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Applied Biosystems CytoFluor 4000 Series User Manual Download Page 62

Setting Scan Parameters

CytoFluor User’s Guide

3-13

3

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.

Gain

Enables you to adjust the voltage on the photomultiplier tube 
in proportion to integer values from 0 to 99 for a scan. For 
example, if you set the value to zero (0), the system turns off 
the photomultiplier tube. If you set the value to 99, the value 
on the photomultiplier tube is approximately 1080 volts (V).

The fluorescence signal level may vary from scan to scan 
depending on your assay and fluorophores. You should start 
scanning with a low value (for example, 40) and gradually 
increase the gain until you find the optimum level(s) for your 
assay. You can usually obtain optimal performance using gain 
settings between 30 and 80. Typically, you use a high gain 
setting for a weak fluorescence signal and a low gain setting 
for a strong fluorescence signal. See Section 3.3, Setting Up 
Multiple Scans in a Cycle, for details.

Auto Scale

Uses the parameters shown in the Auto Scale menu to 
automatically normalize all of your data to the same 
fluorescence reference. You can choose one of the internal 
fluorescence reference supplied with the CytoFluor system or 
use a known concentration of the fluorescent product in your 
assay (control) right on the microwell plate. This option 
minimizes run-to-run variations.

This field must be selected (marked with an x) for the system 
to apply the settings. (See Chapter 5, Setting the Plate Layout 
or Auto Scale Parameters, for details on the how to set the 
Auto Scale menu parameters.) Once you select Auto Scale, 
you cannot edit the Auto Scale menu parameters 
(wavelengths, PMT gain, etc.).

With Auto Scale enabled, the system reads the designated 
reference at the start of each cycle and calculates the scaling 
factor. (CytoFluor multiplies all well readings by this factor as 
acquires them.) To use the same reference for subsequent 
runs, access a previously saved file and adopt the file setup. 
See “Accessing a Previously Saved File” on page 3-4, for 
details. 

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Summary of Contents for CytoFluor 4000 Series

Page 1: ...l service in house repair center WE BUY USED EQUIPMENT Sell your excess underutilized and idle used equipment We also offer credit for buy backs and trade ins www artisantg com WeBuyEquipment REMOTE INSPECTION Remotely inspect equipment before purchasing with our interactive website at www instraview com LOOKING FOR MORE INFORMATION Visit us on the web at www artisantg com for more information on ...

Page 2: ...DRAFT August 30 2001 6 30 pm FLORFM FM5 CytoFluor Series 4000 Fluorescence Multi Well Plate Reader User Guide Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 3: ...eomics Solution 1 SPRINT VISION and Voyager are trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries ICAT is a trademark of the University of Washington in the U S and certain other countries exclusively licensed to Applied Biosystems Group of Applera Corporation MDS is a registered trademark and SCIEX is a trademark of MDS Inc TaqMan is a registered tradema...

Page 4: ...d 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: ...h the instruction manual may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his own expense Note Shielded cables must be used with this unit to ensure compliance with the Class A FCC limits Canadian Safety and EMC Electromagnetic Compl...

Page 6: ...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 Model Name CytoFluor Series 4000 Fluorescence Multi Well Plate Reader Model Number MIFS0C2TR Serial Number FX6CMQ378P and later Year o...

Page 7: ... 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 Model Name CytoFluor Series 4000 Fluorescence Multi Well Plate Reader with Temperature Control Model Number MIFS0C2TC Serial Number FX6CMQ380P and later Year of Manufacture 1997 Artisan Tech...

Page 8: ...emoving the Shipping Restraints 2 13 2 4 3 Connecting the Scanner to Your Computer 2 15 2 4 4 Installing the Software 2 18 2 5 Checking the System 2 21 2 5 1 Starting Up the CytoFluor System 2 21 2 5 2 Accessing the Maintenance Screen 2 23 2 5 3 Checking Scanner Settings 2 24 2 5 4 Running System Diagnostics 2 24 2 5 5 Returning to the Main Setup Screen 2 25 2 6 Shutting Down the System 2 27 Chapt...

Page 9: ...aving 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 4 5 1 Including Header Information 4 27 4 5 2 Including Data in a Table Format 4 29 4 5 3 Including Data in a Linear Format 4 30 Chapter 5 Setting the Plate Layout or Auto Scale Parameters 5 1 Overview of the Plate Layout Screen 5 2 5 2 Accessing the Plate Layout Screen 5 4 5 3 ...

Page 10: ...tom Plate Reading 6 14 6 5 1 Changing the Probe Position 6 14 6 5 2 Checking and Adjusting Probe Height in a Temperature Ready Scanner 6 17 6 5 2 1 Checking and Adjusting Probe Height in Bottom Read Position TR Models 6 17 6 5 2 2 Checking and Adjusting Probe Height in Top Read Position TR Models 6 19 6 5 3 Checking and Adjusting Probe Height in a Temperature Control Scanner 6 21 6 5 3 1 Checking ...

Page 11: ...rd Filter Sets 8 6 8 5 Ordering Information 8 7 Appendix A Introduction to Windows A 1 Appendix B Error Messages B 1 Appendix C Warranty Service Information C 1 C 1 Limited Product Warranty C 1 C 1 Damages Claims Returns C 4 Appendix D Plate Scan Patterns D 1 Appendix E Technical Support and Training E 1 Glossary Index Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www a...

Page 12: ...nvenience there is a glossary of terms at the back of this document If you need more information on Windows refer to the manuals provided with the Windows software Structure of this guide Applied Biosystems CytoFluor Series 4000 Multi Well Fluorescence Reader User s Guide is divided into chapters Each chapter page is marked with a tab and a header to help you locate information within the chapter ...

Page 13: ...le parameters so the system can scale the data as it acquires it Chapter 6 Customizing the CytoFluor System Describes how to customize the system It includes steps to set up and change filter pairs test the scanner drives and lamp and set the lamp saver timer Chapter 7 Maintaining the CytoFluor System Defines how to maintain the CytoFluor system For example it describes how to clean the scanner an...

Page 14: ...TION Warns the user about possible harm to the system or loss of data Appendix B Error Messages Describes and defines CytoFluor system test vectors and error messages Appendix C Warranty Service Information Contains warranty service and return information Appendix D Plate Scan Patterns Provides examples of the scan patterns the CytoFluor system uses when averaging points taken in a well Appendix E...

Page 15: ...s on the system to alert the user to warnings The symbol also appears next to associated warnings in this document Le symbole ci dessous permet d alerter l utilisateur et precede un avertissement Send us your comments We welcome your comments and suggestions for improving our manuals You can send us your comments by e mail at TechPubs appliedbiosystems com Artisan Technology Group Quality Instrume...

Page 16: ... References 1 5 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 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE w...

Page 17: ...n select plate formats from a library of plates or define your own plate format as described in Chapter 5 Setting the Plate Layout or Auto Scale Parameters For plates with larger wells you can choose an option to obtain an average of multiple data points in each well Appendix D Plate Scan Patterns defines the acquisition patterns In addition you can configure the system to read plates from the top...

Page 18: ...ides the ability to hold a plate at a specific temperature or collect data from kinetic experiments See Section 3 5 Controlling the Temperature for more details 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 Artisan Technology Group Quality ...

Page 19: ...u can only change the comments information in a file You start collecting data by selecting the Start button from the main setup screen after you enter the scan setup information The software directs the scanner to move the plate into the detection chamber The scanner mechanism then aligns the probe to read all selected wells row by row A run for a single plate may have up to 200 cycles with up to...

Page 20: ...e Or copy the parameters of an existing file and rename it Chapter 3 Scanning Operations 4 Determine the plate layout to identify particular wells or groups of wells before starting or completing a run optional Chapter 5 Setting the Plate Layout or Auto Scale Parameters 5 Set the auto scale parameters so the system can scale the data as it acquires it optional Chapter 5 Setting the Plate Layout or...

Page 21: ... 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 9 Maintain the CytoFluor scanner Chapter 7 Maintaining the CytoFluor System Step Action Described in Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 22: ... 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 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 23: ...TE See Section 2 2 The CytoFluor Scanner for details CytoFluor system software System Calibration Certificate NOTE It identifies the scanner and software by serial number CytoFluor Series 4000 Fluorescence Multi Well Plate Reader Installation Qualification Certificate CytoFluor Series 4000 Fluorescence Multi Well Plate Reader User s Guide Accessories kit Artisan Technology Group Quality Instrument...

Page 24: ...llen 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 1A 2 5 A Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 25: ...nts for service 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 26: ...ing the CytoFluor System for more details This section defines how each scanner part functions See Section 2 4 Setting Up Your System for information on how to set up the scanner Front of the scanner Figure 2 1 shows the front of the scanner Figure 2 1 Front of Scanner The front of the scanner includes Plate carrier door Opens to extend the plate carrier so you can insert a plate When the system b...

Page 27: ...nger tight CAUTION Be sure to seat the cover properly so the plate carrier can exit the scanner After you follow the steps in Section 2 4 4 Installing the Software click on the Plate In and Plate Out buttons to test the plate carrier If it does not move in and out reseat the cover Figure 2 2 shows the inside of the scanner Figure 2 2 Inside of Scanner NOTE In CytoFluor Series 4000 scanners with te...

Page 28: ...tation and emission signal D Top read mounting block Holds the probe so it can read from the top of the plate E Bottom read mounting block Holds the probe so it can read from the bottom of the plate F Excitation filter assembly Holds the filter that selects the excitation wavelength G Lamp Provides the fluorescent excitation The lamp is located at the rear of the scanner in a separate covered comp...

Page 29: ...r to a computer Pins used 2 Transmit 3 Receive 7 Ground Settings on scanner Com port on computer must be set the same way 9 600 baud 8 data bit 1 stop No parity C Air exhaust fan Forces air out of the scanner to keep it cool D Power switch Enables you to turn the scanner on and off E Power inlet Enables you to connect the power cord F Fuse module Enables you to change the fuses Artisan Technology ...

Page 30: ...nsity disk drive One serial port One parallel port Microsoft Windows version 3 1 or later or Windows 95 software Performance suggestions For optimum performance you should also supply An electrical surge protector most multi outlet power bars include surge protection A mouse pad Site selection Install your system in an area that is well ventilated free from dust and fumes and away from direct sunl...

Page 31: ...uses The CytoFluor Accessories kit contains four 2 5 amp fuses Two UL CSA approved fuses For use in U S and Canada Two IEC approved fuses For use in all other countries The fuses are universal and can be used for 100 to 120 and 200 to 240 voltages WARNING For continued protection against fire hazard replace fuses with those of the same type and rating AVERTISSEMENT Remplacez les fusibles par ceux ...

Page 32: ...ding out the fuse module Figure 2 4 Figure 2 4 Removing the Fuse Module 3 Install the 2 5 amp fuses in the fuse module Figure 2 5 NOTE Install UL CSA approved fuses in the United States and Canada Install IEC approved fuses in all other countries Figure 2 5 Installing the Fuses PB100496 Slot Power module Fuse module PB100493 Fuse module 2 5 amp fuses Artisan Technology Group Quality Instrumentatio...

Page 33: ...the fuse module into the power module until it snaps into place Figure 2 6 Figure 2 6 Replacing the Fuse Module 5 Install the power cord PB100492 Fuse module Power module Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 34: ...he Cover 2 Remove the shipping restraints from the probe and transport assemblies shown in Figure 2 8 Cut the tie wraps with a small wire cutter NOTE CytoFluor Series 4000 Temperature Control models do not have a shipping restraint at position 1 Figure 2 8 You must however remove a piece of tape from the temperature control chamber door Thumbwheel Artisan Technology Group Quality Instrumentation G...

Page 35: ... tight CAUTION Do not over tighten or under tighten the cover thumbwheel or the plate carrier cannot exit the scanner To make sure you closed the cover correctly click Plate Out If the plate carrier does not move out turn off the scanner and turn the thumbwheel further to tighten it Figure 2 9 Closing the Cover PB100532 Shipping restraint position 1 Rails Tie wraps Tie wrap Thumbwheel Artisan Tech...

Page 36: ...tlet Using a grounded plug that has been converted to a non grounded plug can cause electric shock or system damage AVERTISSEMENT Pour les connexions électriques vous devez mettre le système et l ordinateur à la terre Ces composants sont équipés de fiches de mise à la terre Utilisez ces dernières avec une prise de courant reliée à la terre L utilisation d une fiche de mise à la terre transformée e...

Page 37: ...r Make a note of the port you used to connect the scanner Figure 2 10 Connecting the RS 232 Cable to the Computer 2 Connect the other end of the RS 232 cable into the Serial Port 9 pin connector on the rear of the scanner Figure 2 11 Connecting the RS 232 Cable PB100529 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 38: ...nnecting 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 PB100530 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 39: ...ate Windows 3 Insert the CytoFluor diskette into the floppy drive 4 Follow the appropriate steps below for Windows 3 1 or Windows 95 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 If you have Then Windows 3 1 Activate the Windows Program Manager Select Run from the File menu The ...

Page 40: ...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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 41: ...ware contact Applied Biosystems Technical Support See Appendix E Technical Support and Training for the phone number Displaying the software version To check the version of the installed software open the About Cytofluor dialog box To do so select About Cytofluor from the Help menu Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 42: ...o Windows for a brief introduction or run the tutorial under the Windows Help menu Then return to this section 2 5 1 Starting Up the CytoFluor System To start up the CytoFluor scanner CAUTION Do not turn on the scanner unless you have installed fuses as described at the beginning of this chapter 1 Turn on the CytoFluor scanner using the power switch on the rear panel 2 Turn on the computer and sta...

Page 43: ...toFluor Main Setup Screen 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 44: ...e options instead of clicking with the mouse The CytoFluor software shows the key equivalent as an underscored letter in the name of an option For example Maintenance has the key M as its equivalent Press ALT M Enter to choose it The Maintenance screen appears Figure 2 17 CytoFluor Maintenance Screen 2 See Section 2 5 3 Checking Scanner Settings to check the scanner settings Artisan Technology Gro...

Page 45: ...nge the setting 3 Click on the down arrow next to the Port to Reader field to scroll down a list of port selections Highlight the computer port to which you configured the CytoFluor system and release the mouse to select it 4 See Section 2 5 4 Running System Diagnostics to run system diagnostics NOTE Keep a dated record of the settings Update the record when filters are changed or added 2 5 4 Runn...

Page 46: ... Technical Support and Training for the phone and fax numbers 2 Click Print to print a CytoFluor Fluorescence Unit Test Report 3 Click OK to close the box 2 5 5 Returning to the Main Setup Screen If you have been working with the software follow these steps to return to the main setup screen 1 Click the Save button to keep any changes you made before returning to the main setup screen Or click Can...

Page 47: ...ing 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 48: ...de 2 27 2 2 6 Shutting Down the System To shut down the system 1 Select Exit from the File menu ALT F 2 Exit Windows 3 Power down the scanner and computer Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 49: ...Chapter 2 Getting Started 2 28 Applied Biosystems 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 50: ...ns 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 3 24 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 51: ... enter a new file name before or after you set the scan parameters See the following sections for details You can For instructions Enter new settings and create a new file name See Section 3 1 1 Creating a New Original File NOTE If you do not have an existing file in the system follow the steps in this section to create one Access the data of a pre existing file to adopt the settings of that file ...

Page 52: ...ame box up to eight characters Change the directory if necessary Then click on the Save As button to save the file If you want you can save as a template by selecting Template Files from the Save File As Type pull down menu With a template file you can quickly set up future runs by adopting the setup as described in the next procedure If you enter a name that already exists a message is displayed ...

Page 53: ... Section 3 2 Setting Scan Parameters for details To use a previously saved file 1 Pull down the File menu and choose Open ALT F O A dialog box appears containing a list of files in your current directory 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 ...

Page 54: ...s settings for subsequent runs The system displays the file data on your screen whether you chose Yes or No You can see the file name in the title bar 5 Review the data if you selected No Edit the Comments field if necessary then select Save from the File menu to close the file under the same name You cannot edit any other scan parameters If you select New from the File menu the scan setup paramet...

Page 55: ...plate layout information as described in Chapter 5 Setting the Plate Layout or Auto Scale Parameters You cannot change the scan parameters Then save the file under the same name by selecting Save from the File menu Select Save As from the File menu to enter a new file name that has the same parameters as the file you accessed See step 4 and step 5 in Creating a New Original File on page 3 3 for de...

Page 56: ... application you see default settings You can change the parameters before creating naming a file Once you access the main setup screen you can use the Comments field to enter detailed information unique to the experiment assay and laboratory You use the other fields to select the run mode mix time reads per well read location plate type number of cycles up to 200 scans per cycle up to four cycle ...

Page 57: ...use this mode for kinetic studies Manual Scans one plate after another with a minimum amount of manual interaction The system presents the plate at the completion of each cycle enabling you to change the plate or add reagents The system stores all the gathered cycles up to 200 in the same data file You may want to use this mode to run several plates as part of the same experiment The default syste...

Page 58: ...n time The average value is displayed To set this field 1 Click on the down arrow in the Reads well box 2 Highlight your selection Close the choice box by clicking in the Reads well field Center Only For large well plates 6 12 24 and 48 well plates you may want to average readings taken at different locations over the entire well instead of using just one at the center If you deselect the Center o...

Page 59: ...ng the CytoFluor System if you need to adjust the probe height Figure 3 4 Probe Height Adjustment Message 2 Highlight your plate type selection If the warning appeared click OK or press Enter to close the box NOTE If you do not see the plate you want you can define a plate For more information refer to Chapter 6 Customizing the CytoFluor System Cycles For each run you can collect up to 200 cycles ...

Page 60: ...the system displays a message indicating that the value you entered was too small It also shows you what value it used instead If you enter a time of 00 00 00 the scanner will acquire data as quickly as possible with no need to update the Cycle Time field You can use this feature for example to scan at intervals during an ongoing biochemical process This field becomes disabled if you set the mode ...

Page 61: ... selecting Lamp Off from the Excitation menu on the Main Setup screen before you begin a scan Scanning with the lamp off allows you to measure bioluminescence glow This allows you to use the CytoFluor Series 4000 as a luminometer although all luminescent assays may not be optimized on the system Cycle You use this field to indicate the cycle you want to display after the system acquires data To se...

Page 62: ... for a strong fluorescence signal See Section 3 3 Setting Up Multiple Scans in a Cycle for details Auto Scale Uses the parameters shown in the Auto Scale menu to automatically normalize all of your data to the same fluorescence reference You can choose one of the internal fluorescence reference supplied with the CytoFluor system or use a known concentration of the fluorescent product in your assay...

Page 63: ...rescence and time data for each well This allows you to display current rate data during scanning To display rate data during scanning click the By Rate check box When you select By Rate the data are displayed for each well during any given scan as follows NOTE Values that exceed the system limits are not displayed Date Time Displays the data and time of the previously acquired data You cannot edi...

Page 64: ...ate The labels change as the numbering of the wells change This area of the screen represents the position of the wells in your plate As CytoFluor scans the plate you can see the data collected for each well appear in real time in the appropriate position on the screen The top left of the screen displays the post processing selections in effect for the run CAUTION It is safer to give the file a na...

Page 65: ... setup screen to select the multiple scan settings See the following sections for details Select the number of scans 1 Select the number of scans you want in each cycle from the Scan cycle box if you have not done so already See Scans Cycle on page 3 11 for details 2 Click the down arrow in the Scan field to reveal a pull down list 3 Select the scan you want to define 1 2 3 or 4 4 Select the filte...

Page 66: ...lter parameters So if you use custom filters update the software with the correct positions of these filters Also include the correct center wavelength and band pass parameters See Chapter 6 Customizing the CytoFluor System for details CAUTION Do not run a scan with incompatible filter pairs or you will damage the instrument and void the warranty You must select a compatible pair of filters before...

Page 67: ...t different gain settings from low to high This way you can quickly determine the best gain setting for your particular experiment Additional scans Repeat the steps to select the number of scans filter pair and gain for each additional scan you want to run Copying filter and gain settings You can copy the filter and Gain settings from a scan to up to 4 additional scans For example when you scan an...

Page 68: ... 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 5 Click OK Save the file Select Save As from the File menu Name your file if necessary Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 69: ...will lose the data To save the scan parameters 1 Select Save As from the File menu 2 Enter a new name in the File Name box up to eight characters Change the directory if necessary Then click the Save As button You can enter a name that identifies the file as a template Then you can quickly set up future runs by adopting the setup of the file See Accessing a Previously Saved File on page 3 4 for de...

Page 70: ...out screen as a template to use for future scans To save the file as a template 1 Select Save As from the File menu The save as dialog box appears 2 Select Template Files from the Save File As Type pull down menu The file is saved with a MFT extension Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 71: ...trol the temperature to hold the plate at a specific temperature or to perform kinetic experiments that measure rates or endpoints Temperature stability The temperature you set has an accuracy of 0 5 C and is uniform to 0 3 C System temperature The Temp box Figure 3 7 displays the actual system temperature and is updated every 5 seconds as the temperature equilibrates The temperature can take 15 t...

Page 72: ... C to 20 C above ambient temperature in 0 2 C increments up to a maximum of 45 C OFF to turn off the heater If you do not set the temperature the software uses the last temperature value entered to control the temperature Turning off temperature setting To turn off the temperature control setting Select Off from the SetTemp pull down menu Artisan Technology Group Quality Instrumentation Guaranteed...

Page 73: ...ycle to the file as it completes the cycle If you did not name the file you need to save it through the Save As command under File at the completion of the run Otherwise you could lose the data if something disturbed the run for example a power failure 2 Warm up the scanner lamp for a minimum of 10 minutes prior to your first scan You can turn the lamp on by clicking the Lamp On button if necessar...

Page 74: ...ite the data Then select New from File and enter a new name using Save As As the system scans each well you can see the AFU value appear in the corresponding well at the bottom of the screen Accessing other applications You can access other Microsoft Windows applications while performing a scan To access other applications 1 Wait until the scan is between cycles 2 Double click the icon of the appl...

Page 75: ...nts the plate and displays the data on the screen For example you may see data like this Figure 3 10 Main Screen with Data NOTE With Auto mode the Total Time field switches to a countdown timer during a run to the start of the next cycle with multiple cycles This only occurs if the Cycle Time is greater than the actual data acquisition time Artisan Technology Group Quality Instrumentation Guarante...

Page 76: ...ata under that name as it performed the run Data loss protection The data files from each cycle are automatically saved on the hard drive If the power to your system fails all data collected before the power failure is saved and you can retrieve it when the power is restored If you do not define a file name for your data files they are saved with a TMP extension Artisan Technology Group Quality In...

Page 77: ...Chapter 3 Scanning Operations 3 28 Applied Biosystems 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 78: ...cludes 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 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 79: ...the Scaling Screen Overview You use this screen to determine the data display format You can also determine how you want the system to subtract blank values from data points You can designate blank wells in the Plate Layout screen see Chapter 5 Setting the Plate Layout or Auto Scale Parameters for details Once you make your selections you can click on the Update button to view the screen data or s...

Page 80: ...ed scan and the start of the corresponding scan of cycle 1 If the system only acquired one cycle the elapsed time would be 00 00 00 2 Select a cycle from the Cycle pull down list The system applies the post processing parameters to the entire run 3 Select Scaling from the Post processing menu option to display the CytoFluor Scaling screen Figure 4 1 Scaling Screen 4 Select the options you want to ...

Page 81: ...Threshold Ranged Scale To Control The background subtract features are No Background Subtraction Background value Background average of blank wells See the following sections for details Raw Data This feature enables you to see the raw data for each well To display raw data 1 Click on the Raw data button Figure 4 2 Selecting Raw Data Artisan Technology Group Quality Instrumentation Guaranteed 888 ...

Page 82: ...les you to display the data scaled to values from zero 0 to the Max Maximum value entered up to 99999 The maximum data point that the system acquires is set equal to the Maximum data value you enter to determine the scaling factor To display scaled data 1 Click on the Scaled button 2 Enter a value from zero to 99999 Then click Update to return to the CytoFluor main setup screen with a Scaled data ...

Page 83: ...s minus symbols and between the two values as asterisk symbols To display data in the threshold format 1 Click on the Threshold button 2 Edit the Max value and Min value settings if necessary by entering a value from zero 0 to 99999 Click Update to enter the value and return to the main setup screen The Min value should be less than the Max value Otherwise the system makes a beep sound and does no...

Page 84: ...he Max value and Min value settings if necessary by entering a value from zero 0 to 99999 Click Update to enter the value and return to the main setup screen with an updated data display 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 6 Ranged Data See Background Average of Blank Wells on page...

Page 85: ...tem will subtract from each data point To use it 1 Click on the Background Value box 2 Edit the Background value setting if necessary by entering a value from zero 0 to 99999 Then click 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 If you assign a control well as It is used t...

Page 86: ...o subtract from each data point This value is based on the number of blank wells you assign in the Plate Layout screen with a label of bk00 See Chapter 5 Setting the Plate Layout or Auto Scale Parameters for details To enable this feature 1 Click on the Background average of blank wells box NOTE If the plate layout has no wells designated as bk00 the system will subtract a value of zero 0 Artisan ...

Page 87: ...ate data of a kinetics run You do this by determining the maximum change in AFU values between limits you set in the Kinetics Post processing screen The CytoFluor software fits a line to the number of data points you set and determines the maximum slope Accessing the Kinetics Rate Calculation screen To access the kinetics Rate Calculation screen 1 Open a file as described in Chapter 3 Scanning Ope...

Page 88: ...ly acquired one cycle or if cycle 1 is selected the elapsed time would be 00 00 00 2 Click on the down arrow key in Cycle Then select a cycle from the pull down list if you have more than one Click on the down arrow key beside each box to change the data set display The system applies the post processing parameters to the entire run 3 Select Kinetics from the Post processing menu option to display...

Page 89: ...atures This section includes Setting kinetics parameters Plotting kinetics data 4 1 4 1 Setting Kinetics Parameters The Kinetics screen contains the parameters used to calculate the initial rate data and graphs of the scan data for each well 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 Artisa...

Page 90: ...on End Sets the last data point used for the rate calculation AFU Limits Min Sets the minimum AFU value to use in rate calculation Max Sets the maximum AFU value to use in rate calculation Window Size Sets the number of data points number of cycles used to find the maximum slope of the AFU curve Display Scan Sets the scan to display Scale Rate to Control Scales the data to a percentage of the aver...

Page 91: ...To view and print plots for each well 1 Double click the well on the Kinetics Rate Calculation screen Figure 4 10 on page 4 11 The Expanded KineticsPlot screen appears with a graph of the data for the selected well Figure 4 11 Expanded Well Plot 2 Customize the plot parameters if required See Customizing the plots on page 4 18 3 Click Print to print the graph 4 Click Close to return to the Kinetic...

Page 92: ...s and click the Plot button The Expanded Kinetics Plot screen appears with a graph of the standards Figure 4 12 Standards Plot 2 Customize the plot parameters if required See 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 93: ...elect Unknowns and click the Plot button The Expanded Plot screen appears with a graph of the unknown Figure 4 13 Unknowns Plot 2 Customize the plot parameters if required See 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 94: ...trols and click the Plot button The Expanded Plot screen appears with a graph of the controls Figure 4 14 Controls Plot 2 Customize the plot parameters if required See 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 95: ...is labels 1 On any of the previous plots screens double click on the axis to change The Axis labels dialog box appears Figure 4 15 Axis Labels Dialog Box 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE w...

Page 96: ...eturn to the Axis labels dialog box 6 Click OK Axes To customize the axes 1 On any of the previous plots screens double click on the axis to change The Axis dialog box appears Figure 4 17 Axis Dialog Box 2 Change the parameters as desired 3 Click OK to save the changes Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 97: ...e Plot Parameters dialog box appears Figure 4 18 Plot Parameters Dialog Box 2 Change the parameters as desired 3 Click OK to save the changes Legend To customize the legend 1 On any of the previous plots screens double click on the legend The Legend Parameters dialog box appears Figure 4 19 Legend Parameters Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg co...

Page 98: ...t Save As under the File menu ALT F A 4 3 Printing Data Printing an entire run If you currently have data on your screen and you want to print the data of the entire run Click the Print button The data prints using the format selected in the Export Print dialog box when Printer is selected Printing screen data If you only want to print the data currently displayed on the screen instead of the enti...

Page 99: ...m the File menu ALT F E You see a screen like this Figure 4 20 Export Print Dialog Box 2 Select the format you want to export the file in by clicking one of the formats listed under Export format The system will export the data with the post processing options active For example if you selected a background subtraction value through the Post Processing menu all data points in the exported file wil...

Page 100: ...ing 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 Excel Exports a text file with the XLS extension Excel requires the tab delimiter between data fields After you open it in Excel save it as again to retain Excel functions and links Lotu...

Page 101: ...a group To export a group of files select additional file names with the mouse You can also group separate data files into one export file by clicking on the Concatenate button after you select the files to be grouped 5 Select the appropriate Export To option 6 Click the Export button to export the file Or click Cancel to close the box without converting files The system saves files in the export ...

Page 102: ...om 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 Export Current To export the file displayed on the main setup screen click Export Current Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 103: ...format to create in the Format Name text box You can use any characters except commas 4 Type the file extension in the File Suffix text box 5 Select Tab or Comma to separate the data with in the Delimiter pull down list 6 If you want to enclose text with a symbol select the symbol in the Wrap text with pull down list 7 To include header information or export the data in linear or table format use ...

Page 104: ...n 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 Select the parameters to appear in the header An example of a header with all parameters selected is shown in Figure 4 22 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 105: ...g Printing and Exporting Data 4 28 Applied Biosystems 4 Figure 4 23 Header Parameters 3 Click OK to save your changes MAR 9 1997 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 106: ...Export Setup dialog box click Table The Table Setup dialog box appears Figure 4 24 Figure 4 24 Table Setup Dialog Box 2 Select the parameters to include in the header An example of data in table format with all parameters selected is shown in Figure 4 25 Figure 4 25 Table Data Parameters Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 107: ...a Linear Format To export data in a linear format 1 In the Export Setup dialog box click the button to the right of Linear The Linear Setup dialog box appears Figure 4 26 Figure 4 26 Linear Setup Dialog Box 2 Select the parameters to include in the header Header parameters Column parameters Sort parameters Orientation parameters Group parameters Row and Artisan Technology Group Quality Instrumenta...

Page 108: ...OK to save your changes 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 Parameter Description Cycle Vs Well Lists the cycles horizontally and the well names vertically Well Vs Cycle Lists the well ...

Page 109: ...Chapter 4 Displaying Printing and Exporting Data 4 32 Applied Biosystems 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 110: ...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 5 15 5 6 Defining Plates 5 16 5 7 Using 384 Well Plates 5 21 5 8 Setting Auto Scale Parameters 5 25 5 9 Exiting the CytoFluor System 5 28 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 111: ... excluded wells as required by your assay NOTE If your plate is not listed in the main setup screen s Plate type options you can define its parameters in the Define Plate screen The Plate Layout screen looks like this Figure 5 1 Plate Layout Screen Basic editing options Well types Options and Index Selection Box Current plate Plate representation description Concentration parameters Artisan Techno...

Page 112: ...value enables you to identify replicates of the same material on the plate You do not need to enter an index value for wells defined as Empty Hidden or Excluded Concentration parameters Enable you to enter concentration and dilution factors for each group of wells Current Plate Description Allows you to view the size and coordinates of the plate you are using Basic editing options Enable you to ca...

Page 113: ...ures For example you will not be able to access the Exclude well type button See Chapter 3 Scanning Operations for details on how to scan a plate To access the CytoFluor Plate Layout screen 1 Activate Windows Then double click the CytoFluor icon The CytoFluor main setup screen appears Figure 5 2 CytoFluor Main Setup Screen NOTE If you want to open a particular file to review or change the plate la...

Page 114: ...luor Plate Layout Screen The first time you access this screen you see the default plate layout This layout has all unnamed wells You can make changes to any plate layout including the default layout or one of an already saved file If you accessed the plate layout of a pre defined file you see the last saved layout of the plate 4 Review the plate layout To make layout changes see the following sec...

Page 115: ...ons The options consist of four buttons located across the top of the CytoFluor Plate Layout screen See this chart for details Use this Button To do this OK Confirm your changes before saving Cancel Cancel your changes and return to the main setup screen Clear Plate Remove all well assignments You can use this to clear the layout before saving it or to clear the setup of a previously saved file NO...

Page 116: ... enables you to differentiate between different samples of the same type standard unknown etc on the plate NOTE You do not need to enter an index value for wells defined as Empty Hidden or Excluded 3 Select the well s that you want to assign to sample replicates Click a single well to select it For a group of wells start with the pointer at the leftmost corner well and drag it until you highlight ...

Page 117: ...Data Analysis Software for these calculations See Chapter 4 Displaying Printing and Exporting Data for details The following sections describe the options in the order listed Unknown To define a well or group of wells as unknowns 1 Click on the Unknown button in the Plate Layout screen 2 Select an index value from the pull down menu 00 to 99 3 Select the well s on your assay plate that corresponds...

Page 118: ...e plate layout as described in this chapter Or click on OK to save your changes Standard You can use wells assigned as standards to obtain values for plotting standards curves in data analysis applications NOTE If you use CytoCalc software for data analysis you need a minimum of three points to plot a curve and should have at least two replicate wells for each point The CytoCalc software accommoda...

Page 119: ...at the steps in this section for each curve you want to add Assign a different index value for each group of replicates For example sd00 sd01 and sd02 may represent points for one standard curve and sd10 sd11 sd12 and sd13 may represent points for another 5 Make additional changes to the plate layout as described in this chapter Or click on OK to save your changes Control A group of control wells ...

Page 120: ...e See Background Average of Blank Wells on page 4 9 for more information on background subtraction To define wells as blank 1 Click on the Blank button in the Plate Layout screen 2 Select an index value from the pull down menu 00 to 99 3 Select the well s on your assay plate you want as blanks Click with your mouse or click and drag to select a group of wells The system enters the abbreviation bk ...

Page 121: ... time To exclude wells 1 Click on the Exclude button in the Plate Layout screen 2 Select the well s on your assay plate you want to exclude Click with your mouse or click and drag to select a group of wells The system does not enter an Exclude abbreviation in the excluded wells Instead they appear as grayed dimmed wells For example columns 1 and 2 in the figure below are grayed Figure 5 5 Excluded...

Page 122: ... system enters the abbreviation emp into the wells you select 3 Make additional changes to the plate layout as described in this chapter Or click on OK to save your changes Hidden This well option enables you to omit outlying data from calculations The data is not lost but omitted from any calculations For example values that exceed the system limits where appears as the maximum value To define we...

Page 123: ...ed mode See Defined mode on page 5 27 for more details NOTE If you want to select Well s as your auto scale reference in the Auto Scale screen you must define one to three wells as controls There is no limitation as to where you place the Control wells But you can minimize cycle time if define them in the same row near the top of the plate for example 1A 1 Click on the Auto Scale button in the Pla...

Page 124: ...ich you want to assign concentration parameters 2 For standards and controls enter the concentration value in the Value text box and the units in the Unit text box Figure 5 6 Figure 5 6 Concentration Parameters 3 Select Verify to display the parameters for selected wells in the concentration parameters text boxes 4 Make additional changes to the plate layout as described in this chapter Or click o...

Page 125: ...ing a plate Deleting a plate 5 6 1 Preparing the Scanner NOTE The probe must be in the bottom read position when you define plates To insert the plate in the scanner 1 Click Plate Out 2 Place the plate to define in the plate carrier 3 Click Plate In 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 cl...

Page 126: ...efined Plates screen appears Figure 5 7 The name and coordinates of the plate type used during the last scan are displayed Figure 5 7 Defined Plates Screen NOTE You can double click on a plate name in the Defined Plate list to display the coordinates of that plate Enter the Enter the number Enter the number of columns of rows plate name Artisan Technology Group Quality Instrumentation Guaranteed 8...

Page 127: ...yed 5 Enter the number of rows on the plate in the Rows box 6 Enter the number of columns on the plate in the Cols box 7 Click Setup Coordinates The Coordinate Setup screen appears Figure 5 8 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 Arrow Scroll Box Scroll Bar Artisan Technology Group Quality Instrumentation...

Page 128: ...e the plate in increments of 20 units in the direction of the arrow Click the arrow to move the plate in increments of one unit in the direction of the arrow 10 Select X2 Y2 The last well in the plate is positioned over the probe 11 Verify that the well is centered over the probe If the well is not centered center it by using the scroll bar as described in step 9 12 Click Test Move The probe reset...

Page 129: ...closed the cover correctly click Plate Out If the plate carrier does not move out turn off the scanner and turn the thumbwheel further to tighten it 5 6 3 Deleting a Plate To delete a plate from the Defined plate list 1 Select Define Plate from the Plate menu 2 Select the plate to delete 3 Click Delete 4 Click OK If you want to Click add the plate name to the end of the Defined plate list Add add ...

Page 130: ...attern option You can set the scanning pattern of 384 well plates by using the 384 Scan Pattern options on the Plate Layout screen 5 7 1 Defining the 384 Well Plate Before you scan a 384 well plate you must define it using the Define Plates screen See Section 5 6 2 Defining a Plate for detailed instructions See Table 5 1 for the coordinates of standard 384 well plates Table 5 1 384 Well Plate Coor...

Page 131: ...ner reads the plate in four quadrants of 96 wells as shown in Figure 5 9 It reads one quadrant per scan according to the 384 Read Pattern option you select Figure 5 9 384 Well Plate 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 A B C D E F G H I J K L M N O P Quadrant 1 Quadrant 2 Quadrant 3 Quadrant 4 Column 1 Row A Artisan Technology Group Quality Instrumentation Guaranteed 888 ...

Page 132: ... Remaining wells Repeat scan 1 Repeat scan 2 Skip X Skips every other well in row starting at row A column 1 Skips every other well in row starting at row I column 1 Skips every other well in row starting at row A column 2 Skips every other well in row starting at row I column 2 Skip Y Skips every other well in column starting at row A column 1 Skips every other well in column starting at row A co...

Page 133: ...Layout screen appears with the 384 Read Pattern options available Figure 5 10 Figure 5 10 384 Read Pattern Options 3 Select the appropriate Read Pattern option described in Table 5 2 on page 5 23 NOTE The 384 Read Pattern options appear only if a 384 well plate is selected on the main setup screen 4 Click OK NOTE You can save the scanning pattern as a template to use for future scans See Saving as...

Page 134: ... mode Scales data according to the filter pair settings reference and gain you set The defined mode allows you to set up to four different combinations of Auto Scale parameters for each one of four scans Auto Scale off Collects data without auto scaling AutoScale off is the default setting NOTE For the system to apply the settings you must select the Auto Scale field in the CytoFluor main setup sc...

Page 135: ... Figure 5 11 CytoFluor Auto Scale Screen Default mode To scan using the default mode 1 Select the number of scans from the Scans cycle pull down menu 2 Click the appropriate scan number button 3 Click Default Mode 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 Artisan Technology Group Quality Instrumen...

Page 136: ...ou must select a different setting for each filter 6 Select the PMT gain 7 Click Update The reference value is collected and stored 8 Repeat step 1 through step 7 for each scan 9 Click Save to save your Auto Scale information and return to the main setup screen AutoScale Off mode If you select Auto Scale on the main setup screen all scans are auto scaled To turn off Auto Scale for specific scans 1...

Page 137: ... make any changes you can return to the Windows desktop by Selecting Exit from the File menu ALT F E If you made changes to a file or acquired data without saving it the software asks if you want to save Click the appropriate button to save changes and exit ignore them and exit or cancel the exit process Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 138: ...2 6 4 Setting the Lamp Saver Time 6 13 6 5 Configuring the Scanner for Top or Bottom Plate Reading 6 14 NOTE You can define a new plate type if the plate type you are using is not in the CytoFluor plate library See Chapter 5 Setting the Plate Layout or Auto Scale Parameters if you need information on defining plate coordinates 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SO...

Page 139: ...l the filters in the filter wheels and change the corresponding settings in the software you could permanently damage the CytoFluor system and void your warranty Each filter position must contain a filter or a blocking plug 6 1 1 Changing the Excitation and Emission Filters This procedure describes how to change the excitation and emission filters The diagrams show the excitation filter assembly F...

Page 140: ...clicking the Lamp Off button Leave the power on so you can use the Maintenance options 3 Open the cover by turning the thumbwheel counterclockwise and lifting up the cover Figure 6 2 Opening the Scanner 4 Remove the two screws that secure the top cover of the filter wheel assembly Then remove the cover PB100555 Excitation filter assembly Emission filter assembly Thumbwheel Artisan Technology Group...

Page 141: ...the down arrow next to the Excitation Filter box to display a pull down menu when changing the excitation filter Then highlight the position number for loading 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg co...

Page 142: ...Accessing the Filter 7 Place the prongs of the tool into the holes on the top of the filter wheel or blank you need to change Turn the tool to the left until you can lift the filter from the wheel Figure 6 6 Removing the Filter CAUTION Do not apply excessive pressure while turning the filter you could damage the filter wheel And do not touch the glass surfaces of any filter or the instrument s opt...

Page 143: ...r Figure 6 7 Replacing Filters 9 Make a note of the filter position 1 2 3 and so on marked on the filter wheel Also note the center wavelength and bandwidth This information is printed on the outside of each filter For example if the filter is marked 485 20X 485 is the center wavelength and 20 is the bandwidth at one half maximum transmission BWHM of the excitation X filter An M instead of an X de...

Page 144: ... 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 1 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 145: ...toring filters Store unused filters in a cool dry location in sealed plastic bags Figure 6 10 Storing Unused Filters 6 1 2 Changing the Filter Settings in the Maintenance Screen This section describes how to change the excitation and emission filter settings stored in the CytoFluor software system CAUTION After you install new filters in the scanner you must change the filter settings in the Maint...

Page 146: ...igure 6 11 Maintenance Screen 2 Type in the Wavelength and Bandwidth values that correspond to the values of the excitation and emission filters you just installed 3 Click the Save button once you enter the correct new values The system returns to the main setup screen NOTE Click on the Cancel button for the system to disregard your changes and return to the previous settings Artisan Technology Gr...

Page 147: ...the scanner 1 Select Maintenance from the CytoFluor main setup screen You see a screen like this Figure 6 12 Maintenance Screen 2 Click the Test button on the right side of the Maintenance screen The CytoFluor software then automatically checks the scanner drives and lamp The test takes several seconds When complete the Unit Test dialog box appears Artisan Technology Group Quality Instrumentation ...

Page 148: ...ction 7 4 Replacing the Lamp for detailed instructions If any other system fails contact Applied Biosystems Technical Support See Appendix E Technical Support and Training for the phone and fax numbers 3 Click Print to print a CytoFluor Fluorescence Unit Test Report 4 Click OK to close the box Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 149: ...he port setting Otherwise select the Cancel button to return to the main setup screen without saving any changes 2 Click on the down arrow in the Port to reader box to reveal the pull down menu Then highlight the port connection you want to select it 3 Click on the Save button to save any changes If you select an invalid Port to reader setting you see Figure 6 14 Invalid Port Setting 4 Click OK th...

Page 150: ... turning it on and off throughout the day To set the lamp saver time 1 Display the Maintenance screen The default setting or last entered setting for the lamp saver appear in the Lamp saver box To change the setting continue to step 2 Otherwise click on the Cancel button to return to the main setup screen without making changes 2 Enter the hour minutes or seconds in the Lamp saver fields Use two d...

Page 151: ...ecking and Adjusting Probe Height in a Temperature Control Scanner 6 5 1 Changing the Probe Position The default configuration for the system is the bottom read position The illustrations in the following procedure show changing the probe from the top read position to the bottom read position Configuring To change the probe position 1 Make sure the plate transport carrier is inside the scanner If ...

Page 152: ...tion 4 Remove the knurled screw holding the probe to the mounting block Figure 6 16 Removing the Probe Screw CAUTION Pull the probe away from the mounting block to clear the mounting pins CAUTION Do not touch the probe tip or severely twist the fiber optic cables going to the excitation or emission filter modules If you do you could damage the probe or filter connection Artisan Technology Group Qu...

Page 153: ...our Series 4000 TR temperature ready Section 6 5 2 1 Checking and Adjusting Probe Height in Bottom Read Position TR Models Or Section 6 5 2 2 Checking and Adjusting Probe Height in Top Read Position TR Models CytoFlour Series 4000 TC temperature control Section 6 5 3 1 Checking and Adjusting Probe Height in Bottom Read Position TC Models Or Section 6 5 3 2 Checking and Adjusting Probe Height in To...

Page 154: ... height If you set the probe too high the plate carrier can jam against it If you set it too low you lower the signal 1 Slide the plate carrier back to the A1 position until the probe is underneath the edge of the plate carrier If the probe hits the plate carrier skip the remaining steps and proceed to Adjusting probe height in bottom read below 2 Hold the probe height adjustment spacer marked 0 0...

Page 155: ...mage it 5 Tighten the two screws on the rear of the probe mounting block Gently remove the 0 015 inch spacer 6 Slide the plate carrier to the back of the instrument 7 Make sure the fiber optic cables are inside the unit CAUTION The fiber optic cables can be damaged if they are caught between the cover and the base of the scanner 8 Close the scanner cover and seat it properly on the gasket Turn the...

Page 156: ...u lower the signal 1 Insert an empty plate into the carrier 2 Place the probe height adjustment spacer marked 0 020 inch on top of the plate Make sure the spacer is on the highest point of the plate usually across the corner of the plate 3 Slide the probe arm gently over the plate and check the probe height The probe tip should just clear the height adjustment spacer If the probe hits the spacer r...

Page 157: ...it Figure 6 18 Adjusting Probe Height 3 Tighten the two screws on the rear of the probe mounting block Gently remove the 0 020 inch spacer 4 Slide the plate carrier to the back of the scanner 5 Make sure the fiber optic cables are inside the scanner CAUTION The fiber optic cables can be damaged if they are caught between the cover and the base of the scanner 6 Close the scanner cover and seat it p...

Page 158: ...e height in bottom read In the bottom read position the probe tip should be located 0 4 mm the thickness of the 0 015 inch height adjustment spacer below the plate carrier You should rarely have to reset the bottom read probe height because the depth of different plates does not vary widely If you need to adjust the probe height call Applied Biosystems Technical Support for assistance CAUTION The ...

Page 159: ...ment spacer If the probe hits the spacer or is not almost touching the spacer call Applied Biosystems Technical Support When properly adjusted the probe tip is 0 4 mm the thickness of the 0 015 inch height adjustment spacer away from the probe 5 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...

Page 160: ...humbwheel clockwise and lifting up the cover 2 Insert an empty plate into the carrier and push the plate into the temperature control chamber 3 Push the temperature control chamber door open Insert the 12 inch long probe height adjustment spacer marked 0 020 inch into the chamber and place it on top of the plate Make sure the spacer is on the highest point of the plate usually across the corner of...

Page 161: ...be connected to the mounting bracket 2 Slide the probe up or down to the correct height CAUTION Bring the probe head down to just touch the 0 020 inch spacer Do not place excess force on the plate carrier or you could damage it 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 Temperature control chamber 0 020 in...

Page 162: ...ounterclockwise 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 To make sure you closed the cover correctly click Plate Out If the plate carrier does not move out turn off the scanner and turn the thumbwheel further to tighten it Artisan Technology Group Quality Instrumentation Guaranteed 888 88 S...

Page 163: ...Chapter 6 Customizing the CytoFluor System 6 26 Applied Biosystems 6 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 164: ...em 7 This chapter includes the following sections 7 1 Cleaning the Scanner 7 2 7 2 Cleaning the Rails 7 2 7 3 Replacing the Air Filter 7 4 7 4 Replacing the Lamp 7 5 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 165: ... inspect the rails for residue buildup monthly Clean the rails with ethanol or isopropanol if needed CAUTION Do not use acetone to clean the rails Acetone could damage the inside of the scanner Cleaning To clean the rails 1 Turn off the CytoFluor 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 o...

Page 166: ...e scanner CAUTION Do not over tighten or under tighten the cover thumbwheel or the plate carrier cannot exit the scanner To make sure you closed the cover correctly click Plate Out If the plate carrier does not move out turn off the scanner and turn the thumbwheel further to tighten it PB100546 Rails Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 167: ...e the Allen hex wrench provided with the Accessories kit Figure 7 2 Removing the Air Filter 2 Remove and discard the used filter 3 Locate the replacement filter included with the kit The filter is in two 31 mm x 82 mm pieces or one 31 mm x 164 mm piece Insert the new filter and replace the air filter protector Tighten the screws with the Allen hex wrench but do not overtighten CAUTION Do not opera...

Page 168: ...ss the Plate In button from the Maintenance screen if necessary 2 Turn off the CytoFluor scanner and disconnect the power cord Open the scanner cover by turning the thumbwheel counterclockwise then lifting up the cover 3 Locate the lamp cover Remove the retaining screw with a Phillips head screwdriver not included Then lift off the cover Figure 7 3 Removing the Lamp Cover Artisan Technology Group ...

Page 169: ...rior of the reflector They must be free of fingerprints or other material that can interfere with illumination and collect dust You may want to wear lab gloves Locate the tab on the lamp rim Insert the new lamp into the socket so that the it faces the excitation filter wheel with the tab facing up Press lightly on the rear of the lamp to seat and align it Figure 7 5 Replacing the Lamp 6 Place the ...

Page 170: ... 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 171: ...Chapter 7 Maintaining the CytoFluor System 7 8 Applied Biosystems 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 172: ...ions 8 1 Specifications 8 2 8 2 Minimum Computer Requirements You Supply 8 3 8 3 Optical Sets for Fluorophores 8 4 8 4 CytoFluor Standard Filter Sets 8 6 8 5 Ordering Information 8 7 8 6 Technical Support 8 8 8 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 173: ...e delay 250 volt 5 mm x 20 mm UL CSA approved in U S and Canada IEC approved in all other countries Input voltage 90 132 volts AC at 50 60 Hz selectable or 198 262 volts AC at 50 60 Hz selectable Optical Lamp type Tungsten halogen 50 watt Lamp life 3 000 hours nominal Lamp range 320 nm 700 nm Filter wheel 6 positions Detector Electron Tubes Inc 9781 Photomultiplier Tube low noise high gain Probe 3...

Page 174: ...size 45 27 µm 0 0018 in Repeatability 50 µm worst case X Y drive Stepping motor with direct drive belt Plate transport 10 seconds maximum load time Base unit IBM PC compatible 486DX computer 8 MB minimum RAM 240 MB hard drive High density floppy disk drive 3 1 2 inch 1 serial port 1 parallel port for printing Mouse Printer Any compatible Required software Microsoft Windows version 3 1 or later or ...

Page 175: ...ssay CFD A 485 560 Plasma membrane disruption CFD 485 530 pH B Phycoerythrin 485 590 General fluorescent tag DPH 360 460 Membrane probe DAPI 360 460 Nucleic acid stain Quin 2 360 460 Ion concentration Indo 1 360 485 Ion concentration Rhod 2 360 460 Ion concentration Thiolyte 360 460 General fluorescent tag Lucifer yellow 440 530 Gap junction communication Benzoxanthene yellow 360 460 General fluor...

Page 176: ...Nucleic acid stain 485 645 Dual wavelength monit 7 AAD 485 645 Nucleic acid stain Ethidium bromide in solution 485 645 Nucleic acid stain alamar Blue 530 590 Viability assay Ethidium dimer 530 590 Nucleic acid stain SNAFL in base 530 620 pH indicator SNARF 530 620 pH indicator TRITC 530 590 General fluorescent tag Propidium iodide in solution 485 645 Free dye in solution Propidium iodide 530 645 N...

Page 177: ...Monolayer permeability Thiazole Orange 485 560 Nucleic acid stain BODIPY 485 530 General fluorescent tag Green fluorescent protein 395 508 Gene expression Excitation Center Wavelength Full Bandwidth Emission Center Wavelength 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 Dye Excitation Emission Pair Application Artisan Techn...

Page 178: ...m kit Includes Fluorescence Reader Accessories kit 110 V and 220 V power cables RS 232 cable CytoFluor software CytoFluor Fluorescence Multi Well Plate Reader User s Guide MIFS0C2TC with temperature control MIFS0C3TR without temperature control RS 232 cable P40636 Power cable U S P30539 Power cable Europe P30540 CytoFluor 4000 Fluorescence Multi Well Plate Reader User s Guide 601380 Artisan Techno...

Page 179: ...acement Kit includes all parts listed below PIF600884 Probe spacer 0 015 P40633X1 Probe spacer 0 020 P40633X2 Optical filter tool PIFS5TOOL Fuse 2 5 amp time delay 250 volt 5 mm x 20 mm UL CSA approved in U S and Canada P40618X13 Fuse 2 5 amp time delay 250 volt 5 mm x 20 mm IEC approved in all other countries P4619X20 3 5 diskette CytoFluor software PIFS600875 Allen hex wrench 5 64 P40637X1 Combi...

Page 180: ...s 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 A Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 181: ...buttons on its top If you press down on the left mouse button and then release it this signals the computer to initiate an operation This action is called clicking Usually you must position the pointer on something on the screen before you click such as a menu title or a text field To select a section of text you move the pointer to the left end of the text and press and hold down the mouse button...

Page 182: ...file or application in which you re working In the upper right corner of the title bar are two arrows one pointing down and the other up The down arrow makes Microsoft Windows inactive minimizes it the up arrow increases the size of the window on the screen The close box is also found in the title bar in the upper left corner When you position the pointer on the close box and press a mouse button ...

Page 183: ...you choose menu options and commands you often open up dialog boxes In dialog boxes you find buttons scroll bars and check boxes that you can click on to select A 3 Screen Buttons You use screen buttons to make choices and send messages to the software for example you might confirm a command by clicking a button labeled OK or change your mind by clicking a button labeled Cancel Another kind of but...

Page 184: ...m By positioning the pointer over one of the arrows and clicking it you make visible more options on a list In the gray part of the scroll bar there is a small square called a thumb The thumb s position in the gray area is proportional to the viewing position in the list If the thumb is at the bottom of the scroll bar you are looking at the bottom of the list Artisan Technology Group Quality Instr...

Page 185: ...Appendix A Introduction to Windows A 6 Applied Biosystems A Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 186: ...ou may see and defines their meaning Error Code Message Meaning 202 Indicates a bug in the program 203 Failure to initialize the PC S Com port The port may not exist or may already be claimed by Windows or by another program 204 Time out waiting for response from instrument The instrument may not be turned on or connected to the PC or the Com port may be incorrectly configured See error code 206 2...

Page 187: ...internal file 213 Failed to get file system status of a file The file may not exist 214 Failed writing to a file because the disk is full Disk is full 215 Failed to initialize the print engine Check windows printer setup 216 Failed to initialize the main window Out of memory 217 Out of memory Attempt to allocate memory failed Try closing some windows 218 Instrument reports a hardware error 219 Ins...

Page 188: ...e harmful overlap of excitation and emission filters You cannot choose excitation and emission filters with similar or incompatible wavelengths Change one or both of the filter settings Overwrite existing filename You have chosen a file name that already exists Unless you intend to overwrite the file choose Cancel and type a different name Save first Occurs when you attempt to exit CytoFluor or wh...

Page 189: ... port and you selected COM2 Change the selection Time out error The plate may be jammed or incorrectly positioned in the plate transport mechanism 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 CytoFluor system Check all connections The software has lost communic...

Page 190: ...rt For systems that have built in computers installing unauthorized hardware or software may void the Warranty or Service Plan C 1 Limited Product Warranty Limited warranty Applied Biosystems warrants that all standard components of the 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 wi...

Page 191: ...exception of consumable and maintenance items replaceable products or components used on the instrument are themselves warranted to be free of defects in materials and workmanship for ninety 90 days Applied Biosystems warrants that chemicals and other consumable products will be free of defects in materials and workmanship when received by the buyer but not thereafter unless otherwise specified in...

Page 192: ...clusive 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 fitness for a particular purpose whether arising from a statute or otherwise in law or from a course of dealing or usage of trade all of which are expressly disclaime...

Page 193: ...pping damage to the instrument is discovered contact the shipping carrier and request inspection by a local agent Secure a written report of the findings to support any claim Do not return damaged goods to Applied Biosystems without first securing an inspection report and contacting Applied Biosystems Technical Support for a Return Authorization RA number Claims After a damage inspection report is...

Page 194: ...ells as circles The outside circle represents the well wall The dotted circle represents the outside travel diameter for the larger wells The probe travels in a square bound by the dotted circle Each dotted circle contains smaller circles that represent the spot pattern of the probe The wells are drawn to a relative scale See the following examples for details D Artisan Technology Group Quality In...

Page 195: ...Biosystems D 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 196: ...ng E 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 E Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 197: ...oduct Product Area E Mail Address Genetic Analysis DNA Sequencing galab appliedbiosystems com Sequence Detection Systems and PCR pcrlab appliedbiosystems com Protein Sequencing Peptide and DNA Synthesis corelab appliedbiosystems com Biochromatography Expedite 8900 DNA Synthesis System PNA Pioneer Peptide Synthesis System Proteomics Solution 1 PS1 System ICAT reagent FMAT 8100 HTS System Mariner Ma...

Page 198: ...uorescent DNA Sequencing 1 800 831 6844 press 2 then press 2a 1 650 638 5981 Fluorescent Fragment Analysis including GeneScan applications 1 800 831 6844 press 2 then press 3a 1 650 638 5981 Integrated Thermal Cyclers ABI PRISM 877 and Catalyst 800 instruments 1 800 831 6844 press 2 then press 4a 1 650 638 5981 ABI PRISM 3100 Genetic Analyzer 1 800 831 6844 press 2 then press 6a 1 650 638 5981 Pep...

Page 199: ...stem ICAT reagent 1 800 899 5858 press 1 then press 3b 1 508 383 7855 Biochromatography BioCAD SPRINT VISION and INTEGRAL Workstations and POROS Perfusion Chromatography Products 1 800 899 5858 press 1 then press 4b 1 508 383 7855 Expedite 8900 Nucleic Acid Synthesis Systems 1 800 899 5858 press 1 then press 5b 1 508 383 7855 Peptide Synthesis Pioneer and 9050 Plus Peptide Synthesizers 1 800 899 5...

Page 200: ...7899 a 5 30 A M to 5 00 P M Pacific time b 8 00 A M to 6 00 P M Eastern time c 9 00 A M to 5 00 P M Eastern time Product Product Area Telephone Fax Region Telephone Fax Eastern Asia China Oceania Australia Scoresby Victoria 61 3 9730 8600 61 3 9730 8799 China Beijing 86 10 64106608 or 86 800 8100497 86 10 64106617 Hong Kong 852 2756 6928 852 2756 6968 Korea Seoul 82 2 5936470 6471 82 2 5936472 Mal...

Page 201: ...34 0 91 806 1210 34 0 91 806 12 06 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d IJssel 31 0 180 392400 31 0 180 392409 or 31 0 180 392499 United Kingdom Warrington Cheshire 44 0 1925 825650 44 0 1925 282502 European Managed Territories EMT Africa English speaking Johannesburg South Africa 27 11 478 0411 27 1...

Page 202: ... enter the requested information then click Ask Us RIGHT NOW Within 24 to 48 hours you will receive an e mail reply to your question from an Applied Biosystems technical expert For all other EMT countries not listed Central and southeast Europe CIS Middle East and West Asia 44 1925 282481 44 1925 282509 Japan Japan Hacchobori ChuoKu Tokyo 81 3 5566 6230 81 3 5566 6507 Latin America Caribbean count...

Page 203: ...equest Obtaining documents through the web site To view download or order documents through the Applied Biosystems web site 1 Go to www appliedbiosystems com 2 At the top of the page click Services Support at the top of the page then click Documents on Demand 3 In the search form enter and select search criteria then click Search at the bottom of the page 4 In the results screen do any of the foll...

Page 204: ...ser s Guide E 9 E NOTE There is a limit of five documents per fax request but no limit on the number of documents per e mail request Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 205: ...ining 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 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 206: ...the wavelength range nm at 50 of peak transmission Boot To start or restart your computer by loading the DOS operating system The term is short for bootstrapping Starting up is often accomplished by first loading a small program that then loads a larger program into memory The program is said to pull itself up by its own bootstraps Check box A small box inside a dialog box or other window that you...

Page 207: ... quit Current directory The directory in which you are currently working while using the computer For example when using the CytoFluor program you would likely be working in C CYTOFLR which means the CYTOFLR directory on the C drive Data file Any file created within an application As you run scans with the CytoFluor System you are creating data files Data files may have CSV as an extension or they...

Page 208: ... click twice in quick succession This action carries out a command Export To move data into a file that other applications can use Extension A period followed by three letters at the end of a filename Extensions identify what kind of information a file contains For example the extension CSV indicates that the elements in the file are separated by commas The extension EXE identifies a file that the...

Page 209: ...h a minimum amount of manual interaction Maximize box The small box containing an up arrow that is located at the right of the menu bar Mouse users can click the maximize box to enlarge a window to its maximum size Others can use the Maximize command or the Control menu Menu A group listing of available Windows or application commands Menu names appear in the menu bar near the top of the window Yo...

Page 210: ...ou are using the A drive in DOS Sometimes the term prompt is used for the insertion point a flashing bar in a text box that shows where the next typed characters will appear RS 232 The standard serial interface protocol and thus the cable and connector specifications that enable a computer to be linked to the CytoFluor Scanner Restore box The small box containing an up arrow and a down arrow at th...

Page 211: ...s that otherwise require mouse moves or key equivalents such as choosing commands from menus The action of a shortcut key depends on the application program Spooler A Windows program that is automatically run when you choose a print command The Spooler lets you print files and view and control the jobs in the print queue Subdirectory A directory within another All directories are subdirectories of...

Page 212: ... value 3 25 Air exhaust fan 2 8 Air filter 7 4 Air vent 2 8 Applications accessing 3 25 Applied Biosystems world wide web address xiv Auto mode description 3 8 selecting 3 8 Auto Scale accessing screen 5 26 assigning wells 5 14 description of option 3 13 off 5 25 5 27 overview 5 25 setting 5 25 Axes customizing 4 19 Axis dialog box 4 19 B Background average 4 2 4 9 specify value 4 8 subtraction 4 ...

Page 213: ...ile 3 3 Customer training information E 10 Customizing export format 4 26 filters 6 2 kinetic plot labels 4 18 kinetics plot axes 4 19 kinetics plot legend 4 20 kinetics plot parameters 4 20 kinetics plots 4 18 plate reading 6 14 Cycle 3 12 Cycle Time description 3 11 setting 3 11 Cycles setting 3 10 CytoFluor checking system 2 21 customizing 6 1 definition of 1 2 description 2 5 function of 1 4 i...

Page 214: ...le requirements 4 23 Excitation filter assembly 2 7 changing 6 2 setting 3 16 standard sets 8 6 Exclude well 5 12 Exiting CytoFluor 2 27 5 28 Export Current file 4 25 Export format creating 4 26 Export To options 4 24 Exported files custom formats 4 26 names 4 24 Exporting files 4 22 groups of files 4 24 header 4 27 linear data 4 30 options 4 24 table data 4 29 F Features Scaling screen 4 4 Field ...

Page 215: ...a 4 14 Kinetics plot labels customizing 4 18 Kinetics rate data to file check box 4 13 Kinetics screen accessing 4 10 features 4 12 overview 4 10 setting parameters 4 12 L Lamp controlling 3 12 description 2 7 replacing 7 5 scanning with off 3 12 setting saver time 6 13 specifications 8 2 standby mode 6 13 turning off 3 12 Lamp saver time setting 6 13 Layout plate screen 5 2 setting 5 2 Legend Par...

Page 216: ...orientation 4 31 saving 3 20 setting 3 7 Parts of system 2 2 ordering 8 7 Plate 384 well 5 21 clearing 5 6 define coordinates 5 16 define options 5 16 define size 5 17 scan patterns D 1 scanning 3 24 top or bottom read 6 14 Plate carrier description 2 7 door 2 5 moving in or out 3 12 Plate In Plate Out 3 12 Plate Layout screen accessing 5 4 concentration parameters 5 15 editing guidelines 5 6 over...

Page 217: ...op read TC models 6 23 checking and adjusting height top read TR models 6 19 checking height overview 6 14 description 2 7 distance from plate in bottom read position TC models 6 21 distance from plate in bottom read position TR models 6 17 distance from plate in top read position TC models 6 23 distance from plate in top read position TR models 6 19 removing shipping restraints 2 13 R RA number C...

Page 218: ... shutting down 2 27 testing 6 10 Scanner settings checking 2 24 Scanning plates 3 24 with lamp off 3 12 Scans multiple 3 16 setting parameters 3 7 stopping 3 25 Scans Cycle 3 11 Settings filter 6 8 scanner 2 24 temperature 3 23 Setup coordinates 5 18 Shipping restraints 2 13 Shutting down CytoFluor 5 28 Site selection 2 9 Software default directory 2 18 exiting 5 28 installing 2 18 testing 2 21 So...

Page 219: ...Troubleshooting B 1 U 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 V Verify 5 15 Voltage requirements 8 2 W Warnings safety symbols on system xiv Warranty damages claims returns C 4 exceptions C 3 for computers with altered configuration C 1 period C 1 Well assigning 5 7 Auto Scale 5 14 blank 4 9 5 11 clear 5 14 control 5 10 empty 5 13 e...

Page 220: ...nd technical support please call our local office or refer to our web site at www appliedbiosystems com or to the Technical Support and Training appendix in this document Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses www appliedbiosystems com www ...

Page 221: ...l service in house repair center WE BUY USED EQUIPMENT Sell your excess underutilized and idle used equipment We also offer credit for buy backs and trade ins www artisantg com WeBuyEquipment REMOTE INSPECTION Remotely inspect equipment before purchasing with our interactive website at www instraview com LOOKING FOR MORE INFORMATION Visit us on the web at www artisantg com for more information on ...

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