Odyssey LI-COR Operator's Manual
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Odyssey LI-COR Operator's Manual

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Summary of Contents for Odyssey LI-COR

  • Page 2 CE Marking: This product (model number 9120) is a CE-marked product. For conformity information, contact LI-COR Support at biosupport.licor.com. Outside of the U.S., contact your local sales office or distributor.
  • Page 3 Note on Safety LI-COR products have been designed to be safe when operated in the manner described in this manual. The safety of this product can not be guaranteed if the product is used in any other way than is specified in this manual.
  • Page 4 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.
  • Page 5 : +49 (0) 6172 17 17 771 (Serving Europe, Africa, and the Middle East) LI-COR UK Ltd., UK : +44 (0) 1223 422104 (Serving UK, Ireland, and Scandinavia) All other countries, contact LI-COR Biosciences or a local LI-COR distributor: http://www.licor.com/distributors www.licor.com...

  • Page 7: Table Of Contents

    Positioning Microplates......24 Ventilation..........5 Scanning Multiple Microplates ....25 Space Requirements ......... 5 Front Panel Controls........26 Moving the Odyssey System ..... 5 Setting the Network Address From the Electrical Considerations ......7 Front Panel ..........27 Power Cords..........7 Starting Scans From the Front Panel..27 Power Switch ...........
  • Page 8 Chapter 8: Importing and Editing Scanned Images Chapter 5: Accessing the Opening the View Page....... 89 Odyssey Imager With an Opening a Scan Stored on the Odyssey Imager ............90 Internet Browser Changing the Appearance of an Image..92 Overview........... 59 Zooming In and Out .......92 Connecting to the Odyssey Imager Using Cropping an Image .........93...
  • Page 9 ® Updating the Odyssey Instrument Software ..........108 Opening the Update Scanner Page..108 Starting the Update ......110 User Diagnostics ........112 Browser Test..........113 Technician Diagnostics ......115 Chapter 10: Appendices Specifications ..........117 Error Messages........... 118 Scan Setup..........118 Scan Console..........

  • Page 11: Chapter 1: Safety And Operational Information

    Description of detection optics and signal processing. ® • Odyssey Infrared Imaging System operation. • Use and maintenance of the Odyssey scanning bed. • 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.
  • Page 12 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.
  • Page 13 80 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.

  • Page 14: Safety Interlocks

    Be aware of the hazards associated with any chemical before using it. The Odyssey Imager should not be used with any radioactive materials. Placement in the Laboratory The Odyssey Infrared Imaging System weighs approximately 33 kg (72 lb).

  • Page 15: Ambient Laboratory Conditions

    filtered, and the cover serves only as an exhaust outlet. Space Requirements The Odyssey System requires an area approximately 54 cm W (21.3") × 62 cm D (24.4"). 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.
  • Page 16 10BASE-T or 100BASE-TX ® Use a minimum of two people when moving the Odyssey System, as it weighs about 33 kg (72 pounds). Lift under the metal enclosure on each side of the unit, and keep the unit as near vertical as possible.

  • Page 17: Electrical Considerations

    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...

  • Page 18: Fuse Replacement

    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 ® Biosciences or a LI-COR representative.

  • Page 19: Networking Cables

    Networking Cables ® Multiple Cat. 5 networking cabes are provided with the Odyssey Imager. Do not use networking cables other than the ones provided. The use of other networking cables may result in improper electrical performance.

  • Page 21: Chapter 2: Overview And General Description

    Odyssey hard disk to local drives for storage and analysis. Note: Although the Odyssey Imager 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.

  • Page 22: Hardware Description

    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.

  • Page 23: Scanning Surface

    Surface Figure 2-1. Scanning surface on the Odyssey Imager. General Description of Scanning ® Scans can be initiated in any of three ways; 1) using the Odyssey Application Software; 2) using an Internet browser, or 3) from the Odyssey keypad.
  • Page 24 CHAPTER 2 Odyssey Overview and General Description ® When scanning is initiated from the Odyssey 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.

  • Page 25: Continuous Operation

    When idle, the Odyssey Imager uses approximately 0.5 amp of power, about the same as a light bulb. If the Odyssey Imager needs to be powered off (when moving it, for example), see Powering Off The System below.

  • Page 26: 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. Shutdown via the Browser Interface The Odyssey instrument can also be shutdown using the browser interface as described in Chapter 8.

  • Page 27: Chapter 3: Operation

    Chapter 3: Operation Before You Begin... The following procedure is recommended before every scan: 1) Thoroughly wash the glass scanning surface with ultrapure water and wipe with a lint-free tissue. 2) Repeat the wash with isopropanol to remove any visible smears. Use ethanol to remove any remaining residues.

  • Page 28: Using Membranes

    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. Contaminated surfaces in contact with the membrane surface may cause blotches and streaks that cannot be removed with further washing.

  • Page 29: Using Gels

    Odyssey Infrared Imaging system, allowing gels of up to 8 mm to be scanned. Note: Early versions of the Odyssey Imager were limited to a 2.0 mm focus offset, but can be upgraded by installing the Odyssey Server Software version 2.0.0 or above.

  • Page 30: Using Microplates

    Some general consid- erations for microplate selection are provided below. • 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. •...

  • Page 31: Using The Mousepod Accessory

    • 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.

  • Page 32: Positioning Membranes And Gels

    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.
  • Page 33 1 cm larger than the membrane in all dimensions. The larger scan boundary creates an ® image that is easier to analyze in the 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.

  • Page 34: Positioning Microplates

    Microplates can be scanned one at a time using the browser interface or by choosing ® File > Scan in the Odyssey Software and using the Microplate2 scan preset. Alignment Guide Figure 3-4.

  • Page 35: Scanning Multiple Microplates

    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 center the wells on the image for new scans (see the Odyssey User Guide, Chapter 2).

  • Page 36: Front Panel Controls

    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. Figure 3-6.

  • Page 37: Setting The Network Address From The Front Panel

    file called a Preset. These Presets are created and stored in the Odyssey Imager using the Scan page of the Odyssey Server Software (Chapter 6). Once stored, Presets can be chosen when starting scans from the front panel keypad.

  • Page 38: Downloading Scans

    Odyssey Application Software to start the scan rather than the keypad (see the 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.

  • Page 39: File Size And Storage Capacity

    5) Click OK to download the selected scan 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.
  • Page 40 20 x 25 cm 800k 3.5M 14.1M 56.7M 226.7M 25 x 25 cm 1.1M 4.4M 17.6M 70.9M 283.4M ® Can be scanned with the Odyssey Application Software Marginal for the Odyssey Application Software Scan should be started using the browser interface...

  • Page 41: Scanning Limitations

    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 gray 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;...

  • Page 42: Software Options

    ® 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 Odyssey User Guide and Tutorial Manual describe the use of this software.

  • Page 43: Chapter 4: Connecting The Odyssey Imager To A Network

    In the Basic configuration, the Odyssey Imager is connected only to the computer. In the Networked configurations, the Odyssey Imager is connected to the network and can be accessed by any computer on the network. The Odyssey Imager is a network server device that can be connected to a network, and ultimately to a computer, via TCP/IP.

  • Page 44: Firewall Recommendations

    Firewall Recommendations For networks connected to the Internet, the safest way to protect your research and data is to put the Odyssey instrument and computer on a subnet that is behind a firewall. Inexpensive firewall appliances can perform this function. Contact your local IT department for help in selection and configuration if your organization does not already...
  • Page 45 10)Click Finish when installation is complete. Note: When installing the Odyssey software on a computer that has the older Odyssey software installed, the installation application needs to be run once to remove the older software and then again to install the latest Odyssey software.

  • Page 46: Adding Users

    Adding Users If you previously had a user account and password on the Odyssey Imager, it will still be there. If you do not have a user account, you will need to create one before you can use the Odyssey Imager.

  • Page 47: Configuring The Windows System For The Odyssey Software

    Log in to the Odyssey software using an account with Adminis- ® trator access. In the Windows 7 operating system, right click on the Odyssey desktop icon and select Run as admin. b) Insert the CD for the module in your CD-ROM drive.
  • Page 48 CHAPTER 4 Connecting the Odyssey Imager to a Network Odyssey Settings folder. If all of the Odyssey users have Administrator accounts (or use the same Administrator account), it is not necessary to perform this procedure. It is also not necessary to perform this ®...
  • Page 49 6) Click OK to close the Folder Options window. ® 7) Use Windows Explorer to find the Licor folder at the following path: C:\Documents and Settings\All Users\Application Data. 8) Right click the Licor folder and select Properties from the menu. 9) Select the Security tab in the Licor Properties window.
  • Page 50 CHAPTER 4 Connecting the Odyssey Imager to a Network ® 10)Select any users or groups that will use the Odyssey software and select Full Control (Allow column) in the Permissions for Users list. 11)If there are any account names or groups not shown in the list that ®...
  • Page 51 Windows Vista and Windows 7 Instructions ® Follow the instructions below to configure the Windows Vista ® Windows 7 operating system to allow access to the Odyssey settings folder to all users. 1) Open the system Control Panel. 2) Select Appearance and Personalization > Folder Options.
  • Page 52 C:\ProgramData. 8) Right click the Licor folder and select Properties from the menu. 9) Select the Security tab in the Licor Properties window. ® 10)Select any users or groups that will use the Odyssey software and press the Edit button.
  • Page 53 Licor window. Select Full control (Allow column). 12)If there are any account names or groups not shown in the list that ® need to use the Odyssey software, click Add. 13)Enter the names of user accounts or groups and click Check Names.

  • Page 54: Assembling The Basic Hardware Configuration

    3) Turn on the computer and the Odyssey Imager and wait for their start-up procedures to complete. 4) Set up the Odyssey Imager with a static IP address. See Config- uring the Odyssey Imager with a Static or Automatic (DHCP) IP Address later in this chapter.
  • Page 55 When the Odyssey software starts, it goes through an autodiscovery process that finds any Odyssey instruments that are on the same network. 7) To confirm that the Odyssey software can communicate with the Odyssey Imager, choose Settings > System Administration.

  • Page 56: Assembling The Networked Configuration

    DHCP server. 1) Start by turning off both the Odyssey Imager and the computer. 2) Connect the Cat. 5 RJ-45 cable included from the Odyssey Imager directly to the local network port (LAN).
  • Page 57 Imager and computer, but don’t start the Odyssey Application Software. Note: When the Odyssey Imager and computer start up, they will be assigned an IP address automatically by your DHCP server. This can take as long as 5 minutes and it is best to wait for addresses to be assigned before starting the Odyssey software.
  • Page 58 (Settings > Scanners) and clicking Autodiscover in the Scanner List window. If the interval for address expiration is short, you may find it easier to use a static IP address in the Odyssey Imager to avoid loss of communication. See Configuring the Odyssey Imager with a Static...

  • Page 59: Connecting To A Network Using An Ethernet Switch

    Odyssey Imager and computer to the network. With this scheme, it is possible to connect both the Odyssey Imager and the computer to the network even if only one network port is available. Both the Odyssey Imager and the computer are set up for automatic (DHCP) addressing.

  • Page 60: Setting A Static Or Automatic (Dhcp) Ip Address

    Imager and computer, but don’t start the Odyssey Application Software. Note: When the Odyssey Imager and computer start up, they will be assigned an IP address automatically by your DHCP server. This can take as long as 5 minutes and it is best to wait for addresses to be assigned before starting Odyssey software.
  • Page 61 IP address for the Odyssey instrument that you copied down in step 2. 4) On the Odyssey “home” page, click Utilities. 5) When prompted for a user name and password, enter admin in both fields (or use some other administrator account, if you have...
  • Page 62 CHAPTER 4 Connecting the Odyssey Imager to a Network 6) Click the Networking Setup link on the Utilities Page. 7) For automatic addressing, select Use DHCP. For static addressing, select Static IP for the type of IP address. 8) If using static addressing, enter the IP Address and Net Mask...
  • Page 63 field. ® 12)Click the Configure button to send the changes to the Odyssey Imager and then close your Internet browser software. 13)Close the internet browser. Updating the Scanner Settings ®...

  • Page 64: Configuring The Computer With A Static Or Automatic (Dhcp) Ip Address

    CHAPTER 4 Connecting the Odyssey Imager to a Network Configuring the Computer with a Static or Automatic (DHCP) IP Address ® The following are generalized instructions for configuring Windows to use a static or automatic (DHCP) IP address. Consult with your network administrator for specifics on configuring a computer for...
  • Page 65 5) In the Local Area Connection Status window, click Properties on the General tab. 6) Scroll through the list of connection items on the Networking tab, select Internet Protocol Version 4 (TCP/IPv4), and click Properties.

  • Page 66: Connecting Other Computers On The Network

    If you have the Odyssey Imager set for static IP configuration, all you need to do is install the Odyssey software on the new computer and add the Odyssey Imager to the scanner list as follows: 1) Choose Settings >...
  • Page 67 IP address. It is possible that you may not have to do anything but install the Odyssey software. If you are on the same network as the Odyssey Imager, the Odyssey software will find the scanner when the software starts and it will be added to the scanner list.

  • Page 69: Chapter 5: Accessing The Odyssey Imager With An Internet Browser Overview

    Functions that have restricted access are noted where appro- priate throughout the remainder of this manual. Note: Browser-based access to images on the Odyssey instrument 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.
  • Page 70 Odyssey Imager. (Use the IP address supplied by your System Administrator, not the one shown in the graphic.) Note: The current IP address of the Odyssey Imager can also be displayed on the Odyssey front panel as described in Chapter 3. The Odyssey Imager sends a “home page”...

  • Page 71: Checking Instrument Status

    Odyssey Imager’s internal hard disk. Using the Status link on the Odyssey Imager’s home page, a browser on an office computer can be used to find out whether someone is scanning a membrane in the lab.
  • Page 72 Password are case sensitive. 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...
  • Page 73 Odyssey Imager. The status is typically Idle, Paused, or Scanning. The status could also be some error state. When the Odyssey Imager is in operation, as shown above, the user is listed as well as the remaining scan time. Because the browser connection to the Odyssey Imager is not continuous, the remaining scan time is not automatically updated.

  • Page 75: Chapter 6: 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 the browser.
  • Page 76 CHAPTER 6 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. 4) Click the Manage User Accounts link on the Utilities page. The left side of the Utilities page lists all the utilities for account...
  • Page 77 5) Click the Add Account link. The Manage User Accounts page displays a list of all current accounts. Using this page, accounts can be added, deleted, or changed. 6) Set the Account Rights for the new user according to the following definitions: None: When account rights are set to None, the user account becomes •...
  • Page 78 • 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.

  • Page 79: Changing User Account Rights

    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. 2) Use the Account Rights drop-down list next to the User Name to select new account rights.

  • Page 80: Changing Your Own Password

    User and Scan Group Administration Changing Your Own Password ® 1) Follow the instruction in Chapter 4 for logging in to the Odyssey Imager using an Internet browser. 2) Click Utilities on the home page to open the Utilities page.
  • Page 81 4) Click the Change Password link in the Account and Group Utilities section. 5) Enter your current password in the Old Password field. 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.

  • Page 82: Changing Other Users' Passwords

    CHAPTER 6 User and Scan Group Administration Changing Other Users’ Passwords If you are logged in using an account with Administrator access rights, you can change 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.

  • Page 83: Deleting User Accounts

    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. 2) Click Remove User Account to confirm removal of the user account or Cancel to leave the account unchanged.

  • Page 84: Deleting The Original Admin Account

    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.

  • Page 85: Changing Access Permission Of A Scan Group

    2) Enter a name for the group in the Group Name field. 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.
  • Page 86 CHAPTER 6 User and Scan Group Administration 2) Click the Permissions link next to the scan group that you want to change. 3) Use the Permission Level drop-down list next to the user name to change access permission of the user. A permission level of None indicates no access.

  • Page 87: Deleting Scan Groups

    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.

  • Page 88: Viewing And Deleting Scans Within A Scan Group

    CHAPTER 6 User and Scan Group Administration 3) Click the Confirm Remove Group button. 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.
  • Page 89 2) Click the Scans link next to the scan group containing the scans you want to view or delete. 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.

  • Page 91: Chapter 7: Starting Scans Using An Internet Browser

    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 92: Naming The Scan

    CHAPTER 7 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.

  • Page 93: Entering Scan Parameters

    If you are not using Preset parameters skip to Step 4. ® The Odyssey software initially has three sets of Preset parameters – one for membranes and two for gels. LI-COR Presets Membrane DNA Gel Protein Gel Microplate Resolution Quality...
  • Page 94 If the intensity is set too low, the image may not show 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.
  • Page 95 Intensity values from 1 to 10 in increments of 0.5 can be chosen, as well as low intensity values L0.5 to L2.0. L2.0 is the lowest ® intensity value the Odyssey Imager can use for scanning. The Channels check boxes are used to specify whether to detect the 700 channel, 800 channel or both.

  • Page 96: Starting A Scan

    The scan is not actually started until the Start button is clicked, but the Odyssey Imager is reserved for the user who initiated the scan. Other users on the network will not be able to start scans until the...
  • Page 97 (though they can download scans for ® analysis). While the Odyssey Imager is reserved but not scanning, the membrane can be placed on the scan surface without inter- ruption 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.

  • Page 98: Stopping A Scan

    Stopping a Scan ® At the end of a scan, image files are stored on the Odyssey Imager’s internal hard drive in the specified scan group. Images stored on the Odyssey Imager can be downloaded using the Odyssey application software, or using a browser as described in Chapter 7.

  • Page 99: Chapter 8: Importing And Editing Scanned Images

    Chapter 8: Importing and Editing Scanned Images Opening the View Page ® 1) Open the Odyssey home page using a browser as described 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.)

  • Page 100: Opening A Scan Stored On The Odyssey Imager

    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 the Odyssey Imager. 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.
  • Page 101 ® 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.

  • Page 102: Changing The Appearance Of An Image

    CHAPTER 8 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.

  • Page 103: Cropping An Image

    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).

  • Page 104: Changing Image Appearance

    The up and down arrows labeled “1” provide coarse sensitivity adjustment and the arrows labeled “.1” provide a finer adjustment. Note: Changing the sensitivity does not affect the quantification of the image, as the ® software quantifies the data from the Odyssey image file.

  • Page 105: Inverting The Grayscale Map

    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.

  • Page 106: Changing Image Orientation

    CHAPTER 8 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.

  • Page 107: Flipping The Image

    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. Showing and Hiding Image Channels When a scan is opened, the images are initially displayed in color with both image channels overlaid.
  • Page 108 CHAPTER 8 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.

  • Page 109: Displaying Scan Information

    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. The More Information button shows complete information about a completed scan or a scan still in progress.

  • Page 110: Saving Changes To Images

    CHAPTER 8 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. To save the log file for the scan, click Save Scan Log.

  • Page 111: Printing Image Files

    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 the Odyssey Imager operation. The image can then be printed by choosing File > Print.

  • Page 113: Chapter 9: Instrument Utilities And Diagnostics

    Chapter 4 describes opening the Status page for the Odyssey Imager by clicking the Status link on 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.

  • Page 114: Instrument Shutdown

    The Odyssey Imager is normally shut down by pressing the Power key on the keypad, but the Odyssey Imager 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.

  • Page 115: Editing Network Addresses

    Odyssey Imager uses each field is given below. The Network Setup link is found on the Utilities page. Note: For stand-alone (non-network) configurations, the IP Address and Net Mask can be entered from the Odyssey front panel as described in the Installation Manual.

  • Page 116: Dhcp Vs. Static Addressing

    (MAC address is also accessible from the Odyssey front panel.) Using Host Names In order to connect to the Odyssey Imager using a browser, you must enter either the instrument’s IP address or a host name assigned to it.

  • Page 117: Setting Date And Time

    files were created. The Set System Time link on the Utilities page is used to set the clock in the Odyssey Imager. A backup battery maintains the clock when power is discon- nected, so it is generally only necessary to set the clock when the Odyssey Imager is first installed.

  • Page 118: Updating The Odyssey Instrument Software

    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. If the hard disk is full, the oldest scans will be deleted to make room for the update, so make sure all scans are downloaded before proceeding.
  • Page 119 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...

  • Page 120: Starting The Update

    CHAPTER 9 Instrument Utilities and Diagnostics 5) Click the Update Scanner Software link on the Utilities page. Starting 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.
  • Page 121 Technical Support if the update fails. Details of the update can be examined by clicking Show Activity Log. If there is 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.

  • Page 122: User Diagnostics

    Instrument Utilities and Diagnostics 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.

  • Page 123: Browser Test

    The test results can be transferred to a file by clicking the Download button. The file can then be transferred to LI-COR Biosciences via mail or as an e-mail attachment. If you have a gateway address and DNS server address specified on the Network Setup page, you can also e-mail the file directly using...
  • Page 124 CHAPTER 9 Instrument Utilities and Diagnostics To run the browser diagnostic, open the Utilities page and click the Browser Test link. ® If the test fails, download a current copy of the Internet Explorer browser (www.microsoft.com) from the Internet.

  • Page 125: Technician Diagnostics

    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 the ®...

  • Page 127: Chapter 10: Appendices

    Chapter 10: Appendices Specifications Laser/Microscope Laser Lifetime: 40,000 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 µm. 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.

  • Page 128: Error Messages

    CHAPTER 10 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.

  • Page 129: Scan Console

    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.

  • Page 130: Time Setup

    CHAPTER 10 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 >...

  • Page 131: Utilities: User/Technician Diagnostics, View System Log, View Scan Log

    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.

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