Applied Biosystems CytoFluor 4000 Series User Manual
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Applied Biosystems CytoFluor 4000 Series User Manual

Applied Biosystems CytoFluor 4000 Series User Manual

Fluorescence multi-well plate reader
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Applied Biosystems CytoFluor 4000 Series User Manual

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Summary of Contents for Applied Biosystems CytoFluor 4000 Series

  • Page 1 Artisan Technology Group is your source for quality new and certified-used/pre-owned equipment SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT • FAST SHIPPING AND DELIVERY Experienced engineers and technicians on staff Sell your excess, underutilized, and idle used equipment at our full-service, in-house repair center We also offer credit for buy-backs and trade-ins •...
  • Page 2 CytoFluor ® Series 4000 Fluorescence Multi-Well Plate Reader User Guide DRAFT August 30, 2001 6:30 pm FLORFM.FM5 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 3 This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document.
  • Page 4 WARNING For continued protection against fire hazard, replace fuses with those of the same type and rating. AVERTISSEMENT Remplacez les fusibles par ceux de même type et puissance pour éviter les risques d’incendie. Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 5 US Safety and EMC (Electromagnetic Compliance) Standards Safety This instrument has been tested to and complies with standard ANSI/UL 3101-1, “Electrical Equipment for Laboratory Use; Part 1: General Requirements”, 1st Edition. It is an ETL Testing Laboratories listed product. 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 operation.
  • Page 6 EN61010-1 “Safety Requirements for Electrical Equipment for Mea- declared: surement, Control and Laboratory Use” EN55011:1991, Group 1, Class B “Radiated Emissions” EN50082-1:1992 “Generic Immunity” Manufacturer’s Name: Applied Biosystems Manufacturer’s Address: 500 Old Connecticut Path Framingham, Massachusetts 01701 USA Type of Equipment: Laboratory Instrumentation...
  • Page 7 EN61010-1 “Safety Requirements for Electrical Equipment for Mea- declared: surement, Control and Laboratory Use” EN55011:1991, Group 1, Class B “Radiated Emissions” EN50082-1:1992 “Generic Immunity” Manufacturer’s Name: Applied Biosystems. Manufacturer’s Address: 500 Old Connecticut Path Framingham, Massachusetts 01701 USA Type of Equipment: Laboratory Instrumentation...

  • Page 8: Table Of Contents

    Table of Contents Table of Contents How to Use This Guide ................xi Chapter 1 Overview of the CytoFluor System ..........What is the CytoFluor System? ..............How Does It Work? ....Overview of the System Process and Chapter References Chapter 2 Getting Started ............
  • Page 9 ..........Entering Concentration Parameters 5-15 ..............Defining Plates 5-16 5.6.1 Preparing the Scanner ............5-16 5.6.2 Defining a Plate ..............5-17 5.6.3 Deleting a Plate ..............5-20 viii Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 10 Table of Contents ............. Using 384 Well Plates 5-21 5.7.1 Defining the 384 Well Plate ...........5-21 5.7.2 Selecting the Read Pattern Option ........5-22 ..........Setting Auto Scale Parameters 5-25 ............ Exiting the CytoFluor System 5-28 Chapter 6 Customizing the CytoFluor System ............
  • Page 11 ............Limited Product Warranty ............Damages, Claims, Returns Appendix D Plate Scan Patterns ............. D-1 Appendix E Technical Support and Training ......E-1 Glossary Index Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 12: How To Use This Guide

    How to Use This Guide Purpose of this Applied Biosystems CytoFluor Series 4000 Multi-Well Fluorescence Reader User’s Guide describes how to set up, guide ® use, and maintain the CytoFluor Series 4000 Fluorescence Multi-Well Plate Reader. This system enables you to scan data on soluble and cell-associated fluorescence.
  • Page 13 Technical Information Appendix A, Provides basic information on how to Introduction to use Microsoft Windows and defines Windows basic Microsoft Windows terms Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 14 Appendix B, Error Describes and defines CytoFluor Messages system test vectors and error messages. Appendix C, Contains warranty, service, and return Warranty/Service information. Information Appendix D, Plate Provides examples of the scan Scan Patterns patterns the CytoFluor system uses when averaging points taken in a well. Appendix E, Describes how to contact Technical Technical Support...
  • Page 15 Send us your We welcome your comments and suggestions for improving our manuals. You can send us your comments by e-mail at comments TechPubs@appliedbiosystems.com. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 16: Chapter 1 Overview Of The Cytofluor System

    NOTE: Complete and return the provided CytoFluor installation qualification report. Applied Biosystems must receive your completed installation qualification report before you can receive technical support and product update information. The registration number for your system software is on the program disk.

  • Page 17: What Is The Cytofluor System

    In addition, the scanner requires little maintenance. The most important routine maintenance task is changing the air filter. (See Chapter 7, Maintaining the CytoFluor System, for instructions.) Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 18 CytoFluor Series 4000/TR—Temperature-ready model not equipped with a temperature control chamber. TR models can be upgraded with a temperature control chamber. Contact Applied Biosystems for more information. CytoFluor User’s Guide Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 19: How Does It Work

    CytoFluor System. The system stores scanned information and the setup in a CytoFluor data file. You can save and export file data from within the application. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 20: Overview Of The System Process And Chapter References

    Overview of the System Process and Chapter References 1.3 Overview of the System Process and Chapter References This chart overviews the basic steps you follow to use CytoFluor and refers you to the appropriate chapter for details: Step Action Described in … Set up the scanner.
  • Page 21 Section 8, Accessing Technical Information, contains system specifications and catalogue numbers; Appendix E, Technical Support and Training, provides information on how to contact the Applied Biosystems Technical Support Department by phone, fax, or through the internet. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 22 Getting Started This chapter includes the following sections: 2.1 Parts of the CytoFluor System ....2-2 2.2 The CytoFluor Scanner......2-5 2.3 Computer System Requirements ....2-9 2.4 Setting Up Your System......2-10 2.5 Checking the System....... 2-21 2.6 Shutting Down the System ....... 2-26 CytoFluor User’s Guide Artisan Technology Group - Quality Instrumentation ...

  • Page 23: Parts Of The Cytofluor System

    CytoFluor Series 4000 Fluorescence Multi-Well Plate Reader Installation Qualification Certificate CytoFluor Series 4000 Fluorescence Multi-Well Plate Reader User’s Guide Accessories kit Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 24 Parts of the CytoFluor System Accessories Kit Parts Diagram RS-232 cable Two Allen (hex) wrenches Power cord Fuses, 2.5 amp (2-IEC, 2-UL) Filter installation tool Probe height adjustment spacers (shims), 0.015-inch and 0.020-inch Test plate (for Service use only) Replacement air filter Spare lamp CytoFluor User’s Guide Artisan Technology Group - Quality Instrumentation ...
  • Page 25 If you have all the parts, complete the Installation Qualification Certificate and return it to Applied Biosystems. If you did not receive all the equipment in your kit, call the Applied Biosystems Technical Support Department. See Appendix E, Technical Support and Training, for the phone number.

  • Page 26: The Cytofluor Scanner

    The CytoFluor Scanner 2.2 The CytoFluor Scanner The scanner contains all the parts necessary to scan a variety of plates. Once you connect the scanner to your computer and load the CytoFluor software, you can control how it functions. You can also determine the way the scanner reads the plate wells and customize it to suit your needs.
  • Page 27 NOTE: In CytoFluor Series 4000 scanners with temperature control, the plate carrier is contained in a temperature control chamber with an additional door. These features are not shown. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 28 The CytoFluor Scanner Letter Part Name Function Plate carrier Holds the plate so the scanner can read the well contents. Emission filter Holds the filter that determines the fluorescence assembly emission wavelength to monitor. Probe Transmits and receives the excitation and emission signal.
  • Page 29 Enables you to turn the scanner on and off. Power inlet Enables you to connect the power cord. Fuse module Enables you to change the fuses. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 30: Computer System Requirements

    Computer System Requirements 2.3 Computer System Requirements You supply the computer to use with the CytoFluor system. Your computer must meet these minimum requirements: ® • IBM-PC -compatible type with 486DX computer • 240 megabyte hard drive • 8 megabytes of memory (RAM) •...

  • Page 31: Setting Up Your System

    AVERTISSEMENT Remplacez les fusibles par ceux de même type et puissance pour éviter les risques d’incendie. 2-10 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 32 Setting Up Your System Installing To install the fuses: 1. Remove the warning label from the power module. 2. Remove the fuse module by inserting a small flathead screwdriver in the slot beside the power plug and sliding out the fuse module (Figure 2-4). Slot Power module Fuse module...
  • Page 33 4. Slide the fuse module into the power module until it snaps into place (Figure 2-6). Power module Fuse module PB100492 Figure 2-6 Replacing the Fuse Module 5. Install the power cord. 2-12 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 34: Removing The Shipping Restraints

    Setting Up Your System 2.4.2 Removing the Shipping Restraints To remove the shipping restraints: Open the scanner cover by turning the thumbwheel counterclockwise and lifting up the cover. Thumbwheel Figure 2-7 Opening the Cover 2. Remove the shipping restraints from the probe and transport assemblies shown in Figure 2-8.
  • Page 35 Out. If the plate carrier does not move out, turn off the scanner and turn the thumbwheel further to tighten it. Thumbwheel Figure 2-9 Closing the Cover 2-14 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 36: Connecting The Scanner To Your Computer

    Setting Up Your System 2.4.3 Connecting the Scanner to Your Computer After you install fuses in the scanner, and you remove the shipping restraints, you can connect the scanner to your computer. WARNING You must electrically ground the system and computer. These components are equipped with grounding plugs.
  • Page 37 2. Connect the other end of the RS-232 cable into the Serial Port (9-pin connector) on the rear of the scanner. PB100529 Figure 2-11 Connecting the RS-232 Cable 2-16 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 38 3. Connect the power cable to the scanner. PB100530 Figure 2-12 Connecting the Power Cable 4. Plug all power cords into grounded, electrical outlets. (Applied Biosystems recommends that you also use a surge protector.) Figure 2-13 Connecting the Power Cable to an Electrical Outlet CytoFluor User’s Guide...

  • Page 39: Installing The Software

    5. Type a:\setup.exe and click OK. The CytoFluor installation screen appears and prompts you through the installation procedure. The default destination path is C:\CytoFlr. 2-18 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 40 Setting Up Your System The Setup Complete dialog box appears when the installation is complete. Figure 2-14 Installation Complete Dialog Box 6. Select Yes, Launch the program file and click on Finish to bring up the CytoFluor main setup screen: Figure 2-15 CytoFluor Main Setup Screen CytoFluor User’s Guide 2-19...
  • Page 41 Getting Started You can now check the system as described in the Section 2.5, Checking the System. If you have problems installing the software, contact Applied Biosystems Technical Support. See Appendix E, Technical Support and Training, for the phone number.

  • Page 42: Checking The System

    Checking the System 2.5 Checking the System After you complete the set up steps, you must check the CytoFluor system before you can use it. This involves: • Starting up the CytoFluor system • Accessing the Maintenance screen • Checking the scanner settings •...
  • Page 43 Chapter 3, Scanning Operations, contains details on how to use this screen to set run parameters. 4. Access the Maintenance screen as described in Section 2.5.2, Accessing the Maintenance Screen. 2-22 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 44: Accessing The Maintenance Screen

    Checking the System 2.5.2 Accessing the Maintenance Screen To check your scanner settings, use the Maintenance screen. To access this screen: Pull down the Maintenance menu (or press ALT, M, and Enter). NOTE: You can use key equivalents to choose options instead of clicking with the mouse.

  • Page 45: Checking Scanner Settings

    The CytoFluor software automatically checks the scanner drives and lamp. The test takes several seconds. When testing is completed, the Unit Test dialog box appears (Figure 2-18). 2-24 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 46: Returning To The Main Setup Screen

    Checking the System Figure 2-18 Unit Test Dialog Box If all systems pass, the scanner is ready for use. If the Lamp Status fails, then replace the lamp. See “Replacing the Lamp” on page 7-5 for detailed instructions. If any other system fails, contact Applied Biosystems Technical Support.
  • Page 47 2. Begin working with the system. Continue to Chapter 3, Scanning Operations, for details on how to perform scans. Or, shut down the system as described in Section 2.6, Shutting Down the System. 2-26 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 48: Shutting Down The System

    Shutting Down the System 2.6 Shutting Down the System To shut down the system: Select Exit from the File menu (ALT, F). 2. Exit Windows. 3. Power down the scanner and computer. CytoFluor User’s Guide 2-27 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 49 Chapter 2 Getting Started 2-28 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 50 Scanning Operations This chapter includes the following sections: 3.1 Creating a New File ........3-2 3.2 Setting Scan Parameters ......3-7 3.3 Setting Up Multiple Scans in a Cycle ..3-16 3.4 Saving Scan Parameters ......3-20 3.5 Controlling Temperature ......3-22 3.6 Scanning Plates ........

  • Page 51: Chapter 3 Scanning Operations

    Section 3.2, Setting Scan Parameters, for details. You can save a file and enter a new file name before or after you set the scan parameters. See the following sections for details. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 52: Creating A New, Original File

    Creating a New File 3.1.1 Creating a New, Original File If you want to clear the data of an existing file or set the parameters of a new file, follow these steps: Start up CytoFluor as described in Chapter 2, Getting Started.

  • Page 53: Accessing A Previously Saved File

    Figure 3-1 Selecting a File 2. Scroll through the list of files or change directories until you see the name of the file you want. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 54 Creating a New File 3. Click on the name of the file to select it. Then click on the Open button. You see this prompt: Figure 3-2 Accepting Setup From File 4. Select Yes to use the parameters of that file for subsequent runs.
  • Page 55 (See step 4 and step 5 in “Creating a New, Original File” on page 3-3 for details on using the Save As… command.) Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 56: Setting Scan Parameters

    Setting Scan Parameters 3.2 Setting Scan Parameters Overview As soon as you enter the CytoFluor software, you see the main setup screen. It displays the scan settings of the last run. For example, you may see information like this in your main setup screen: Figure 3-3 Main Setup Screen If this is the first time you entered the application, you see...
  • Page 57 To select the run mode: Click on the down arrow in the Mode box. 2. Highlight your selection. Then close the choice box by clicking in the Mode field. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 58 Setting Scan Parameters Mix Time When running multiple cycles, you might want to mix the well contents of your plate before re-scanning. You may mix the plate contents for up to 99 seconds at the start of each cycle. To set the mix time: Click on the down arrow in the Mix Time box.
  • Page 59 Click on the down arrow in the Cycles box. 2. Highlight your selection. Then close the choice box by clicking in the field. 3-10 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 60 Setting Scan Parameters Scans/Cycle You can have up to four scans for each cycle. You can also use a different filter pair and gain setting for each scan, or use the same ones. To select the number of scans per cycle: Click on the down arrow in the Scans/cycle box.
  • Page 61 See Section 3.3, Setting Up Multiple Scans in a Cycle, for details. 3-12 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 62 Setting Scan Parameters Excitation Enables you to select the excitation filter for a scan. See Section 3.3, Setting Up Multiple Scans in a Cycle, for details. Emission Enables you to set the emission level of the filter for a scan. See Section 3.3, Setting Up Multiple Scans in a Cycle, for details.
  • Page 63 NOTE: Values that exceed the system limits are not displayed. Date/Time Displays the data and time of the previously acquired data. You cannot edit this field. 3-14 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 64 Setting Scan Parameters Total Before a run, displays the total run time. During the run, displays the time elapsed between the current scan and the Time/Elapsed same scan number acquired during the first cycle. You cannot edit this field. During a run, this field doubles as a countdown timer to the start of the next cycle.

  • Page 65: Setting Up Multiple Scans In A Cycle

    2. Highlight the filter pair you want to use. 3. Click on the down arrow in the Emission field to display the list of choices. 3-16 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 66 Setting Up Multiple Scans in a Cycle 4. Highlight the filter you want to use. The system displays an error message if you try to start a run with incompatible filter pairs that overlap enough to damage the photomultiplier tube. Figure 3-5 Filter Overlap Error If you see a message, click on OK and make another selection.
  • Page 67 Set the filters and gain as described in “Select the filter pairs for a Scan” on page 3-16 and “Select the Gain” on page 3-18. 3-18 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 68 Setting Up Multiple Scans in a Cycle 2. Select CopyFilterTo from the Plate menu. The Filter/Gain Copy dialog box appears. Figure 3-6 Filter/Gain Copy Dialog Box 3. Select the scan settings to copy from the Copy From buttons. 4. Select the scans to which you want to copy the settings from the Copy To buttons.

  • Page 69: Saving Scan Parameters

    Select Yes to overwrite the previous data, or No to enter another name. CAUTION If you select Yes, you overwrite any information previously in the file. 3-20 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 70 Saving Scan Parameters Saving as a You can save the parameters from the main setup screen and Plate layout screen as a template to use for future scans. To template save the file as a template: Select Save As from the File menu. The save as dialog box appears.

  • Page 71: Controlling The Temperature

    15 to 20 minutes to stabilize. When scans are running, the temperature is updated at the beginning of each scan. Current temperature SetTemp pull-down menu Figure 3-7 Setting the Temperature 3-22 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 72: Controlling Temperature

    Controlling the Temperature Setting the To set the temperature from the main setup screen: temperature Select the temperature from the SetTemp pull-down menu (Figure 3-7). Valid temperature settings are: • 5°C to 20°C above ambient temperature in 0.2°C increments, up to a maximum of 45°C •...

  • Page 73: Scanning Plates

    A1 is at the top left (towards the back of the scanner) as shown: Figure 3-8 Seating the Plate in the Carrier 3-24 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 74 Scanning Plates Running Click the Start button to start the run. If you start a run before the lamp has been on for 10 minutes, you see a screen message asking if you want to start the run. Select Yes to continue or No to wait. If you select Yes, you may not receive optimal results since the lamp was not warmed up completely.
  • Page 75 This only occurs if the Cycle Time is greater than the actual data acquisition time. 3-26 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 76 Scanning Plates Saving Save the data through the Save As… command under File and enter a file name, unless you gave the file a name before you started the run. If you already named the file, the system automatically stored the data under that name as it performed the run.
  • Page 77 Chapter 3 Scanning Operations 3-28 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 78 Displaying, Printing, and Exporting Data This chapter includes the following sections: 4.1 Overview of Post Processing ..... 4-2 4.2 Saving Post Processing Selections..4-21 4.3 Printing Data ........... 4-21 4.4 Exporting Files ......... 4-22 4.5 Creating an Export Format ...... 4-26 CytoFluor User’s Guide Artisan Technology Group - Quality Instrumentation ...

  • Page 79: Overview Of Post Processing

    NOTE: The system displays the “Adopt setup from file?” prompt. Click on Yes or No; you do not have to adopt the setup of the file to continue with post processing. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 80 Overview of Post Processing You then see the data and setup of the file you chose. The wells display the values obtained from the run. The Cycle and Scan boxes are active, and the Data format box displays the current post processing choice. The Date/time box displays the date and time the scan was started.

  • Page 81: Using Scaling Features

    This feature enables you to see the raw data for each well. To display raw data: Click on the Raw data button. Figure 4-2 Selecting Raw Data Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 82 Overview of Post Processing 2. Click Update to return to the main setup screen with raw data. If you had one of the background features selected, they affect what you see on the screen. You may see a screen like this: Figure 4-3 Raw Data NOTE: The system always retains raw data, regardless of options you choose.
  • Page 83 (The Min value should be less than the Max value. Otherwise, the system makes a “beep” sound and does not accept the value.) You see a screen like this: Figure 4-5 Threshold Feature Applied Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 84 Overview of Post Processing (See “Background Average of Blank Wells” on page 4-9 and “Using the Kinetics Rate Calculation Screen” on page 4-10, if you want the system to subtract values from the data also.) Ranged Use this feature to display data above the maximum as plus symbols (+++), below the minimum as minus symbols (---), and between the two values as integer values from 0 to 9.
  • Page 85 Update to return to the main setup screen with the subtracted background value. For example a background of 26 is subtracted from the raw data: Figure 4-7 Background Value Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 86 Overview of Post Processing NOTE: If the subtracted data is less than -9999, a minus sign is displayed as shown in Figure 4-8. Figure 4-8 Subtracted Value Less Than -9999 Background Use this feature to automatically calculate a value to subtract from each data point.

  • Page 87: Using The Kinetics Rate Calculation Screen

    NOTE: The system displays the “Adopt setup from file?” prompt. Click on Yes or No; you do not have to adopt the setup of the file to continue with post processing. 4-10 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 88 Overview of Post Processing You then see the data and setup of the file you chose. The wells display the values obtained from the run. The Cycle and Scan boxes are active, and the Data format box displays the current post processing choice. The Date/time box displays the date and time the scan was started.

  • Page 89: Using Kinetics Features

    You can customize the graphs by setting the following parameters: • Point Limits • AFU Limits • Window size • Scan to Display • Scale Rate to Control • Display Mode 4-12 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 90 Overview of Post Processing The kinetics parameters are described in the table below: Parameter… Description… Point Limits • Start—Sets the first data point used for the rate calculation. • End—Sets the last data point used for the rate calculation. AFU Limits •...

  • Page 91: Plotting Kinetics Data

    “Customizing the plots” on page 4-18. 3. Click Print to print the graph. 4. Click Close to return to the Kinetics Rate Calculation screen. 4-14 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 92 Overview of Post Processing Plotting standards To view and print plots for standards: On the Kinetics Rate Calculation screen (Figure 4-10 on page 4-11), select Standards and click the Plot button. The Expanded Kinetics Plot screen appears with a graph of the standards. Figure 4-12 Standards Plot 2.
  • Page 93 “Customizing the plots” on page 4-18. 3. Click Print to print the graph. 4. Click Close to return to the Kinetics Rate Calculation screen. 4-16 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 94 Overview of Post Processing Plotting controls To view and print plots of controls: On the Kinetics Rate Calculation screen (Figure 4-10 on page 4-11), select Controls and click the Plot button. The Expanded Plot screen appears with a graph of the controls. Figure 4-14 Controls Plot 2.
  • Page 95 2. Select the appropriate parameters. 3. To change the axis label text, click on Text Parameters. The Text Parameters dialog box appears. Figure 4-16 Text Parameters Dialog Box 4-18 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 96 Overview of Post Processing 4. Type the appropriate text and change the parameters as desired. 5. Click OK to save the changes and return to the Axis labels dialog box. 6. Click OK. Axes To customize the axes: On any of the previous plots screens, double-click on the axis to change.
  • Page 97 To customize the legend: On any of the previous plots screens, double-click on the legend. The Legend Parameters dialog box appears. Figure 4-19 Legend Parameters 4-20 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 98: Saving Post Processing Selections

    Saving Post Processing Selections 2. Type the appropriate text and change the parameters as desired. 3. Click OK to save the changes. 4.2 Saving Post Processing Selections To save the post processing selections under the same file name: Select Save under the File menu (ALT, F, S). To save the selections under a different name: Select Save As…...

  • Page 99: Exporting Files

    For example, if you selected a background subtraction value through the Post Processing menu, all data points in the exported file will have the value subtracted. 4-22 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 100 Exporting Files Some software packages have special requirements as described here: Software Requirement Grafit Exports a text file containing group average and concentration data to be used with Grafit Kinetics Analysis Software. Grafit is an option offered with the CytoFluor scanner. Well unknowns or standards must be defined before using this format.
  • Page 101 For example, the export file containing the data from cycle 1 and scan 4 of file TEST.MFR would have the name TEST.014. 4-24 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 102 Exporting Files Concatenate To combine several files into one for export: Select the files to combine from the Files in list. 2. Click Concatenate. The selected files are exported into one file. The new file has the same name as the first file selected to export.

  • Page 103: Creating An Export Format

    7. To include header information or export the data in linear or table format, use the procedure in the following sections. 8. Click on OK to save the setup. 4-26 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 104: Including Header Information

    Creating an Export Format 4.5.1 Including Header Information To include header information with your custom exported data: In the Export Setup dialog box, click the button to the right of Header. The Header dialog box appears (Figure 4-22). Figure 4-22 Header Dialog Box 2.
  • Page 105 Chapter 4 Displaying, Printing, and Exporting Data MAR 9 1997 Figure 4-23 Header Parameters 3. Click OK to save your changes. 4-28 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 106: Including Data In A Table Format

    Creating an Export Format 4.5.2 Including Data in a Table Format To include data formatted in a table that corresponds to the plate layout: In the Export Setup dialog box, click Table. The Table Setup dialog box appears (Figure 4-24). Figure 4-24 Table Setup Dialog Box 2.

  • Page 107: Including Data In A Linear Format

    Sort parameters Orientation parameters Row and Column parameters Group parameters Figure 4-26 Linear Setup Dialog Box 2. Select the parameters to include in the header. 4-30 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 108 Creating an Export Format 3. Select the sort parameters: Parameter Description Sort on Well Sorts data alphabetically by well name. Sort on Group Sorts data by group name in the order shown in the Include Groups section of the screen. When you select Sort on Group, Group Average becomes a row or column option.
  • Page 109 Chapter 4 Displaying, Printing, and Exporting Data 4-32 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 110 Setting the Plate Layout or Auto Scale Parameters This chapter includes the following sections: 5.1 Overview of the Plate Layout Screen ..5-2 5.2 Accessing the Plate Layout Screen ... 5-4 5.3 Plate Layout Overview........ 5-6 5.4 Using Well Types Options ......5-8 5.5 Entering Concentration Parameters ..

  • Page 111: Overview Of The Plate Layout Screen

    The Plate Layout screen looks like this: Current plate Concentration Basic editing options description parameters Well types Options and Index Selection Plate representation Figure 5-1 Plate Layout Screen Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 112 Overview of the Plate Layout Screen The Plate Layout screen includes the following features: • Well Types Options and Index Selection box— Enable you to specify characteristics of particular wells and define replicates. The system may use the data of specific wells to perform calculations, for example, background subtraction.

  • Page 113: Accessing The Plate Layout Screen

    Figure 5-2 CytoFluor Main Setup Screen NOTE: If you want to open a particular file to review or change the plate layout, see step 2. Otherwise skip to step 3. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 114 Accessing the Plate Layout Screen 2. Choose Open from the File menu (ALT, F, O). Then select the file you want to open from the pull-down menu and click on Open. The data of the file you selected appears in the CytoFluor main setup screen.

  • Page 115: Plate Layout Overview

    Setting Auto Scale Parameters, for details. Undo Cancel your latest changes and return to the last assignment you made. You cannot access this button unless you made changes. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 116 Plate Layout Overview NOTE: To change the assignment value of any well, select the new Well types button first, then select the well. Follow the steps in this section for general well assignment steps: Click the Well type button that corresponds to the sample type on the plate.

  • Page 117: Using Well Types Options

    (Click with your mouse, or click and drag to select a group of wells.) The system enters the abbreviation “un” and the index value into the wells you select. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 118 Using Well Types Options For example: Figure 5-4 Defining Unknowns NOTE: If you have more than one group of unknowns on a single plate, repeat step 2 and step 3, changing the index value as necessary. You may assign as many different unknown groups as your experiments require.
  • Page 119 To define wells as controls: Click on the Control button in the Plate Layout screen. 2. Select an index value from the pull-down menu (00 to 99). 5-10 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 120 Using Well Types Options 3. Select the wells on your assay plate you want as a control group. (Click with your mouse, or click and drag to select a group of wells.) You do not have to place controls in contiguous wells.
  • Page 121 1 and step 2. 3. Make additional changes to the plate layout as described in this chapter. Or click on OK to save your changes. 5-12 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 122 Using Well Types Options Empty Use this option to define any wells on your assay plate that have been left unfilled or ones you do not want considered in the assay. NOTE: The system does not treat Empty wells the same way it treats Blank wells.
  • Page 123 Auto Scale 00 All scans Auto Scale 01 Scan 1 Auto Scale 02 Scan 2 Auto Scale 03 Scan 3 Auto Scale 04 Scan 4 5-14 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 124: Entering Concentration Parameters

    Entering Concentration Parameters 5.5 Entering Concentration Parameters After you assign well types, you can use the Concentration section of the Plate Layout screen to enter concentration values and units for standards. To enter concentration parameters: Select a well in a group to which you want to assign concentration parameters.

  • Page 125: Defining Plates

    4. Set the gain to zero on the main setup screen to disable the photomultiplier tube and prevent damage. 5. Open the scanner by turning the thumbwheel clockwise and lifting up the cover. 5-16 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 126: Defining A Plate

    Defining Plates 5.6.2 Defining a Plate To define a plate type: Click Lamp On, if necessary. 2. Set the Gain to zero to turn off the photomultiplier tube. 3. Select Define Plate from the Plate menu. The Defined Plates screen appears (Figure 5-7). The name and coordinates of the plate type used during the last scan are displayed.
  • Page 127 Scroll Box Figure 5-8 Coordinate Setup Screen 8. Select X1-Y1 from the Coordinate list. The first well in the plate is positioned over the probe. 5-18 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 128 Defining Plates 9. Verify that the well is centered over the probe. NOTE: If your scanner has a temperature control chamber, gently lift up the edges of the slit in the insulation on the temperature control chamber to see the well. If the well is not centered, center it by using the scroll bar: •...

  • Page 129: Deleting A Plate

    To delete a plate from the Defined plate list: Select Define Plate from the Plate menu. 2. Select the plate to delete. 3. Click Delete. 4. Click OK. 5-20 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 130: Using 384 Well Plates

    NOTE: CytoFluor systems manufactured before April 1997 with serial numbers with the last three digits lower than 593 require a hardware modification to read an entire 384 well plate. Contact Applied Biosystems Technical Support for details. To use 384 well plates you must: •...

  • Page 131: Selecting The Read Pattern Option

    11 12 13 14 15 16 17 18 19 20 21 22 23 24 Row A Quadrant 3 Quadrant 4 Figure 5-9 384 Well Plate 5-22 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 132 Using 384 Well Plates When you select a 384 Read Pattern option the CytoFluor software scans the plate according to the pattern described in Table 5-2. Table 5-2 Read Patterns Read Pattern Option Scan 1 Scan 2 Scan 3 Scan 4 Quadrants (with >8 Upper left Upper right...
  • Page 133 NOTE: You can save the scanning pattern as a template to use for future scans. See “Saving as a template” on page 3-21 for details. 5-24 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 134: Setting Auto Scale Parameters

    Setting Auto Scale Parameters 5.8 Setting Auto Scale Parameters Overview The CytoFluor Auto Scale screen allows you to select how you normalize your data using the following modes: • Default mode—Scales data according to the filter pair you set and the internal reference and gain the scanner automatically sets.
  • Page 135 4. Click Update. The reference value is collected and stored. 5. Click Save to save your Auto Scale information and return to the main setup screen. 5-26 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 136 Setting Auto Scale Parameters Defined mode If you are using replicate wells as references, you must define them as Auto Scale wells on the Plate Layout screen before setting the Auto Scale parameters. See “Auto Scale” on page 5-14 for more details. To scan using the Defined mode: Select the number of scans from the Scans/cycle pull-down menu.

  • Page 137: Exiting The Cytofluor System

    Click the appropriate button to save changes and exit, ignore them and exit, or cancel the exit process. 5-28 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 138 Customizing the CytoFluor System This chapter includes the following sections: 6.1 Replacing Optical Filters......6-2 6.2 Testing the Scanner ......... 6-10 6.3 Checking or Changing the Communication Port ........ 6-12 6.4 Setting the Lamp Saver Time....6-13 6.5 Configuring the Scanner for Top or Bottom Plate Reading ....

  • Page 139: Chapter 6 Customizing The Cytofluor System

    Follow the same steps when changing either type of filter. Figure 6-1 shows the position of the excitation and emission filter assemblies inside the scanner. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 140 Replacing Optical Filters Excitation filter assembly Emission filter assembly PB100555 Figure 6-1 Filter Assemblies Make sure the plate transport carrier is inside the scanner. If it is not inside, click on the Plate In button. 2. On the main setup screen, set the Gain to 0 and turn the lamp off by clicking the Lamp Off button.
  • Page 141 Click on the Position button to the left of the Excitation Filter field. For the emission filter, click Position button. Figure 6-4 Selecting the Filter Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 142 Replacing Optical Filters The scanner filter wheel finds the home position, then presents the selected location at the top of the filter assembly. 6. Fold down the gasket in the filter assembly to gain access to the filter (Figure 6-5). Then locate the filter installation tool provided with the Accessories kit.
  • Page 143 Make sure the filter is installed in the position you selected in the Maintenance screen. An overlap of filters could damage the CytoFluor system and void your warranty. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 144 Replacing Optical Filters Figure 6-8 Checking Filter Position 10. Replace the cover on the filter wheels and tighten the screws. Do not overtighten. Figure 6-9 Replacing the Filter Wheel Assembly Cover CytoFluor User’s Guide Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 145: Changing The Filter Settings In The Maintenance Screen

    If you do not set the values correctly, your data will be invalid. You could also damage the system, voiding your warranty. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 146 Replacing Optical Filters To change the filter settings through the software: In the Maintenance screen, drag the cursor across the appropriate Position 1 through Position 6 box under Excitation Filters or Emission Filters to select them. Figure 6-11 Maintenance Screen 2.

  • Page 147: Testing The Scanner

    The CytoFluor software then automatically checks the scanner drives and lamp. The test takes several seconds. When complete, the Unit Test dialog box appears. 6-10 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 148 Testing the Scanner Figure 6-13 Unit Test Dialog Box If all systems pass, the scanner is ready for use. If the Lamp Status fails, then replace the lamp. See Section 7.4, Replacing the Lamp, for detailed instructions. If any other system fails, contact Applied Biosystems Technical Support.

  • Page 149: Checking Or Changing The Communication Port

    Figure 6-14 Invalid Port Setting 4. Click OK, then repeat step 2 to make another selection. Once you save the new setting, the system activates it. 6-12 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 150: Setting The Lamp Saver Time

    Setting the Lamp Saver Time 6.4 Setting the Lamp Saver Time The lamp saver feature enables you to extend the life of the lamp. For example, you can set the lamp to turn off when there is no scanner activity. The default setting is 60 minutes.

  • Page 151: Configuring The Scanner For Top Or Bottom Plate Reading

    When the probe is in the top-read position, the upper fiber-optic cable goes to the emission module and the lower fiber-optic cable goes to the excitation module. 6-14 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 152 Configuring the Scanner for Top or Bottom Plate Reading NOTE: In scanners with a temperature control chamber, place the probe in the slit on top of the temperature control chamber. Figure 6-15 Moving the Probe Arm (Probe in Top-Read Position) 4.
  • Page 153 Section 6.5.3.1, Checking (temperature-control) and Adjusting Probe Height in Bottom-Read Position (TC Models) • Section 6.5.3.2, Checking and Adjusting Probe Height in Top-Read Position (TC Models) 6-16 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 154: Checking And Adjusting Probe Height In A Temperature-Ready Scanner

    Configuring the Scanner for Top or Bottom Plate Reading 6.5.2 Checking and Adjusting Probe Height in a Temperature-Ready Scanner Use the following procedures to check and adjust probe height in scanners without a temperature control chamber. 6.5.2.1 Checking and Adjusting Probe Height in Bottom-Read Position (TR Models) Checking probe In the bottom-read position, the probe tip should be located...
  • Page 155 Plate Out. If the plate carrier does not move out, turn off the scanner and turn the thumbwheel further to tighten it. 6-18 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 156: Checking And Adjusting Probe Height In Top-Read Position (Tr Models)

    Configuring the Scanner for Top or Bottom Plate Reading 6.5.2.2 Checking and Adjusting Probe Height in Top-Read Position (TR Models) Checking probe In the top-read position, the probe tip should be located 0.5 mm above the plate to maximize the signal. You can adjust height in top-read the probe height for the top-read position to accommodate different plate heights.
  • Page 157 6. Close the scanner cover and seat it properly on the gasket. Turn the thumbwheel counterclockwise until finger tight. Turn on the scanner. 6-20 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 158: Checking And Adjusting Probe Height In A Temperature Control Scanner

    If you need to adjust the probe height, call Applied Biosystems Technical Support for assistance. CAUTION The probe must be set at the correct height. If you set the probe too high, the plate carrier can jam against it.
  • Page 159 3. Slide the probe until it is underneath the edge of the plate carrier. If the probe hits the plate carrier, skip the remaining steps and call Applied Biosystems Technical Support. 4. Push the temperature control chamber door open and insert the 12-inch long probe height adjustment spacer marked 0.015-inch through the oven door and hold it...

  • Page 160: Checking And Adjusting Probe Height In Top-Read Position (Tc Models)

    Configuring the Scanner for Top or Bottom Plate Reading 6.5.3.2 Checking and Adjusting Probe Height in Top-Read Position (TC Models) Checking probe In the top-read position, the probe tip should be located 0.5 mm (the thickness of the 0.020-inch height adjustment height in top-read spacer) above the plate to maximize the signal.
  • Page 161 0.020-inch spacer Figure 6-20 Adjusting Probe Height 3. Tighten the two screws on the rear of the probe mounting block. Gently remove the 0.020-inch spacer. 6-24 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 162 Configuring the Scanner for Top or Bottom Plate Reading 4. Make sure the fiber-optic cables are inside the unit. Close the scanner cover and seat it properly on the gasket. Turn the thumbwheel counterclockwise until finger-tight. Turn on the scanner. CAUTION Do not over-tighten or under-tighten the cover thumbwheel or the plate carrier cannot exit the scanner.
  • Page 163 Chapter 6 Customizing the CytoFluor System 6-26 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 164: Chapter 7 Maintaining The Cytofluor System

    Maintaining the CytoFluor System This chapter includes the following sections: ......7.1 Cleaning the Scanner 7.2 Cleaning the Rails ........7-2 ......7.3 Replacing the Air Filter ......7.4 Replacing the Lamp CytoFluor User’s Guide Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 165: Cleaning The Scanner

    2. Open the scanner cover by turning the thumbwheel counterclockwise and lifting up the cover. 3. Clean the rails shown in Figure 7-1 with ethanol or isopropanol. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 166 Cleaning the Rails Rails PB100546 Figure 7-1 Rails 4. Close the scanner cover and seat it properly on the gasket. Turn the thumbwheel counterclockwise until finger tight. Turn on the scanner. CAUTION Do not over-tighten or under-tighten the cover thumbwheel or the plate carrier cannot exit the scanner.

  • Page 167: Replacing The Air Filter

    Tighten the screws with the Allen (hex) wrench, but do not overtighten. CAUTION Do not operate the scanner without an air filter or you may reduce the performance quality. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 168: Replacing The Lamp

    Replacing the Lamp 7.4 Replacing the Lamp This section describes how to replace a faulty lamp with a new one. (See Chapter 8, Accessing Technical Information, if you need to order one.) Make sure the plate carrier is inside the scanner. Press the Plate In button from the Maintenance screen, if necessary.
  • Page 169 Figure 7-5 Replacing the Lamp 6. Place the cover over the lamp compartment. Then insert and tighten the screw. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 170 Replacing the Lamp 7. Close the scanner cover, reconnect the power cable, and turn on the power. Then make sure the plate transport carrier moves smoothly into position using the Plate In and Plate Out buttons from the Maintenance screen. (If necessary, close the scanner cover again.) NOTE: Click the Lamp On and Lamp Off buttons if you want to test the new lamp.
  • Page 171 Chapter 7 Maintaining the CytoFluor System Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 172 Accessing Technical Information This chapter includes the following sections: ......... Specifications Minimum Computer Requirements ..........(You Supply) ..... Optical Sets for Fluorophores ....CytoFluor Standard Filter Sets ........ Ordering Information Technical Support ..........8-8 CytoFluor User’s Guide Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 173: Chapter 8 Accessing Technical Information

    6 positions Detector Electron Tubes, Inc. 9781 Photomultiplier Tube (low noise, high gain) Probe 3.0 mm quartz Filters 6-cavity design interference filters, optimized for CytoFluor Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 174: Minimum Computer Requirements (You Supply)

    Minimum Computer Requirements (You Supply) X-Y Scanning Step size 45.27 µm (0.0018 in) Mechanism Repeatability ± 50 µm worst case X-Y drive Stepping motor with direct drive belt Plate 10 seconds maximum load time transport 8.2 Minimum Computer Requirements (You Supply) Note: The recommended requirements are: 4 MB of RAM, 250 MB hard drive, and a 100 percent compatible base unit that is powerful enough to run Windows efficiently.)

  • Page 175: Optical Sets For Fluorophores

    Ion concentration Thiolyte 360/460 General fluorescent tag Lucifer yellow 440/530 Gap junction communication Benzoxanthene yellow 360/460 General fluorescent tag Dansyl P. E. 360/530 General fluorescent tag Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 176 Optical Sets for Fluorophores Excitation/ Application Emission Pair BCECF 485/530 Vital dye, pH indicator Carboxy fluorescein 485/530 Vital dye, pH indicator Fluo-3 508/560 concentration ™ PicoGreen 485/530 Nucleic acid quantitation ™ SNAFL (in acid) 485/530 pH indicator Acridine orange 485/530 Nucleic acid stain Rhodamine 123 485/530...

  • Page 177: Cytofluor Standard Filter Sets

    8.4 CytoFluor Standard Filter Sets Excitation Center Wavelength/ Emission Center Wavelength/ Full Bandwidth* Full Bandwidth* 360/40 460/40 450/50 530/25 485/20 580/50 530/25 620/40 590/20 645/40 *Wavelengths measured in nanometers Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 178: Ordering Information

    Ordering Information 8.5 Ordering Information Table 8-1 lists the part numbers of the CytoFluor System kit Table 8-2 lists the part numbers of the Accessories kit. . Table 8-1 CytoFluor System Kit Part Numbers Description Part Number CytoFluor System kit— MIFS0C2TC—...

  • Page 179: Technical Support

    Appendix E, Technical Support and Training. When you contact Technical Support, be prepared to provide your CytoFluor model number, serial number, and software version. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 180: Appendix A Introduction To Windows

    Introduction to Windows This appendix provides basic information on how to use ® ® Microsoft Windows . For example, it provides details on using the following: • Mouse and on-screen pointer • Windows • Screen buttons • Pull-down menus and scroll bars If you need further information, see the manuals provided with the Microsoft Windows software.
  • Page 181 This action is called dragging. You can drag to select text or other contiguous objects on the screen; for example, groups of wells on the CytoFluor plate layout. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 182 Windows A.2 Windows A window is a rectangular area on the screen in which you do work in a program. The window can be manipulated—opened and closed, moved and resized, and shuffled—just like a sheet of paper on top of a desk. Title bar Close box Menu bar...
  • Page 183 Clicking the box puts an X in it, which means the option is selected. Clicking the box again removes the X and deselects the option. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 184 Menus and Scroll Bars A.4 Menus and Scroll Bars You use scroll bars to move through long lists or window areas where part of the contents are hidden. A scroll bar looks like a long rectangle with arrows at the top and bottom. By positioning the pointer over one of the arrows and clicking it, you make visible more options on a list.
  • Page 185 Appendix A Introduction to Windows Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 186: Appendix B Error Messages

    Error Messages This appendix lists error messages you may see while using the CytoFluor software. The CytoFluor software displays a system error in a message box and makes a beep sound to draw your attention to it. Many error messages display a negative error code (number).
  • Page 187 -222 Reading aborted with ESC key. You pressed the Escape key. Delete <filename>? Occurs when you are deleting a file as a double-check before deletion. Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 188 Error Code/ Message Meaning Disk full. The disk chosen as a destination has insufficient room for the file(s) you’re trying to copy. Error reading <filename>. The file selected for opening is an invalid type. Error writing <filename>. The file cannot be saved. Check that the path selected is correct and that a disk is inserted in the floppy disk drive, if selected.
  • Page 189 Do not try to force the mechanism or correct the problem yourself. Turn off the scanner, disconnect the power, and contact Applied Biosystems Technical Support. Unable to communicate with The software has lost communication with the CytoFluor system.

  • Page 190: Appendix C Warranty/Service Information

    Cytofluor Series 4000 Flourescence Multiwell Plate Reader will be free of defects in materials and workmanship for a period of ninety (90) days. Applied Biosystems will repair or replace, at its discretion, all defective components during this warranty period. After this warranty period, repairs and replacement components may be purchased from Applied Biosystems at its published rates.
  • Page 191 Biosystems will repair or replace, at its discretion, defective accessories during this warranty period. After this warranty period, Applied Biosystems will pass on to the buyer, to the extent that it is permitted to do so, the warranty of the original manufacturer for such accessories.
  • Page 192 The foregoing provisions set forth Applied Biosystems’ sole and exclusive representations, warranties, and obligations with respect to its products, and Applied Biosystems makes no other warranty of any kind whatsoever, expressed or implied, including without limitation, warranties of merchantability and...

  • Page 193: Damages, Claims, Returns

    No agent, employee, or representative of Applied Biosystems has any authority to bind Applied Biosystems to any affirmation, representation, or warranty concerning the product that is not contained in this Limited Warranty Statement. Any...

  • Page 194: Appendix D Plate Scan Patterns

    Plate Scan Patterns This appendix shows the scan patterns the system uses when averaging points taken in a well. It includes graphic examples on plates of this size: • Six-well • 12-well • 24-well • 48-well NOTE: The graphics represent wells as circles. The outside circle represents the well wall.
  • Page 195 Plate Scan Patterns Figure D-1 A Six-Well Plate Pattern Figure D-2 A 12-Well Plate Pattern Figure D-3 A 24-Well Plate Pattern Figure D-4 A 48-Well Plate Pattern Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 196: Appendix E Technical Support And Training

    Technical Support and Training This appendix contains the following sections: E.1 Contacting Technical Support ......E-2 E.2 Obtaining Technical Documents..... E-8 E.3 Obtaining Customer Training Information..E-10 ® CytoFluor Series 4000 User’s Guide Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 197 Appendix E- Technical Support and Training E.1 Contacting Technical Support Overview You can contact Applied Biosystems for technical support: • By e-mail • By telephone or fax • Through the Applied Biosystems web site NOTE: For information on obtaining technical documents such as Applied Biosystems user documents, MSDSs, and certificates of analysis, see “Obtaining Technical...
  • Page 198 By telephone or To contact Applied Biosystems Technical Support in North America, use the telephone or fax numbers in the table below. fax (North America) NOTE: To schedule a service call for other support needs, or in case of an emergency, dial 1.800.831.6844, then press 1.
  • Page 199 Peptide Synthesis (Pioneer 1.800.899.5858, press 1, 1.508.383.7855 9050 Plus Peptide Synthesizers) then press 5 PNA Custom and Synthesis 1.800.899.5858, press 1, 1.508.383.7855 then press 5 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 200 8:00 A.M. to 6:00 P.M. Eastern time. c. 9:00 A.M. to 5:00 P.M. Eastern time. By telephone or To contact Applied Biosystems Technical Support or Field Service outside North America, use the telephone or fax fax (outside North numbers below.
  • Page 201 91 11 653 3743 91 11 653 3138 91 11 653 3744 Poland, Lithuania, Latvia, and 48 22 866 4010 48 22 866 4020 Estonia (Warszawa) Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 202 1230 020 9102 55 11 5070 9694/95 Uruguay 0004 055 654 55 11 5070 9694/95 Through the To contact Technical Support through the Applied Biosystems web site: Applied Biosystems web Go to www.appliedbiosystems.com site 2. Click Services & Support at the top of the page, then click Frequently Asked Questions.
  • Page 203 Biosystems user documents, MSDSs, certificates of analysis, and other related documents for free, 24 hours a day. You can obtain documents: • By telephone • Through the Applied Biosystems web site Ordering To order documents by telephone: documents by From the U.S. or Canada, dial 1.800.487.6809, or from telephone outside the U.S.
  • Page 204 NOTE: There is a limit of five documents per fax request, but no limit on the number of documents per e-mail request. ® CytoFluor Series 4000 User’s Guide Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 205 Appendix E- Technical Support and Training E.3 Obtaining Customer Training Information To obtain Applied Biosystems training information, go to www.appliedbiosystems.com, click Services & Support at the top of the screen, then click Training. E-10 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 206: Glossary

    Glossary Active Boot —Describes a window that is —To start or restart your selected; that is, the one in which you’re computer by loading the DOS operating currently able to work. Also refers to system. The term is short for commands or options that are currently bootstrapping.
  • Page 207 Device driver menu or double-click it to quit. —A program that controls how your computer and a device, such as the CytoFluor Scanner, interact. Glossary-2 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 208 Dialog box Export —An on-screen box —To move data into a file that that either requests or provides other applications can use. information. For instance, if you choose Extension —A period followed by the Export .CSV command, a dialog box three letters at the end of a filename.
  • Page 209 Open —To make available; to display the contents of a file in a window. Glossary-4 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 210 Option button RS-232 —A small round —The standard serial on-screen button that selects an option interface protocol, and thus the cable when clicked. An option affects the way and connector specifications, that in which a command is carried out. enable a computer to be linked to the Within a group of related option buttons, CytoFluor Scanner.
  • Page 211 CytoFluor System equivalents, such as choosing take place in windows. commands from menus. The action of a shortcut key depends on the application program. Glossary-6 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 212: Index

    Index Numerics and Symbols Applied Biosystems world wide web address xiv --- in data display 4-6, 4-7 Auto mode +++ in data display 4-6, 4-7 description 3-8 selecting 3-8 Auto Scale accessing screen 5-26 384 well plates assigning wells 5-14...
  • Page 213 3-3 Data, printing 4-21 Customer training, information E-10 Date/Time 3-14 Customizing Default mode 5-25, 5-26 export format 4-26 filters 6-2 Define Plate Options 5-3 Index-2 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 214 Defined mode 5-25, 5-27 setting 3-16 standard sets 8-6 Defined plate adding 5-20 Exclude well 5-12 inserting 5-20 Exiting CytoFluor 2-27, 5-28 replacing name 5-20 Export Current file 4-25 Defining Export format, creating 4-26 384 well plates 5-21 Export To options 4-24 plate 5-17 Exported files X1-Y1 coordinate 5-18...
  • Page 215 Main setup screen overview 4-10 accessing 2-22, 2-25 plotting data 4-14 saving parameters 3-20 plotting standards 4-15 setting parameters 3-7 plotting unknowns 4-16, 4-17 Index-4 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 216 Maintenance saving 3-20 cleaning rails 7-2 setting 3-7 cleaning scanner 7-2 Parts replacing air filter 7-4 of system 2-2 replacing lamp 7-5 ordering 8-7 Maintenance screen 2-23, 6-1 Plate Manual mode 384 well 5-21 description 3-8 clearing 5-6 selecting 3-8 define coordinates 5-16 define options 5-16 MFT files 3-21...
  • Page 217 TC models 6-23 checking and adjusting height, starting 3-25 top-read, TR models 6-19 stopping 3-25 checking height, overview 6-14 description 2-7 Run mode, selecting 3-8 Index-6 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 218 Scans multiple 3-16 setting parameters 3-7 Saving stopping 3-25 files 3-19, 3-27 Scans/Cycle 3-11 post processing selections 4-21 scan parameters 3-20 Settings filter 6-8 Saving template files 3-21 scanner 2-24 Scaled data, displaying 4-5 temperature 3-23 Scaling data to control 4-8 Setup coordinates 5-18 Scaling screen Shipping restraints 2-13...
  • Page 219 Unit Test dialog box 2-25, 6-11 Unknown well 5-8 Unknowns, plotting 4-16, 4-17 Unpacking the system 2-2, 2-10 X1-Y1 coordinate, defining 5-18 X2-Y2 coordinate, defining 5-19 Index-8 Applied Biosystems Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 220 Phone: +1 650.638.5800 Toll Free (In North America): +1 800.345.5224 Fax: +1 650.638.5884 Worldwide Sales and Support Applied Biosystems vast distribution and service network, composed of highly trained support and applications personnel, reaches into 150 countries on six continents. For sales...
  • Page 221 Artisan Technology Group is your source for quality new and certified-used/pre-owned equipment SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT • FAST SHIPPING AND DELIVERY Experienced engineers and technicians on staff Sell your excess, underutilized, and idle used equipment at our full-service, in-house repair center We also offer credit for buy-backs and trade-ins •...

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