11 3M 5x25 cm 220k 875k 3 5M 14 2M 10x10cm 10x15cm 264k 1 0M 4 1M 10 x20 cm 352k 1 4M 5 6M 10x25 cm 440k 1 7M 7 0M 15x15cm 396k 1 6M 6 3M 15 x 20 cm 528k 2 1M 8 4M 15x25cm 20 x 20 cm 704k 2 8M 20x25cm 800k 3 5M 25 X25 cm 1 1M 4 4M File size is small enough to scan with Odyssey Application Software Marginal for Odyssey Application Software Scan should be started in using the browser interface Scanning Limitations It is important to note that there are limits to scanning files with the Odyssey Application Software with respect to scan resolution and file size these
28. ange the password for any user account as follows 1 On the Manage User Accounts page click the Password link next to the appropriate User Name to change that user s password Odyssey Administration Level Administration Netscape Eile Edit View Go Communicator Help 3 3 28 d3 G N Back Foward Reload Home Search Netscape Print Security Stop d Bookmarks 4 Location com scanapp admin admin index action ManageUserAccounts amp What s Related C4 SufSaver amp Instant Message E WebMail E Contact E People E YellowPages E Download C4 Chan Odyssey QJ Home QP Scan lt View Utilities PD Heip Account and Group Status Utilities e Change Password Add Account e Manage Groups Change Account Ri G Manage User Accounts admin Password Remove jan Password Remove Instrument Utilities kevin Password Remove e Instrument Status mike Password Remove e Delete Preset ton Password Remove Shutdown the tech Password Remove Instrument 2 Enter the new password in the New Password field and confirm that it is correct by typing it again in the New Password Confirm field Selected User ron The old password is not New Password freee required which makes it New Password Confirm rere easy to assign anew password to users who Change Password Cancel have forgotten theirs 3 Click Change Pa
29. cribed in Chapter 4 2 Click the maximize button on the browser window Images are often large and it is best not to resize the browser window while viewing an image 3 On the home page click the View link to open the Image View page Odyssey Netscape File Edit View Go Communicator Help Server Software LICOR Copyright 2000 LI COR Inc All rights rese f 62 CHAPTER 7 Importing and Editing Scanned Images Opening a Scan Stored on Odyssey The View page is used to open edit and save image files located on the Odyssey Imager All editing and file management functions can be accessed using the toolbar in the top frame of the View page When the View link on the home page is clicked a page for opening scans is displayed The Open button in the View toolbar can also be used to display this page The Open page is used to open image files stored on Odyssey The image files can then be saved to a local storage drive using the Save button Other functions on the View page are used to edit the image while it is open Follow the steps below to open an image 1 Select the scan group where the file is located from the Group drop down list 3 View Scan Netscape iof xj File Edit View Go Communicator Help Z 3 3 a u sts E F Back Forward Reload Home Search Netscape Print Security Stop zl wt Bookmarks 4 Location http 7195 44 23 174 scanapp imaging nonjava index z G What s Related
30. e Odyssey Application Software or an Internet browser The Odyssey Imager can also be connected directly to the computer in stand alone non network configurations Image data run parameters and security protocols can be viewed and or changed over the network finished scans are then downloaded from the Odyssey hard disk to local drives for storage and analysis Although Odyssey has an internal hard disk it should be used for temporary storage only when the hard disk is full the oldest files are overwritten to make space Files can also be erased from the hard disk using the browser interface see Chapter 5 Viewing and Deleting Scans Within a Scan Group Unique password protected User Accounts allow access rights to be established for multiple users 2 CHAPTER 2 Odyssey Overview and General Description Hardware Description Two solid state diode lasers simultaneously provide light excitation at 685 and 785 nm Collimating lenses optical bandpass filters and a focusing lens focus and tune the laser beams to produce an excitation spot on the scanning surface The microscope electronics then modulate the laser beams to discriminate the infrared IR dye signal fluorescence from background fluorescence The scanner detection optics focus on the excitation spot and collect light from the fluorescing IR dyes After collection by the microscope objective the light is passed to a dichroic mirror The mirror splits the light and e
31. e from light until it has been scanned e Keep the membrane wet if you plan to strip and re use it For Western blots store dry or in PBS buffer at 4 C e Use clean containers to avoid cross contamination and reduce background e Multiple membranes can be washed together provided there is ample volume so each membrane moves freely e If the signal on the membrane is too strong re scan at a lower intensity setting Using Gels e The fluorescent signal on the membrane will remain stable for several months or longer if protected from light A protocol for in gel Westerns is provided in the Odyssey Application Protocols manual Coomassie stained gels can also be scanned since Coomassie Blue dye can be seen clearly in the 700 nm channel and faintly in the 800 nm channel To scan a gel follow these procedures 1 Thoroughly rinse the gel with de staining solution or water to remove dye particulates 2 When placing the gel on the scanning surface take care not to trap air bubbles underneath Cover the gel with plastic wrap to prevent drying if desired 3 Scan the gel in the 700 nm channel 4 Adjust the focus offset for the gel thickness The correct focus offset is 1 2 the thickness of the gel for a 1 mm gel set the focus offset to 0 5 mm The maximum offset is 4 mm in the most current edition of Odyssey allowing gels of up to 8 mm to be scanned Early versions of Odyssey were limited to a 2 0 mm focus offset but ca
32. eaning the Scanning Surface The scanning surface is plate glass which can be cleaned with any non abrasive glass cleaner Warm soapy distilled water or isopropyl alcohol can also be used Do not use scouring compounds or abrasive scouring pads the glass can scratch which can affect the scanned image 18 CHAPTER 3 Operation It is very important that the glass and silicone mat be free of smudges dust and dye before placing membranes or gels onto the Odyssey Imager Dirty surfaces in contact with the membrane surface may cause blotches and streaks that can not be removed with further washing Using Membranes For Western blotting methods nitrocellulose or PVDF membranes may be used For best performance pure cast nitrocellulose membranes are recommended For Northern blotting methods nylon membranes optimized for use with the Odyssey Imager are available from LI COR Detailed blotting procols can be found in the Odyssey Application Protocols There are some general tips however for using membranes with the Odyssey Imager e Do not touch the membrane handle only with a clean forceps Lift the membrane only by the corners Fingerprints even from a glove will show clearly when imaged e Always use the silicone mat included to cover the membrane s before scanning This helps keep the membrane flat Use the 4 soft roller included to flatten the membrane and remove any air bubbles that may be present e Protect the membran
33. ed in the Installation Manual IP Address C Use DHCP Static IP IP Address Net Mask MAC Address Host Name Name Gateway Address Name Configure k 157 44 22 251 255 255 0 0 00 A0 CC 65 E2 6E sara fus7 44 22 1 m Domain Name Servers 78 CHAPTER 8 Instrument Utilities and Diagnostics DHCP vs Static Addressing Your local network will either use static IP addresses for devices on the network or IP addresses will be assigned automatically using Dynamic Host Configuration Protocol DHCP Your network admin istrator will tell you whether to select Use DHOP or Static IP If Static IP is selected you must enter the IP Address and Net Mask assigned by your network administrator The MAC Address listed below Net Mask is the address of the network card in the Odyssey Imager Your network administrator may request the MAC address during configu ration MAC address is also accessible from the Odyssey front panel Using Host Names In order to connect to Odyssey using a browser you must enter either Odyssey s IP address or a host name assigned to Odyssey If your network has a domain name server a host name may be a conve nient alternative to using an IP address to log onto Odyssey A host name is generally a common name that is easy to remember rather than a series of numbers A host name is also useful on networks using DHCP where addressing may be dynamic and the IP address
34. ed on the Network Setup page you can also e mail the file directly using the Transfer Options area The Send To address for LI COR technical support is already entered Fill in your e mail address in the Reply Back To field add any descriptive Comments and click the E mail button If you are using a dial up account make sure you are logged on before clicking E mail Browser Test Odyssey should be used with Netscape or Internet Explorer version 4 0 or above or their equivalent If you don t know the version number of your browser or are using some other browser you should run the browser test on the Utilities page to verify that your browser can run Odyssey software With some older browsers certain pages may display correctly but important functions like scanning may not work correctly To run the browser diagnostic open the Utilities page and click the Browser Test link Browser Test Netscape oj x Fie Edit View Go Communicator Help Odyssey gy Home Gp Scan lt 2 View Utilities ED Help Check Browser Version Account and Group Test Successfull Utilities Your web browser Netscape 4 6 should run this application correctly e Change Password e Manage Groups e Manage User Accounts Instrument Utilities e Instrument Status e Delete Preset e Shutdown the Instrument Networking Setup e Set System Time e Scan Test Pattern Update Scanner Software Diagnostic Utilities e User Diagnostics e
35. ed to another language without prior written consent of LI COR Inc Printing History Publication Number 984 08464 Printed June 2006 The Odyssey System and LI COR chemical reagents are produced and distributed for research purposes only In no instance is any product offered for drug or clinical use in humans LI COR is an ISO9001 registered company 2001 2006 LI COR Inc Specifications subject to change LI COR Odyssey MousePOD and IRDye are trademarks or registered trademarks of LI COR inc The Odyssey Infrared Imager and IRDye reagents are covered by U S patents foreign equivalents and patents pending Federal Communications Commission Radio Frequency Interference Statement WARNING This equipment generates uses and can radiate radio frequency energy and if not installed in accordance with the instruction manual may cause interference to radio commu nications It has been tested and found to comply with the limits for a Class A computing device pursuant to Subpart J of Part 15 of FCC rules which are designed to provide a reasonable protection against such interference when operated in a commercial environment Operation of this equipment in a residential area is likely to cause interference in which case the user at his own expense will be required to take whatever measures may be required to correct the interference 4647 Superior Street e P O Box 4000 e Lincoln Nebraska 68504 USA Technical Support 800 645 4260 Nor
36. er the wells on the image for new scans see Odyssey User Guide Chapter 2 25 26 CHAPTER 3 Operation Front Panel Controls The front panel display is a 2 line 20 character Vacuum Fluorescent Display VFD for displaying operating parameters and software command codes The front panel keypad Figure 3 6 is used to enter software commands and to edit operating parameters OFO stop start Figure 3 6 Odyssey keypad and display The front panel controls are as follows Power Powers the instrument On Off Also performs instrument reset if held down for 4 seconds Stop N Stops or pauses scanning or cancels option currently visible on LCD display Start Y Starts scanning or confirms option currently visible on LCD display Next Scrolls through available options for front panel opera tions The display and keypad should be cleaned only with warm water and a damp cloth Setting the Network Address From the Front Panel Using the front panel keypad you can select the method DHCP or Static by which the network IP address is assigned to instrument These functions as well as other network parameters can also be set using the browser software as described in Chapter 8 To enter the IP address follow these steps 1 Press the Stop and Next buttons simultaneously 2 Toggle to Static or DHCP using the Next button For the purpose of this discussion choose Static and press Start Y 3 To enter the first
37. eviewing the collected scans use the focus offset with the highest signal to noise as your focus offset for experiments with the alternate plates e The Intensity scan parameter for both 700 and 800 nm channels should be set to 5 for initial scanning If the image signal is saturated or too high re scan using a lower intensity setting i e 2 5 Likewise If the image signal is too low re scan using a higher intensity setting i e 7 5 e For satisfactory images with minimal scan time the Quality scan parameter should be medium with Resolution set to 169 um Higher scan quality and resolution may be used but scan time will increase Using the MousePOD Accessory The optional Odyssey MousePOD Accessory fits over Odyssey scanning surface for in vivo imaging of up to three mice in a temperature controlled enclosure Operation of the MousePOD Accessory is described in the Odyssey In vivo Imaging Guide Figure 3 1 MousePOD Accessory 22 CHAPTER 3 Operation Positioning Membranes and Gels Membranes are placed on the scanning surface with the sample surface down and the top of the membrane facing the front of the instrument as shown in Figure 3 2 Gels are placed in a similar orientation Figure 3 2 Membranes and gels are placed with sample surface down with top of the membrane facing the front of the instrument Important Handle membranes only with a clean forceps and touch only the corners Fingerprints eve
38. fety of this product can not be guaranteed if the product is used in any other way than is specified in this manual Equipment markings The product is marked with this symbol when it is necessary for you to refer to the manual or accompanying documents in order to protect against damage to the product The product is marked with this symbol when a hazardous voltage may be present The product is marked with this symbol for a Chassis Ground connection WARNING Warnings must be followed carefully to avoid bodily injury CAUTION Cautions must be observed to avoid damage to your equipment Manual markings WARNING Warnings must be followed carefully to avoid bodily injury CAUTION Cautions must be observed to avoid damage to your equipment NOTE Notes contain important information and useful tips on the operation of your equipment Notice The information contained in this document is subject to change without notice LI COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE LI COR shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing performance or use of this material This document contains proprietary information which is protected by copyright All rights are reserved No part of this document may be photocopied reproduced or translat
39. ging Groups 47 Creating a New Scan Group 47 Changing Access Permission of a EE e E T 48 Deleting Scan GroUPS sssscsesssisisisiscsssrsasi 50 Viewing and Deleting Scans Within a Scan GHOUP ese nns niinn teaceevereeeceseees 51 Chapter 6 Starting Scans Using an Internet Browser Using the Scan Setup Window 0 53 Naming the Scamisesiescsssshvecnesatdssagvebvcene 54 Entering Scan Parameters 0ceee 55 Starting a SCAM rsss s as ean i 58 Stopping ASCAM ssis sosis ikr eesin 60 Saving and Deleting Preset Parameters 60 Chapter 7 Importing and Editing Scanned Images Opening the View Page cee 61 Opening a Scan Stored on Odyssey 62 Changing the Appearance of an Image 64 Zooming In and Out eee 64 Cropping an IMage ccceseeseeseeeseeeee 65 Changing Image Sensitivity 0 0 66 Inverting the Grayscale Map 005 67 Changing Image Orientation 68 Rotating the Image eeeeeeeeeeeee 68 Flipping the Image cece 69 Showing and Hiding Image Channels 69 Displaying Scan Information 00 71 Saving Changes to Images seen 72 Printing Image Files ssesseseneeeeees 73 Chapter 8 Instrument Utilities and Diagnostics INSEPUMMENE Status ns ccssscssscesscevesestesssvepeesess ses 75 Instrument Shutdown cece esses 76 Editing Network Addresses 0 0ceeee 77 DHCP vs Static Address
40. ing 04 78 Using Host Names cccceceeseeseeeeeeees 78 Entering a Gateway Address 00 78 Setting Date and Time 79 Updating the Odyssey Instrument SONWANE ipaa aa e n ERE 80 Opening the Update Scanner Page 80 Starting the Update ee eee 82 User DiagnhostiC Sirei 85 Browser OSU cc iec2dc sieve inn aE 86 Technician Diagnostics cesses 88 Chapter 9 Appendices Specificato Sissies ireren 89 Error Message Srorssriere enesik 90 Scan SOUP iiss rinine inie 90 Scam CoNsOl Eseia 91 MASI G o cs tscsssetevsesteecsscdeeteebiettestestesedeess 91 Software Upgrage Errors s ssseessseereeeeeeeee 91 TIME SGUD recs a 92 Utilities Change Password cece 92 Utilities Manage GroupS ceeeee 92 Utilities User Technician Diagnostics View System Log View Scan Log 93 Chapter 1 Safety and Operational Information In This Manual The following topics are discussed in this manual e Safety considerations e Instrument placement and power considerations e Description of detection optics and signal processing e Odyssey Infrared Imaging System operation e Use and maintenance of the Odyssey scanning bed e Troubleshooting for the Odyssey Infrared Imaging System Safety Considerations Laser Safety The Center for Devices and Radiological Health CDRH was estab lished in October 1982 by the U S Food and Drug Administration FDA to protect the public hea
41. limitations do not pertain when a browser is used to initiate a scan in Odyssey Server Software Table 3 1 shows approximate file sizes for various combinations of sample area and scan resolution All combinations can be scanned using the Odyssey Server Software The light grey shaded cells indicate those combinations that may or may not be able to be scanned using Odyssey Application Software depending on the system resources memory available a notification in the form of a warning message may appear before you start scanning The dark grey cells indicate those combinations that can not be scanned with Odyssey Application Software Anything that affects the computer s system resources may also influence the ability to start scans with the Application Software For example if you are running other applications at the same time as the Odyssey Application Software fewer system resources will be available causing the system to run out of memory As a general rule it is good practice to close all other applications when using Odyssey Application Software Note too that Table 3 1 applies to computer systems with 256 Mb RAM if your computer has additional RAM installed you may be able to scan larger files As mentioned earlier there are no limitations to scanning with the browser interface software Large files can be scanned and then smaller portions of the scan file can be cropped out and imported into the application software for ana
42. ll continue until the entire scan area specified in the Preset has been scanned File names are automatically assigned to scans started from the keypad using the first 7 characters of the chosen Preset file followed by the date and a sequential index number An example would be Membran 12 10_5 in which Membrane was the Preset name December 10 was the month and day of the scan and this was the 5th scan initiated from the front panel keypad on December 10 Scans initiated from the Odyssey front panel are stored in the public scan group They can then be downloaded for analysis with the Odyssey Application Software Downloading Scans The following procedure can be used to download scans with Odyssey Application Software Complete details can be found in the Odyssey User Guide 1 Create a new Odyssey project or open an existing project 2 Choose File gt Download Scan 3 Select the scanner and enter your name and password Scanner Login gt Odyssey Imager User Name roger Password trantan Logout 4 Select the public scan group and select the scan in the Available Scans list Download Scan Scan Name Scan Groups Available Scans 2003 Jul 01 SA4M 2 2003 Jul 30 4PM 1 2003 Jul 30 4PM 2 2003 Jul 30 4PM 3 2003 Jul 30 4PM 3_1 2003 Jun 30 4PM 1 2003 Jul 01 94M 1 jen 2003 Jun 30 4PM 2 5 Click OK to download the selected sc
43. ltered and the cover serves only as an exhaust outlet Space Requirements The Odyssey System requires an area approximately 52 cm W 20 5 x 60 cm D 23 5 With the hood fully open the Odyssey Imager requires 74 cm 29 of vertical clearance Moving the Odyssey System Be cautious when moving the instrument Always be sure to move the motor lock switch on the instrument back panel to the Up Transport position before moving the instrument Use the tip of a pen or a small screwdriver to move the motor lock switch After 6 CHAPTER 1 Operational Information moving the instrument return the motor lock switch to the Down Operate position The following label is located next to the motor lock switch a TRANSPORT Figure 1 4 MOTOR LOCK OPERATE A 10BASE T or 100BASE TX w Use a minimum of two people when moving the Odyssey System as it weighs about 32 kg 70 pounds Lift under the metal enclosure on each side of the unit and keep the unit as near vertical as possible Gently set the Odyssey Imager at its new position The instrument can be leveled after it is moved if necessary The instrument does not need to be level for proper operation it may be helpful however if the laboratory bench is not level to prevent moistened membranes from sliding on the scanning surface Each of the 4 plastic feet on the bottom of the instrument case has a threaded metal insert that can be turned in either direction t
44. lth in the fields of medical devices and radiological health Manufacturers of products subject to performance standards under the Radiation Control for Health and Safety Act of 1968 are required to furnish various reports to the CDRH 2 CHAPTER 1 Operational Information The Odyssey Infrared Imager is certified as a Class laser product containing a Class Illb laser This means that hazardous laser radiation is not emitted outside the instrument Radiation emitted inside the instrument is confined within protective housings and external covers A series of safety interlocks ensures that the laser beam cannot escape during any phase of user operation The CDRH implemented regulations for laser products on August 1 1976 CDRH radiation performance standard 21 Code of Federal Regulations Chapter 1 Subchapter J Compliance for products marketed in the United States is mandatory The label that must be attached to laser products marketed in the United States is Figure 1 1 and is located on the rear panel of the Odyssey System indicating compliance with CDRH regulations EUT Figure 1 1 100 127V 8A 200 240V 5A 50 60HZ DISCONNECT POWER BEFORE SERVICING THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS 1 THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED
45. lysis there is a 20 25 Mb file size limit on computers with 256 Mb RAM See the Odyssey User Guide for more details CHAPTER 3 Operation Software Options Odyssey Application Software The Odyssey Application Software provides a simple interface for analyzing the image files created on the Odyssey Imager The core Odyssey application includes scan control band sizing quantifi cation project management and reporting The In Cell Western Module for Odyssey software also has analysis software for analyzing In Cell Western Assays The Odyssey User Guide and Tutorial Manual describe the use of this software Browser Interface The Odyssey Imager has a built in internal server that provides scanner control data storage and user access control Internet browsers such as Netscape Navigator version 4 5 or above and Internet Explorer version 5 0 or above can be used to access Odyssey to start scans view and manipulate image files collected by the instrument or retrieve files stored on Odyssey s hard disk Users with Administrator rights can also use the browser to manage user accounts The remainder of this manual describes how to use the internal server software i Chapter 4 Accessing Odyssey With an Internet Browser Overview The Odyssey Imager has an internal server that provides scan control as well as temporary data storage and user access control Internet browsers such as Netscape Navigator Internet Explorer
46. me and Password are case sensitive 44 CHAPTER 5 User and Scan Group Administration 4 Click the Change Password link in the Account and Group Utilities section h Odyssey Administration Level Selection Page Netscape Eile Edit View Go Communicator Help Odyssey gy Home QP Scan lt View Utilities PD Help Account and Group Utilities e Change Password Manage Groups Manage User Accounts Instrument Utilities e Instrument Status e Delete Preset Shutdown the Instrument Networking Setup e Set System Time Scan Test Pattern Update Scanner Software Diagnostic Utilities e User Diagnostics Technician Diagnostics 5 Enter your current password in the Old Password field 3 Odyssey Browse Level Administration Netscape Jol x File Edit View Go Communicator Help Odyssey gy Home QP Scan lt gt View Utilities 2c Account and Group Utilities Old Password ppp Ia Change Password New Pamard pe o Manage Groups Manage User Accounts New Password Confirm F zara Instrument Utilities e Instrument Status Execute N Cancel e Shutdown the Tnetriment 6 Enter the new password in the New Password field and confirm it by typing it again in the New Password Confirm field 7 Click Execute to change the password 45 Changing Other User s Passwords If you are logged in using an account with Administrator access rights you can ch
47. me input field 93 Utilities User Technician Diagnostics View System Log View Scan Log Error Message The Default Gateway is not defined Please proceed to the Administration Level Network Setup Page to define the default Gateway Description The instrument has not been configured to allow e mail of log or diagnostic information directly from the instrument Error Message The Domain Name Server is not defined Please proceed to the Administration Level Network Setup Page to define the Domain Name Server Description The instrument has not been configured to allow e mail of log or diagnostic information directly from the instrument
48. n be upgraded by installing Odyssey Server Software version 2 0 0 or above 5 After removing the gel clean the glass surface to remove any residual dye If dye particulates remain wipe the gel gently with a gloved finger or a wet cloth before scanning 6 The ruler included can be placed on the scanning surface adjacent to the gel as a reference when cutting lanes out of the gel after scanning 20 CHAPTER 3 Operation Using Microplates Microplates that meet certain physical characteristics can be scanned directly on the Odyssey scanning surface Proper selection of microplates significantly affects the results of your analysis as each plate has its own characteristics including well depth plate autoflu orescence and well to well signal crossover Some general consid erations for microplate selection are provided below e Plate dimensions must be such that the distance from the Odyssey scanning surface to the target detection area of the plate is 4 0 mm or less e In order to avoid well to well signal spread black well clear bottom plates should be used for assays that involve imaging of a liquid Since In cell Western assays use detection at the well surface with no liquid present both clear and black well plates can be used Consult protocols in the Application Protocols manual for specific recommendations e Do not use plates with white wells because the auto fluorescence from the white surface will create significant n
49. n from a glove will show clearly when imaged 23 Figure 3 3 shows how to place membranes or gels with respect to the etched X Y axes on the scan surface It is a good practice to leave a gap 1 cmor so between the sample and either axis This allows you to specify a scan boundary that is 1 cm larger than the membrane in all dimensions The larger scan boundary creates an image that is easier to analyze in Odyssey software If the sample is placed too near either axis or if the scan boundary is too close to the membrane annotations in the Odyssey Application Software may be truncated in some views Scan Boundary Figure 3 3 Leave a 1 cm gap between membranes or gels and the origin 0 0 on all sides Multiple membranes and or gels can be scanned at one time portions of the scan file can then be cropped out and downloaded for analysis Note that orientation of the samples on the scanning surface is not critical as scanned samples can be rotated and otherwise manipulated before downloading However membranes are generally easier to analyze if the sides are parallel to the X Y scan axes 24 CHAPTER 3 Operation Positioning Microplates The plastic microplate alignment guide P N 9891 080 should be placed on the scan surface so the corner of the guide contacts the front left corner of the bezel surrounding the scan surface Push the guide into the corner until it contacts the bezel on both the front and left sides Put the mic
50. n surface without interruption from another user 6 Place the membrane gel or microplate on the scan surface as described in Chapter 3 and click Start in the Scan Console to begin the scan When the scan is started the scan information page in the View section is displayed i View Scan Netscape Eile Edit View Go Communicator Help Odyssey fa Home e Scan gt Vi Utilities E Help Scan Information Scan Name fp3016116 Group Name 6116 Dimensions 296x21 File Size 0 01 MB Channel More Information Auto Update Image Off On Off Time Left 00 00 00 Progress MEE 100 To see the image as it is being scanned make sure Auto Update Image is On click the On Off button as needed The percentage of the scan that has been completed is shown in the Progress bar All of the scan parameters entered in the scan setup window can be examined by clicking More Information If you need to stop or pause a scan click the Scan C button in the toolbar to display the Scanner Console window 59 0 CHAPTER 6 Starting Scans Using An Internet Browser Stopping a Scan At the end of a scan image files are stored on Odyssey s internal hard drive in the specified scan group Images stored on Odyssey can be downloaded using the Windows based Odyssey application software or using a browser as described in Chapter 7 To interrupt a scan before automatic completion click Pause in the Scan Console To complete
51. nd 2 0 Description The user entered a number out of the valid range or a number that is not valid Error Message You must select at least one channel to scan Description At least one channel needs to be checked Error Message Enter valid x dimensions OR Enter valid y dimensions Description The dimensions that the user entered are out of range 0 25 cm Error Message The scan dimensions must be in cm Description The value entered is not a number Error Message Scanner is busy Description A scan is currently in progress Error Message Scan already exists Description Attempt to start a scan with a name that is already in the group 91 Error Message Permission denied Description The user does not have permission to place scans in that group Scan Console Error Message Lid open Description Close the lid before starting a scan Imaging Error Message Image not open Description No image open to work with Error Message You must select a scan group Description On the open page you must select a scan group Error Message You must select a scan name Description On the open page you must select a scan name Software Upgrade Errors Error Message Signatures on files do not match Description The file transferred is not a LI COR update Error Message Could not find install file Description After the file is uploaded the application could not find the file to install it Error Message Can
52. ne shown in the graphic Netcenter Netscape File Edit View Go Communicator Help 324 2 t i Back Formsard Reload Home Search Net AE Bookmarks A Goto rttp 195 44 23 174 ss Odyssey Netscape iof x Odyssey sends a home File Edit View Go Communicator Help page with four links that correspond to pages for scanner operation image viewing and manipulation system utilities and scanner status Access beyond this page is password protected Your access level determines which functions you can actually use LI lOR Biosciences Server Software Scan View Utilities Status 39 Checking Instrument Status Odyssey is configured as a server allowing multiple users to be logged on at the same time In other words one user may be operating the scanner while others are retrieving and analyzing scans stored on Odyssey s internal hard disk Using the Status link on Odyssey s home page you can use a browser in your office to find out whether someone is scanning a membrane in the lab 2 Click the Status link on the Odyssey home page f Odyssey Netscape Jol x File Edit Yiew Go Communicator Help Odyssey Server Software Scan View Utilities 3 In the password window enter the Odyssey User Name and Password assigned to you Username and Password Required x Enter username for LICOR Odyssey at 195 44 23 174 UserName fimin S The User Name and Pass
53. not read from input Description The file can not be uploaded Error Message Error opening file filename for writing Description Can not write the file sent Probably a permission problem on the scanner Error Message No data was written to the file Description The file was transferred but non of the data could be written 92 CHAPTER 9 Appendices Time Setup Error Message Enter a month between 1 and 12 Description Must enter a numerical month 1 Jan 2 Feb etc Error Message Enter a day between 1 and 31 Description Out of range day Error Message Enter a valid year Description Year must be gt 2000 Error Message Enter an hour between 1 and 12 Description Hours must be 1 12 No 24 hour time allowed Error Message Enter minutes between 0 and 59 Description Minutes must be between 0 and 59 No fractions accepted Error Message All entries must be numerical values Description Illegal non numeric characters were entered Utilities Change Password Error Message The new password and the new password confirm do not match Description The new password and the new password confirm must match to change the password Error Message One or more of the password input fields was empty Description All password change fields must be filled in Utilities Manage Groups Error Message The Group input field was empty Description When adding a group a group name must be provided in the group na
54. o adjust its height Adjust the feet as necessary until the instrument is level Instrument base Metal insert Figure 1 5 Turn the metal inserts on the feet to adjust the height Electrical Considerations Power Cords The Odyssey Imager is equipped with a 3 wire grounding type plug This plug will only fit into a grounding type outlet This is a necessary safety feature If you are unable to insert the plug into the outlet you will need to replace the outlet Do not defeat the purpose of the grounding type plug Do not locate the Odyssey Imager where the power cord will be walked on or exposed to water or chemical spills The Odyssey Imager draws approximately 3 amperes at 120V If an extension cord is used make sure the total of the ampere ratings on the instruments plugged into the extension cord does not exceed the extension cord ampere rating Also make sure the total amperage of instruments plugged into the wall outlet does not exceed the amperage capacity for the outlet In the U S this is usually 15 or 20 amperes Fuse Replacement Caution Replace fuses only with fuses of the specified type and current ratings The power supply fuses are located inside the sealed instrument power supply and are not user serviceable If the instrument fails to power up and you suspect that a fuse has blown contact LI COR or a LI COR representative A single 5A fast blow fuse protecting the Digital Signal Processor D
55. oise e For In Cell Western assays requiring sterile plates for tissue culture growth the following plates recommended by LI COR Biosciences 96 well format Nunc Nalgene Part Number 161093 Clear 96 well format Nunc Nalgene Part Number 165305 Black 96 well format Falcon Part Number 353075 Clear 96 well format Falcon Part Number 353948 Black 384 well format Nunc Nalgene Part Number 164688 Clear 384 well format Nunc Nalgene Part Number 164730 Black 384 well format Falcon Part Number 353961 Clear 384 well format Falcon Part Number 353962 Black e Before plate scanning clean the bottom plate surface with a moist lint free paper to remove any obstructions Additionally the Odyssey scanning surface should be thoroughly cleaned using procedure described earlier in this chapter 21 e Protect plates from light before imaging to ensure highest sensitivity When storing plates after imaging protect plates from light at room temperature e A Focus Offset of 3 0 mm should be entered in the scan parameters Chapter 2 Odyssey User Guide when using the plates specified above Plates other than those recommended above may require lower or higher focus offsets for optimal resolution and detection If alternative plates are used an initial optimization scan will be necessary Scan a plate containing experimental and control samples at 0 5 1 0 2 0 3 0 and 4 0 mm focus offsets Use the same intensity settings for each scan After r
56. olution scans make the scan area about 1 cm larger than the membrane or gel on all four sides For example if you have a 5 cm x 5 cm membrane set the scan Width and Height to 7 cm and set the Origin to 0 0 The membrane would then be placed at the 1 cm x 1 cm position on the scan surface 58 CHAPTER 6 Starting Scans Using An Internet Browser Focus Offset for scans of membranes should be zero For gels Focus Offset should be half the gel thickness in millimeters A focus offset of 3 0 mm is usually accurate for standard microplates The maximum allowable focus offset is 4 mm 8 mm gels Comments Comments can be used to identify the scan In Odyssey software comments can be included in reports Starting a Scan Before starting a scan an estimate of the scan time can be calculated by clicking the Calculate Scan Time button at the bottom of the Scan Setup window 5 Click Configure to send the scan parameters to Odyssey After Odyssey is configured the Scan Console window is displayed 3 Scan Console Netscape Be x Scan Console Start stop Pause Cancel Leise The scan is not actually started until the Start button is clicked but Odyssey is reserved for the user who initiated the scan Other users on the network will not be able to start scans until the current scan is complete though they can download scans for analysis While Odyssey is reserved but not scanning the membrane can be placed on the sca
57. ontrol Level Administration Netscape Odyssey fal Home qe Scan 42 View Utilities C 20 Help ccount and Group tilities e Change Password e Manage Groups e Manage User Accounts Selected Group mike Status test A Remove Scan jtesi2 Remove Scan strument Utilities e Instrument Status i Chapter 6 Starting Scans Using an Internet Browser Scans can be started from the Odyssey instrument keypad from Odyssey Application Software or using an Internet browser Only the Internet browser method of starting scans is discussed in this chapter Using the Scan Setup Window 1 Open the Odyssey home page by entering the IP address or host name of the Odyssey Imager as described in Chapter 4 2 On the home page click the Scan link to open the Scan Setup page Odyssey Netscape ol x File Edit View Go Communicator Help 54 CHAPTER 6 Starting Scans Using An Internet Browser Naming the Scan 1 Enter a name for the scan in the Name field 2 Select a scan group from the Available Groups drop down list Initially the scan groups listed may include only your own group and the public scan group Chapter 5 describes how to create additional groups and how to let other users access your groups lolx Scan Setup Netscape File Edit View Go Communicator Help Odyssey fy Home REP Scan lt View Utilities ED telp Name fityscan Group public Available Groups
58. ration 4 Click Change to implement the new permission level Deleting Scan Groups Any user with Control rights and Change permission to a scan group can delete the scan group using the Manage Groups link on the Utilities page Users with Administrator rights can delete any scan group Important Deleting a scan group deletes all scans within the group Once a group is deleted it is not possible to retrieve scans that were in the group 1 Click the Manage Groups link on the Utilities page Odyssey Administration Level Selection Page Netscape Odyssey fal Home me Scan 42 View Utilities C2 Help Manage Groups e Manage User Accounts 2 Click the Remove link next to the scan group that you want to delete 3 Odyssey Control Level Administration Netscape Mi x File Edit Yiew Go Communicator Help Account and Group Utilities e Change Password IO Manage Groups Status e Manage User Accounts Group Nama me Instrument Utilities Instrument Status e Delete Preset jim Permissions Remove Scans Shutdown the public Permissions Remo Scans Instrument ERD cre caer eee 51 3 Click the Confirm Remove Group button Odyssey Control Level Administration Netscape Mi x File Edit View Go Communicator Help Odyssey gy Home QP Scan lt 2 View Utilities ED Hep Odyssey Control Level Administration Account and
59. roplate on the scanning surface and slide it into place until it contacts both the front and left side of the alignment guide The first well in the first row A1 should be toward the back and left side of the alignment guide as shown below Microplates can be scanned one at a time using the browser interface or by choosing File gt Scan in Odyssey Software and using the Microplate2 scan preset Figure 3 4 The microplate alignment guide should be placed in the front left corner and should contact the bezel surrounding the scan surface Scanning Multiple Microplates Up to six microplates with standard dimensions can be scanned by choosing File gt Scan Multiple Plates in Odyssey Software not available from the front panel or browser software Individual scan files are produced for each microplate When scanning fewer than six microplates add the plates in one through six order as shown below Alignment Guide Figure 3 5 Plate order for multiple microplates The first well in the first row A1 for each microplate should be in the upper left corner as you face the Odyssey instrument Consult the Odyssey User Guide for details on the Scan Multiple Plates function Note If the microplates are poorly centered in the images try adjusting the grid template to match the grid to the wells in the image If some wells are truncated or the grid is off the image the Multiple Scan Settings can be used to change the scan offset to cent
60. ser connection to Odyssey is not continuous the remaining scan time is not automatically updated If you are waiting for a scan to finish and the Status page has been displayed for a while click Refresh to get the latest status information id Chapter 5 User and Scan Group Administration Adding User Accounts Adding user accounts requires Administrator access rights 1 Log in to the Odyssey server by entering http plus the IP address of the Odyssey Imager in the Location URL field of your browser 3 Odyssey Netscape File Edit View Go Communicator Help Odyssey Server Software 2 Click Utilities to open the Utilities page 38 CHAPTER 5 User and Scan Group Administration 3 In the password window enter the User Name and Password of a current account with Administrator rights User Name and Password are case sensitive Username and Password Required 4 Click the Manage User Accounts link on the Utilities page X Odyssey Administration Level Selection Page Netscape The left side of the Utilities page lists all the Odyssey A Home S Scan 4 View Utilities utilities for account management Instrument ilities maintenance and Change Password diagnostics Manage Groups Manage User Accounts Account and Group Instrument Utilities Instrument Status e Delete Preset e Shutdown the Instrument Networking Setup e Set System Time e Scan Test Pattern Update Scanner Software
61. so be shutdown using the browser interface as described in Chapter 8 An account with Administrator access is required to use the Shutdown function Resetting the Instrument In the event that the front panel keypad is unresponsive and you cannot connect to the instrument using an Internet browser the instrument can be reset by holding down the Power key for at least 4 seconds until the instrument turns off This procedure cuts power to the instrument and internal hard disk so it should only be used when communication cannot be established by any other means Odyssey should resume normal operation after the Power key is pressed again to turn the instrument back on though start up may take several minutes Chapter 3 Operation Before You Begin The following procedure is recommended before every scan 1 Thoroughly wash the glass scanning surface with distilled water and wipe with a dust free cloth 2 Repeat the wash with isopropanol to remove any remaining residues If dye contamination continues to be a problem slightly wet a cloth with acetone and wipe the glass Important the acetone must not contact anything other than the glass The paint can be damaged by acetone 3 If you are using the silicone mat rinse it under warm water Gentle lab soap may be used but the soap must be completely rinsed away before use The silicone mat may also be rinsed in isopropanol if needed Dry the silicone mat with a dust free cloth Cl
62. ssentially sorts the fluorescent signals by transmitting the light above 810 nm and reflecting light below 750 nm Transmitted and reflected light travels two independent paths through optics designed to remove scattered and stray light The light is ultimately focused onto one of two avalanche photodiodes that converts the light to an electrical signal for processing by the microscope detection electronics In the microscope electronics the signal is amplified filtered and finally converted to a digital value by an analog to digital converter The digital signal is demodulated filtered again and coordinated with the microscope position by a Digital Signal Processor DSP to produce the image file The entire compact laser microscope assembly travels on a platform that moves beneath the scanning surface below along both the X and Y axes Scanning Surface The scanning surface is a 25 cm x 25 cm glass plate below upon which the samples to be scanned are placed The scanning surface is sealed from the instrument interior so no moisture can penetrate to the detection optics and electronics below Scanning Surface Figure 2 1 Odyssey scanning surface General Description of Scanning Scans can be initiated in any of three ways 1 using the Windows Application Software 2 using an Internet browser or 3 from the Odyssey keypad 14 CHAPTER 2 Odyssey Overview and General Description When scanning is initiated from
63. ssword Note If you need to change the account name delete the existing account and add a new account with the correct name 46 CHAPTER 5 User and Scan Group Administration Deleting User Accounts 1 On the Manage User Accounts page users with Administrator access rights can remove a user by clicking the Remove link next to the user name to be remove Odyssey Administration Level Administration Netscape File Edit Yiew Go Communicator Help gt 3 3 2 u amp BF Back Foward Reload Home Search Netscape Print Security Stop z wt Bookmarks Ae Location com scanapp admin admin index action ManageUserAccounts J EI What s Related C4 SufSaver amp instant Message E WebMail E Contact E People E YellowPages E Download C4 Chan Odyssey gy Home QP Scan lt gt View Utilities ED telp Account and Group Utilities Status Change Password Add Account Manage Groups Change Account Rights O Manage User Accounts admin Password Remove jan Password Remove Instrument Utilities kevin Password Remove e Instrument Status mike Password Remove e Delete Preset ron Password Remove Shutdown the tech Password Remove Instrument Networking Setup a Ou OW Cane 2 Click Remove User Account to confirm removal of the user account or Cancel to leave the account unchanged Status
64. t Note Creating a new account automatically creates a new scan group for the account that has the same name as the account name Use the Manage Groups link to give other users access to the group if desired Adding Users in Odyssey Application Software Matching user accounts must also be created in the Windows based Odyssey Application Software The Odyssey User Guide gives complete details on adding users A summary is given below 1 Start the Odyssey Software 2 Choose Settings gt Users User List Authorized Scanner Users 3 Click Add to add a new user 4 Enter a User Name that exactly matches an existing account name in the Odyssey Imager user names are case sensitive Add User Entry of the e mail address is not required since itis not currently Email Address jsrith location com used on Odyssey software 5 Click OK and then click OK again in the Add User window Name John Smith 42 CHAPTER 5 User and Scan Group Administration Changing User Account Rights If you are logged in using an account with Administrator access rights you can change the account rights of any user as follows 1 Account rights can be upgraded or downgraded by clicking the Change Account Rights link on the Manage User Accounts page Odyssey A Home Gp Scan lt gt Vie Account and Group Satie Utilities e Change Password Add Account Manage Groups Change Accoun
65. t Rights Manage User Password Remove Accounts admin Pacawnrd Remnwe gt a Back Foward Reload Howe Search Netscape Print Security Stop 3 Bookmarks Ai Location tp 1 5 44 23 174 scanapp admin admin inde SurfSaver amp Instant Message ebMail E Contact E E People E YellowPages E Download C4 Cha x action Change ccountRights Odyssey Q Home B Scan lt gt View Utilities DP telp Account and Group User Name Account Rights Utilities x Change Password admin Administrator z e Manage Groups jim conto E Manage User Accounts r kevin contrat z Instrument Utilities mike Con E Instrument Status e Delete Preset fon Browse H e Shutdown the Instrument Bumen op E EN Set System Time e Scan Test Pattern 2 Use the Account Rights drop down list next to the User Name to select new account rights Account rights are described in Adding User Accounts above 3 Click Change to save any changes 43 Changing Your Own Password 1 Follow the instruction in Chapter 4 for logging in to Odyssey using an Internet browser 2 Click Utilities on the home page to open the Utilities page XY Odyssey Netscape of x Eile Edit View Go Communicator Help Scan View Utilities Status 3 In the password window enter your User Name and Password User Na
66. t System Time Account and Group Date Utilities Month faz Day 06 Year feooo e Change Password Manage Groups Time e Manage User Accounts Hour 03 Minute 02 Pm z Instrument Utilities Set Time e Instrument Status Delete Preset e Shutdown the Instrument eee Enter Date and Time and IO Set System Time 4 i e Scan Test Pattern click Set Time Update Scanner ID A fhrrava Important Check instrument status before setting date and time If you attempt to set the clock during a scan the scan will be aborted 80 CHAPTER 8 Instrument Utilities and Diagnostics Updating the Odyssey Instrument Software Updates to the Odyssey instrument software will be posted on LI COR s FTP site and made available on CD ROM Update notifica tions will be sent that detail how to get the update on CD and will also include FTP address name and password information so the files can be downloaded on line IMPORTANT Updating the Odyssey software requires about 100 MB internal hard disk Ifthe hard disk is full the oldest scans will be deleted to make room for the update so make sure you have downloaded all scans before proceeding In many cases the Odyssey Application Software will be updated at the same time as the instrument software Instructions for installing the application software will be provided with the update files Opening the Update Scanner Page Whether you have an
67. tarting the Update 6 If you have an update CD insert the CD into the drive If you downloaded the update file make sure the file is accessible on your computer or network drive 83 7 Click the Browse button and use the standard file selection window to select the update file from CD or disk drive If the upload file name is not displayed make sure the file type is set to All Files in the file selection window 1 Upload Netscape oy xi File Edit View Go Communicator Help ate 324A 2 as amp B i Back Foward Reload Home Search Netscape Print Security Stap z A Bookmarks A Location http 195 44 23 174 scanapp util upload E Whats Related C4 SufSaver Q Instant Message E WebMail E Contact E People E Yelow Pages E Download C4 Chan Odyssey gy Home QP Scan lt d View Utilities GD Heip Software Update Account and Group Utilities e Change Password iaoei Browse Manage Groups Upload Manage User Accounts Instrument Utilities e Instrument Status Delete Preset Shutdown the Instrument Networking Setup e Set System Time Scan Test Pattern iO Update Scanner Software Diagnostic Utilities e User Diagnostics Technician Diagnostics 8 Click the Upload button to load the new software into the Odyssey scanner Odyssey reports on the success of the update procedure by displaying a list of updated components If the upda
68. te was successful each update component will have a green check mark next to it If there was a problem during the update a red will be placed next to the update component that failed and a failure message will be displayed Contact LI COR Technical Support if the update fails 84 CHAPTER 8 Instrument Utilities and Diagnostics Details of the update can be examined by clicking Show Activity Log If you have a failure during an update LI COR Technical Support may ask you to e mail or print the activity log Note Error and warning messages are a normal part of the activity log even for successful updates Only LI COR Technical Support can interpret the activity log All changes take affect as soon as the update is completed Click Go To Home Page to continue using the Odyssey instrument User Diagnostics If you have a problem with your Odyssey Imager LI COR Technical Support staff may ask you to perform the User Diagnostic function If you suspect a problem with the instrument the User Diagnostic can also be used to verify a problem before contacting technical support To start the User Diagnostic open the Utilities page and click the User Diagnostics link F Odyssey Diagnostics Viewer User Level Netscape File Edit View Go Communicator Help Odyssey gy Home Gp Scan 4 View Utilities iol xi C2 Help Account and Group Utilities e Change Password e Manage Groups e Manage User Accounts
69. th America 800 645 4267 International 402 467 0700 e 402 467 0819 LI COR GmbH 49 0 6172 17 17 771 LI COR UK Ltd 44 0 1223 422104 www licor com Serving Austria Czech Republic Germany Hungary Slovakia and Switzerland Table of Contents Chapter 1 Safety and Operational Information In This Manual cceeeceeseeseeeseeesreeereeereees 1 Safety Considerations ccceeseeeeeteeeteeeeees 1 laser Saey rera nr nnn OAR 1 Safety InterlocKsyrennan nnna n 4 Chemical Saleyonaninnn ern nanna 4 Placement in the Laboratory s s s ssesesse 4 Ambient Laboratory Conditions 5 Ventilation c i i sens cevssent cant carscavdias caneaicass 5 Space ReguihemMents nsnsssunenni inna 5 Moving the Odyssey System 0 0 5 Electrical Considerations 0 0 0 0 cece 7 Power COrdSisc csc esceesccsaxeos deus cdvndees corseevsiaes 7 Fuse Replacement sscessseesseeeeereeees 7 Routine MaintenanCeseessrne tare aroas 8 Chapter 2 Odyssey Overview and General Description OVEIVIEW cen visssinsacesacessustoonsesesndeiocassentiesseds 11 Hardware Description s s s ssesesesererereren 12 Scanning Surface sssececcsseseeeeeeeeaes 13 General Description Of Scanning 13 Continuous OperatiOn seiesarsnisarsnieneni 15 Powering Off the System n s 16 Power BUTON 0 lt hcessccesdencepseascennosassensens 16 Software Shutdown cceeeeeeeeees 16 Resetting the Instrument sesser
70. the Application Software or an Internet browser the user is presented with a representation of the scanning surface from which the origin of the scan and the size of the area to be scanned are chosen 2 8 gt vo X Y 0 5 10 15 20 25 X Axis cm Figure 2 2 Scan origin and size of sample are chosen in software Scanning starts at the lower left hand corner of the scanning surface when facing the front of the instrument and progresses first across the X axis and then steps up incrementally along the Y axis of the scanning surface as shown in Figure 2 3 The scan will again progress along the X axis until the specified area has been scanned Figure 2 3 Scans start at the lower left hand corner of the scanning surface and progresses across the X axis and up the Y axis Continuous Operation The Odyssey Imager and network switch are designed to operate continuously During idle times the Odyssey Imager can remain powered on or be powered off at your discretion If the Odyssey Imager needs to be powered off when moving it for example see Powering Off The System below 16 CHAPTER 2 Odyssey Overview and General Description Powering Off the System Power Button Briefly press the Power button on the front panel keypad to shut down the Odyssey Imager You will be asked to confirm that you want to shut down Press the Y start button to shut down Software Shutdown The Odyssey instrument can al
71. the Odyssey home page That discussion describes how to use the Status page to determine whether the instrument is in operation who the user is and how much time remains in the current scan The Status page can also be accessed by clicking the Instrument Status link on the Utilities page Odyssey Administration Level Selection Page Netscape Eile Edit View Go Communicator Help Odyssey fal Home Gp Scan 4 View Utilities C2 Help Account and Group Utilities e Change Password e Manage Groups Manage User Accounts Instrument Uses ge e Instrument Status e Delete Preset e Shutdown the Instrument 76 CHAPTER 8 Instrument Utilities and Diagnostics Instrument Shutdown The Odyssey Imager is normally shut down by pressing the Power key on the keypad but Odyssey can also be shut down using the Shutdown The Instrument link on the Utilities page Check the instrument status to make sure it is idle before shutting down the instrument Odyssey Administration Level Administration Netscape File Edit View Go Communicator Help XZ 3 4 2 a sts S amp S ww Back Foward Reload Home Search Netscape Print Security Stop 1 SE Bookmarks A Location 44 23 174 scanapp admin admin index action InitiateShutdown QE What s Related C SutSaver amp Instant Message E WebMail E Contact E People E YellowPages E Download C4 Chan Odyssey fey Home QP Scan lt gt View Utilities ED Help
72. w any signal even though there is adequate fluorescence from the samples LI COR Presets use an intensity value of 5 0 for membranes 8 0 for DNA gels 5 0 for protein gels and 5 0 for microplates These settings may need to be optimized for your scans due to the differing background fluorescence of various materials Intensity values from 1 to 10 in increments of 0 5 can be chosen as well as low intensity values LO 5 to L2 0 L2 0 is the lowest intensity value Odyssey can use for scanning 57 The Channels check boxes let you specify whether to detect the 700 channel 800 channel or both When both are selected fluorescence from each dye is detected separately and stored in a separate image file Scan Area is used to specify the portion of the 25 x 25 cm scan surface that will be scanned 25 N o r Width 1 Y Axis cm ry a Height uo Origin X Y XH ra 0 5 10 15 20 25 X Axis cm For the Origin enter the X and Y offset of the left front corner of the area to be scanned Only integer values representing centimeters can be entered The front left corner of the scanning surface has an Origin of X 0 Y 0 The tip of the white arrow on the scan surface is the 0 0 position In general it is best not to place the membrane or gel at the 0 0 position The scan area should always be larger than the membrane or gel so labels placed on the image during analysis will be displayed properly For low res
73. word are case sensitive 36 CHAPTER 4 Accessing Odyssey With An Internet Browser The Status page is a typical Odyssey page The navigation bar at the top of the page indicates that the Status page is in the Utilities section The left side panel has navigation links for the various utility functions t Odyssey Instrument Status Netscape oO x Eile Edit View Go Communicator Help Odyssey fal Home amp p Scan 42 View Utilities C2 Help Account and Group Scanner Status scanning Utilities e Change Password Current User Pat Percent Complete 44 p isece Time Ri a 5 00 05 05 e Manage User Accounts EEN sae Lid Status closed Instrument Utilities IO Instrument Status Refresh e Delete Preset e Shutdown the Instrument e Networking Setup e Set System Time e Scan Test Pattern e Update Scanner Software Diagnostic Utilities e User Diagnostics e Technician Diagnostics e View System Log e View Scan Log e Browser Test Links for system administration and technician functions are shown however only users accounts with Administrator or Technician access will be able to use those functions In the main body of the page is a box showing the status of the Odyssey Imager The status is typically dle Paused or Scanning The status could also be some error state When Odyssey is in operation as shown above the user is listed as well as the remaining scan time Because the brow
74. y The sensitivity on each channel can be adjusted independently by entering a value or by clicking the arrow buttons The up and down arrows labeled 1 provide coarse sensitivity adjustment and the arrows labeled 1 provide a finer adjustment 67 Inverting the Grayscale Map When only a single image channel is displayed see Showing and Hiding Image Channels below the grayscale image map can be inverted by clicking Invert in the toolbar and then clicking the Black White button Clicking Black White toggles between a white image background with black bands and a black background with white bands X View Scan Netscape Iof x Eile Edit View Go Communicator Help Odyssey fg Home gt Vi Utilities Corr Scan Background Background white Black White 3 View Scan Netscape Eile Edit View Go Communicator Help Odyssey gy Home Gp Scan Viv Ter T Scan Background Background black BlackWhite 68 CHAPTER 7 Importing and Editing Scanned Images Changing Image Orientation Rotating the Image If an image was scanned upside down or in some other orientation the image can be rotated in 90 degree increments by clicking Rotate in the toolbar and then clicking 90 CW or 90 CCW The 90 CW and 90 CCW buttons rotate the image 90 degrees in either a clockwise or counter clockwise direction respectively 3 View Scan Netscape ioj x Eile Edit View Go Communicator Help Odyssey
75. ze 1 1 Large images may be displayed at a reduction to fit the window 64 CHAPTER 7 Importing and Editing Scanned Images Changing the Appearance of an Image Zooming In and Out When large images are opened they are often displayed at a reduction to fit the window Images may be displayed at 1 2 1 4 or even smaller To enlarge an image click the Zoom button and then click the image When the Zoom Factor reaches 1 1 actual size clicking the image will no longer enlarge it To reduce the image click Reset Image to return the image size it was when the window was opened 3 View Scan Netscape iof x Eile Edit View Go Communicator Help 3 4a u ds amp amp Back Forward Reload Home Search Netscape Print Security Stop 3 E Bookmarks 4 Location htr 195 44 23 174 scanapp imaging nonjava index gt Ge What s Related j SurfSaver amp Instant Message E WebMail J Contact S People E Yellow Pages E Download Chant Odyssey gy Home Gp Scan lt 2 View Utilities ED Heip Zoom Zoom Factor 1 1 Reset Image 65 Cropping an Image To crop an image start by clicking Crop in the toolbar Next define a rectangular crop area by clicking the mouse at the upper left and lower right corners of the area to be cropped as shown below cross hair marks are show for illustration only View Scan Netscape Of x Fie Edit View Go Communicator Help Odyssey gy Home Utilities Hei
76. ze the Preset parameters by editing individual scan parameters using the scan parameter definitions given below Resolution can be set to 21 42 84 169 or 337 um For typical scans of membranes or gels 169 um scans should suffice Resolution can be increased as needed however note that the file sizes can get very large If you intend to analyze the images with Odyssey Application Software choose a resolution that keeps the file size of individual images under 10 MB 20 MB for both images Quality controls scanning speed and ultimately how many detector readings are processed for a given area on the membrane to make a pixel on the image For typical scans Medium is recommended but there are five settings Choosing Highest quality will reduce noise in the image data but significantly increase scanning time due to the slower scanning speed Similarly choosing Lowest will decrease scanning time but increase noise in the image data For high resolution scans where samples have very little fluorescence High or Highest may be a better choice than Medium When quality is set too low the image will become noisy or grainy particularly in the background The Intensity fields control the detector sensitivity and affect the band intensity on the image If the intensity is set too high the detector may saturate which produces white areas in the middle of intense bands dots on color images If the intensity is set too low the image may not sho

Odyssey Infrared Imaging System Operator`s Manual v 2.1

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