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CellWorks© Short Manual - NPI Electronic Instruments

1. aka rae n REL A display shows the CHART sweep selected Ocal parameters in the CHART table BESSERES Figure 14 CW Chart Editor 5 6 Edit PULSE sequences in the Pulse Editor This chapter briefly describes the CW Pulse Editor which is used to define fast voltage protocols pulses or ramps for the two analog output channels Ao0 and Aol of the interface board and simultaneously perform synchronous Ai recording The Pulse Editor window is very similar to the Chart Editor window see chapter 5 5 As in CHARTS segments are the smallest temporal components of PULSES The parameter settings of five pulses are shown in the module window see Figure 15 The list at the left side contains the available PULSES and after selection of a PULSE the parameter settings are updated immediately In addition CellWorks reads these parameters and displays the corresponding traces in the graph which has various display and scaling features For DACO seven parameters can be set for each segment Segment Type Constant or Ramp value time and four parameters to define increments for voltage and or time Furthermore all voltages can be set in relation to a Reference Voltage to simplify pulse protocols for different holding potentials e g the user can define voltage steps defined as step amplitude for an I V curve in relation to a certain holding Reference potential This Reference potential is for display only T
2. Figure 1 assembling the hardware Installation 11 Nu Figure 2 INT 20X front panel Installation Front panel Number Short name Signal name Description Ai0 Ail5 ACHO ACH15 Analog input channels Analog Input 16 BNC connectors providing the 16 analog input channels of the E Series board AGND Analog input ground This connector supplies the 2 AISENSE Analog Input Sense reference point for all analog input channels 3 GND Ground Chassis potential 4 Ao0 Aol Analog output channels These BNC connectors provide DACO DACI Analog Outputs the 2 analog output channels of the MIO board 5 Do0 Do7 Digital output ports These output ports provide the 8 Digital I O digital lines from the E Series board 6 GND Ground Compare to number 3 7 DGND Digital ground This connector supplies the DGND Digital Ground reference point for all digital signals 8 TRIG Manual trigger This push button triggers the MIO board manually 9 TRIG Trigger input This BNC connector provides TRIG the timing signal PFII TRIGI from the E Series board for connecting an external trigger device with active low logic 10 PC TRIG PWR PC connection Trigger LED PC indicates the connection Power supply connection between the computer and the breakout box computer must be switched on LED TRIG indicates the Trigger status green trigger active red wa
3. l I 1 1 I D 1 I 1 j I I 1 I I I I U 1 I 200 400 600 3800 1000 120 1600 1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800 4000 Er pay shows His Local parameters PULSE Sweep for the editor display Figure 15 CW Pulse Editor after adding a segment in the example above Note SNAPSHOTS are PULSES for Ai with very high sampling rate only Ao is disabled In some Low cost E Series boards e g the PCI 6024E the maximum analog input sample rate is higher than the maximum update rate of the analog outputs Therefore before working with fast PULSES sample frequency gt 10kHz refer to the technical limitations described in the board documentation You may also wish to consider using SNAPSHOTS instead of PULSES 5 7 Linking CHARTS PULSES SNAPSHOTS and INSTRUCTIONS to EXPERIMENTS This chapter describes the CW Experiment Editor which is used to link the preprogrammed CHART and PULSE protocols The CW Experiment Editor also controls hard and software settings via INSTRUCTIONS to perform automated execution of complex experiments 29 How to Use CellWorks CellWorks allows scheduling of previously defined CHARTS and PULSES as well as additional INSTRUCTIONS and SNAPSHOTS in any order for complete control and automatic execution of a whole experiment The user can assemble CHARTS PULSES SNAPSHOTS and INSTRUCTIONS to a schedule list called EXPERIMENT in the CW Experiment Editor Remember that SNAPSHOTS are PULS
4. Note The basic procedure of manipulating CHARTS and PULSES too is to duplicate an existing CHART and then configure the new CHART You cannot create a new CHART without copying an existing one Gv How to create a new CHART a Open the CW Chart Editor with the corresponding button in the CW Manager a Double click a CHART name in subeditor field left where all available CHARTS are displayed CellWorks provides some default CHARTS these CHARTS can be edited deleted and duplicated in order to generate new ones The subeditor window opens a Ifthe Order Locked button is red turn it to gray by pushing it Now the Duplicate and Delete buttons are available a Click the button Duplicate and rename the copied CHART in the small upper text field a Move the new CHART to the desired location in the list we recommend always adding new CHARTS at the end of the CHART list How to Use CellWorks 25 Note CellWorks generally refers to list items by their position and not by their name a OK the subeditor The new CHART will be added to the CHART list Now you can modify the new CHART as desired You can define two independent groups of digital outputs the organization of digital output lines is performed in the CW Setup module see chapter 5 3 set analog output Ao values increments and delays for each segment see below CHARTS are organized hierarchically i e they consis
5. Pulse in chart Remember that these parameters concern only the monitor buffer a Chart Buffer II time base for included pulses Remember that this parameter concerns only the monitor buffer a Chart Monitor I Chart Monitor settings Mode X axis scaling Trace selection a Chart Monitor II Chart Monitor settings Monitor Size Background color Grid Display settings a Pulse Buffer Pulse buffer settings similar to Chart Buffer I and II a Pulse Monitor I II Pulse monitor settings data reduction or not a Till I I settings for the Till monochromator chapter 7 2 e g Wavelength Integration Time a Chart Monitor II further configuration of the X axis in the Chart monitor a Chart Monitor IV configuration of the Y axis in the Chart monitor a Chart Monitor V cursor handling in the Chart monitor a Pulse Monitor III IV V Pulse monitor settings similar to Chart Monitor III IV and V a Online I from file Online module configuration settings These Instructions are used to set module options by loading a configuration file In the upper part of the window the user selects an Online Module and the corresponding configuration file for loading In the lower part of the window the user selects the part s of the Online module e g Options 30 How to Use CellWorks Export or Trace to be configured a
6. ib Online XY Monitor P SUTIOnline0 File Edit Operate Layout Help IA LC A x ImSeconds_ y x ess y i y Ewe I Exporting Off Switch A Number 0 Last File Next File 2002318400 a0 2000 4000 6000 8000 10000 12000 Figure 27 the Online XY Monitor P If the user has selected Online XY Monitor P in the user module a click to the Online button in the CW Manager opens the Online XY Monitor P window Figure 27 The window looks similar to the Pulse Monitor and several functions and menu commands are the same On the top of the window the user finds elements for zooming and cursor control as in the Pulse Monitor see chapter 5 8 and on the right settings for export as in Online Sweep Analysis P see above The big difference from the Pulse Monitor is that the user can select for both axis an analog input channel by clicking to the pull down menu top left Figure 27 How to Use CellWorks 54 The File menu contains the same commands except Options as in the Online Sweep Analysis P module see earlier in this chapter Operate and Layout menu are the same as in the Pulse Monitor module see chapter 5 8 Online XY Monitor II P The Online XY Monitor II P expands the Online XY Monitor P so that several storing functions are added All menus and functions are the same except some commands in the Operate menu and
7. shows the beginning of the file B shows the end of the first sweep and the beginning of the second sweep and C shows the end of the file with the calculated data and Notes How to Use CellWorks exported analog file name input channels definition 50 export format definition export full pulse or data marked by marker 1 or marker 2 sport Format Ascii Columns Export Channels File Name Data Header Data Mames FE U IE 1 s el CH CH lea Prefix npi Data Name Header Switch is included here m a Include Number CH a e Sf SS amp Lei 2 a eyo SS Increment He Infix Name Infix Number by Cale Data Header Calc Data Header amp tmr Ss Include Sweep Data in File One File per Pulse _ amp BR amp O Ea L L m o m a Calc Data Trailer Cale Data Trailer name suffis This is an example of export settings Notes Header Hotes_Header Calc Data Names Notes Trailer Default Names Motes Trailer Figure 24 export configuration window File Name amis Include Date L4 Prefix pi Switch is included here Include Number am I Increment Sr Number by vi 1 Data in File One F
8. The appendix has some sample settings for a variety of npi instruments How to Use CellWorks 21 Another set of important configuration parameters are the Solutions These settings are used to determine user defined solutions or other devices that can be controlled by digital output lines e g shutter of a microscope or stepper motor controller and to assign them to Output names the outputs have to be set in the CW Hardware module chapter 5 2 Furthermore the user can group solutions in lists to define a complete sequence of solution changes in an experiment In a chart consisting of several sweeps the solutions in the list will be changed consecutively sweep per sweep as they are listed e g if the list contains solution 1 2 and 3 in that order in sweep 1 solution 1 will flow in sweep 2 solution 2 will flow and in sweep 3 solution 3 will flow If a chart consist of more sweeps than solutions in the list the valve will be closed Def off For a detailed description see CW Manual 4 0 Note CellWorks generally refers to list items by their position and not by their name Also note that CW starts counting with 0 zero and not with 1 eo Sample settings in the subeditor Software Gain Factors etc for a npi TEC amplifier e g TEC 10CX Amplifier data COMMAND INPUT and CURRENT 10mV STIMMULUS INPUT POTENTIAL OUTPUT PEL 10mV Open the CW Setup module and the subeditor Software Gain
9. 20kHz alen and or control amplifier set manually e g E E analog output values Default Contig or activate solutions Online Modules Experiment list containing all a available CHARTS PULSES SNAPSHOTS EXPERIMENTS poup menu to select CHARTS PULSES SNAPSHOTS and EXPERIMENTS Experiment indicates whether CHARTS PULSES SNAPSHOTS and or INSTRUCTIONS are set options written to file Cw TT a 5 data recording Doing status indicator actual max a 3 d M control the running CHART PULSE Abort C PS Dn Out A Solution Out B SalutionO2 DACH 0 DACI QU information about Rev ffsetv 0 44 the current protocol Time Base ms 1 0000 Actual Sampling Hz 1000 00 DO Flow ml min e g actual sampling rate DAC value Figure 18 CW Execution module 35 How to Use CellWorks Note If analog telegraph lines are used the values are read once before each chart or pulse starts and stored until the next pulse starts That means changes of the gain position switch at the amplifier are not detected by CellWorks during a CHART or a PULSE The NPI bidirectional communication is active during a chart The update period is Is for slow CHARTS CHARTS sampling below the user interface silencing limit frequency set in the Hardware module The Gain value is written to file only once at the first segment
10. Groups i e a collection of up to four digital lines that are associated with the group name Thus it is possible to associate a single Output with up to twelve TTL lines four individual lines plus two Groups of lines See the CW Manual 4 0 for a complete description of the output settings After closing the module a dialog box opens where the user can save all settings to a hardware configuration file or quit the module window without saving Nevertheless the actual configuration settings remain in memory for this CW session Thus one can test and probably alter the settings and save them to the configuration file not until everything works well After initial configuration the CW Hardware module will probably be accessed rarely Consequently configuration of those terms and elements of the hardware environment that may change from experiment to experiment can be made in the CW Setup module How to Use CellWorks 18 Note Once the three environment configuration modules Hardware Setup and User module have been configured we recommend to create a new USER At this time also make a BACKUP of your default configuration files chapter 7 4 This is perhaps the most difficult part in setting up CW but usually HW configuration rarely needs to be changed For a number of configurations especially for amplifier interfacing you will find examples in the appendix four subeditors devided define Groups of by dotted lines
11. Select Duplicate from the popup menu A further segment is generated with identical parameters The Pulse Editor display should now show the pulse as shown in Figure 15 How to Use CellWorks 28 PULSE table lists all in this user configuration available PULSE protocols es base and sampling rate segment move number of sweeps parameter buttons segments and Markers E E Pulse Editor DEFIPul se Timing a Segments l5 R HE Time Base ms 1 0000 Ten No of Sweeps B 10 Spike z o Jump Series DACO 0 SS d 3 P H P Sweep Int s 1 0 Fast Snapshot Semen Type nom DACO Value y 0 00 D 50 00 DH nm D nm f om Malbec oR 2 E a A A A a rer M M Time ms ei 100 00 el 500 00 z 1000 00 1000 00 el 500 00 Deka V mv om 1000 1800 f 1000 f om DACI Levels Pr 0 Post 0 Delta V Facte zl 1 00 f 1 00 f 100 f 100 f 1 00 Deka Tims W 0 00 000 ooo 000 g Pulse Display Delta TFactor 1 00 100 100 E 100 Update Interval ms 100 SweepNo t 0 DACI i n n x Ref Voltage mw 0 00 Window is editor field Deis tet zoo wj 000 e 11 00 e 11 00 x A unit mSecond Scale X to largest DACI Value ff 300 om sooo f 5000 E B Length ms 4 100 am 4 soo A sooo amp Shortest Sweep 3200 00 Show DACI Longest Sweep 3200 00 Don t autoscale Y
12. When a new user is created a subdirectory for the new user is created and the configuration files from the DEF user are copied to this directory Source of the configuration files The source of the HARDWARE SETUP CHART PULSE and EXECUTION configuration files is selected in the User module by the corresponding buttons Hardware How to Use CellWorks 23 Setup The user can decide whether the corresponding configuration file is taken from the DEF folder Default file or from the USER folder User File We recommend always load the hardware and setup configuration from the DEF default user Figure 13 This avoids configuration problems and makes it easier to adapt new hardware to all users E User TST User File Edit Help usr ST A pull down menu to set user specific Log in categories Location of Files Hardware Default File Setup Default File Chart Pulse Experiment button to change current user the user location of the source files Figure 13 CW User module Configuration file format and date format In CellWorks it is possible to export the configuration files and comments in simple text Word or Word Perfect format The year format can be displayed and stored with two or four digits year 2000 or year 00 In order to choose the text format of exported configuration files and the date format select Date and Text from the popup
13. You may not use this software for medical purposes e g for diagnosis or treatment of humans nor for any other life supporting system Licensor expressly disclaims any watranties for such a purpose Licensor warrants that the Software will perform substantially in accordance with the accompanying written materials for a period of 90 days from the date of your receipt of the Software Any implied warranties on the Software are limited to 90 days Some countries or states do not allow limitations on duration of an implied warranty so the above limitation may not apply to you LICENSOR DISCLAIMS ALL OTHER WARRANTIES EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE AND NON INFRINGEMENT WITH RESPECT TO THE SOFTWARE AND THE ACCOMPANYING WRITTEN MATERIALS This limited warranty gives you specific legal rights You may have others which vary from country to country or state to state Software License Agreement 6 LICENSOR S ENTIRE LIABILITY AND YOUR EXCLUSIVE REMEDY SHALL BE AT LICENSOR S CHOICE EITHER A RETURN OF THE PRICE PAID OR B REPLACEMENT OF THE SOFTWARE THAT DOES NOT MEET LICENSOR S LIMITED WARRANTY AND WHICH IS RETURNED TO LICENSOR WITH A COPY OF YOUR RECEIPT Any replacement Software will be warranted for the remainder of the original warranty period or 30 days whichever is longer This Limited Warranty is void if failure of the Software has
14. and Offset voltages open or close valves and modify the flow rate of connected pumps Furthermore the user can select a PULSE protocol in the lower popup menu and execute this protocol repetitively by clicking the button Do repetitive pulse The button turns red and the pulses are executed until the Do repetitive pulse button is pushed again To leave the manual mode click OK Note The manual mode is very convenient to apply test pulses to the electrode or specimen After execution has been started by double clicking the desired CHART PULSE SNAPSHOT or EXPERIMENT list item the status of execution is shown in the Doing field i e the CHART PULSE SNAPSHOTS or EXPERIMENT protocol that is currently 38 How to Use CellWorks executed by CellWorks is displayed see Figure 18 When performing an EXPERIMENT the name of the EXPERIMENT is shown in the first row and the name of the currently executed protocol e g Simple jump is displayed in a second row The two columns of numbers display the number of the currently executed segment sweep or EXPERIMENT left column and the total number right column When execution is finished Done is displayed in the Doing field Further information on the status of execution as well as several parameter settings 1 e digital outputs Out A and Out B DAC values Reference and Offset voltages Time Base Actual Sampling frequency are
15. delete recorded elements from file load old data files and replay the CHARTS PULSES EXPERIMENTS and INSTRUCTIONS Monitor Monitor the acquired CHART the acquired PULSE data in the Chart Monitor data in the Pulse Monitor Options Options to configure the Monitor to configure the Monitor in the menu bar of this in the menu bar of this module module Analyze and Export the acquired PULSE data in one of the preselected Online modules Export the acquired PULSE data and the calculated data in ASCII Igor Autes or Axon format Flow chart of using the CW modules 16 How to Use CellWorks 17 5 2 Configure the hardware in the Hardware module This chapter briefly describes how to configure the existing hardware interface boards using the CW Hardware module If you use the Demo version you can skip this paragraph because the Demo Version has preconfigured hardware and these settings have no effect please read also the ReadMe file on the CellWorks Demo CD For a complete description of the hardware editor module refer to CW 4 0 Manual which is on the CellWorks CD as well During start CellWorks checks whether the actual hardware configuration matches the configuration stored in the hardware configuration file If CellWorks recognizes different hardware which is e g the case when starting the CW Manager the first time this is indicated by a red blinking field in the CW Manager status
16. use the up to four digital scrollbar to see all sub output lines configure pumps editors Hardware Configuration D FlHardware File Edit Help Board Interface Configurktion Groups double click here to on configure the analog ario d inputs Ai and analog outputs Ao ofthe PCI MIO board 100 Flow ml min 4 200 IR Driver smatec Port None Outputs Lines Groups Mark link digital output DEE e lines and Groups to e e s Outputs 04 Quppardd 3 double click here to MONS e a configure the digital output ports Do Lines 14 113 4 2 1 Groupe None Nore Mark 1 i Figure 6 CW Hardware module Sample settings for a setup consisting of PCI 6024E npi amplifier TEC 10CX with the additional bidirectional interface npi breakout box INT 20X and the 8 channel perfusion system BPS 8 from ALA scientific Start Hardware module double click all four Board Interface Configuration subeditors and set the parameters as shown Figure 7 Figure 10 Analog Main Board Chart Target Ai Samping Rate Hz gt 300 Board Device Pe ge Interface siencing above sample rate 19 __ Channels PACO DAcL_ Se Mode Chart Pulse D AC TT singe edel Use Use Pube aoco TC singeended ue Use _ Ao Channels PACD DACIL ADC02 r10v singeended Oontuse Dontuse em anc
17. 0 1 Sensed Gain none Units mV Long Names voltage Ao a Channel 00 Gain Factor 10 Long Name Voltage out short name Vo a Channel 01 normally not used in this configuration Low cost E series board PCI 6024E with breakout box INT 20X telegraph reading and mode control read write 68 pole 1 1 breakoutbox analog lings 7 computer cable with INT 20X name direction SCSI female wite CeallWork 6 comes amplifier gain all filter all mode write mode digital lines VC CC TEC 10 for TEC 10 and RPEL TEC 10 4 ve RCEL TEC 10 BR SEC 10 4 REL SEC 10 gain filter read telegraph lines for all TECs and SECs Connection SEC TEC a 68 pole 1 1 cable with SCSI female connectors from the PCI board inside the computer to the front panel connector PCI E SERIES BOARD INT20X a BNC cable from digital line 0 Do0 front panel breakout box INT 20X to connector RPEL rear panel TEC a BNC cable from digital line 1 Do1 front panel breakout box INT 20X to connector VC rear panel TEC a BNC cable from digital line 2 Do2 front panel breakout box INT 20X to connector CC rear panel TEC a BNC cable from digital line 3 Do3 front panel breakout box INT 20X to connector RCEL rear panel TEC 10 a BNC cable from analog input channel 0 A10 front panel breakout box INT 20X to connector CURRENT OUTPUT front panel SEC TEC 61 Appendix a BNC cable from analo
18. 300 500 700 ERR 230 04 275 1 Name Prefix CO1_rName Infix O2name suffix CW Channel 1 CW Made Pulse CW Name Simple Ramp CW _ Segment 1 CW OutA Def Off CW OutB DeF Of CW ChannelAiShort C01 CW ChannelAiLong Voltage CW UnitAi m CW DACO 0 00 CW DACT 0 00 CW FlowRate Oml min g Current l min Ws 2001c16pulsenoo Bereit Figure 26 structure of an Ascii export fil Is e How to Use CellWorks 52 Ascii export format The Ascii export file is structured as follows First the raw data are listed The first column contains the time information and the other columns contain the data of the exported analog input channels i e Ail Ai2 If set so in the export configuration window the first row in the first column contains the File Header The first row in the following columns contain the Data Names and the Ai channel numbers i e C00 CO1 The second row in the first column contains the Data Name Trailer and the first time data point In the second row of the following columns are the analog input data The other rows contain the time and A1 channel data respectively Sweeps of the PULSE are separated by the Data Trailer and Data Names of every single sweep Second the calculated data are listed The data of the four monitors are saved in six columns Columns 1 and 2 CW Calc00 and CW Calc01 contain the Y data of monitor 1 and 2 which produce one value per s
19. B all buttons off Control on Read on Manual off opt TEC SEC Attenuation of Ai Signals 1 1 Digital Write to Amp needs additional digital I O board e g PCI 6503 Port A needs additional digital I O board e g PCI 6503 Port A Digital Read to Amp needs additional digital I O board e g PCI 6503 Port B needs additional digital I O board e g PCI 6503 Port B Setup module subeditor Software Gain Factors etc Ai a Channel 00 Gain Factor 0 001 Sensed Gain Gain A Units pA Long Names current a Channel 01 Gain Factor 0 1 Sensed Gain none Units mV Long Names Voltage a Channel 00 Gain Factor 0 001 Sensed Gain Gain A Units nA Long Names current a Channel 01 Gain Factor 0 1 Sensed Gain none Units mV Long Names Voltage a Channel 00 Gain factor 10 Long Name Voltage out Short Name Vo a Channel 01 usually not used in this configuration a Channel 00 Gain factor 10 Long Name Voltage out Short Name Vo a Channel 01 usually not used in this configuration 64 Appendix 7 4 File and directory structure and management This chapter describes the CellWorks folder and file structure After installing and starting CellWorks the default user folder CWE default will be created automatically by the program This folder is absolutely necessary to run CellWorks even if you log in under a different USER name because this fo
20. Don t update and Monitor see also PULSE and CHART Monitors and to set autoscaling for the analyze windows In addition there are two commands concerning the preferences Reset to Preferences and to create new default settings Make current settings new Preferences How to Use CellWorks 49 Data export Using the export functions all recorded data and also the calculated data can be saved to a file on the hard disk Various export preferences can be set by selecting Export Settings in the File menu To turn ON the automatic export function click to the popup menu Exporting on the top right of the Online Sweep Analysis P window Figure 23 The names of the export files are built automatically by CellWorks according to the settings of Switch Number and various parameters of Export Settings Figure 24 Selecting Export Settings in the File menu opens a window with several parameters and settings a data Export Format field with the format setting popup menu Here the user selects whether to export the data in ASCII rows or columns Igor text Autes or Axon binary format Note When you open Export Settings for the first time be sure to set the Export Format from None to the desired format Otherwise no data will be exported even if the automatic export function in Online Sweep Analysis P window is turned on a Export Channels field inclu
21. FOUR FILES are required for reloading e g in CW Reader Thus if you want to transfer data to another location copy all four types of CW data files Furthermore there is only ONE Nme file per daily folder i e per experiment day and therefore this file type should never be deleted manually unless you want to delete the whole folder The status of execution as well as several parameter settings 1 e digital outputs Out A and Out B DAC values Reference and Offset voltages Time Base Actual Sampling frequency are monitored in the lower half of the window To the left of the status fields are several buttons to influence execution The user can Pause or abort execution of CHARTS PULSES SNAPSHOTS or INSTRUCTIONS Abort C P S I or abort the whole EXPERIMENT Abort Exp Furthermore it is possible to skip the running segment or sweep and continue with the next Next Seg Next Sweep Manual Mode Sometimes it is necessary to change or adapt parameters of the experimental protocol due to unexpected behavior of the tissue or simply to test the experimental configuration or tissue at the beginning of an experiment Therefore CellWorks has a Manual Mode of operation Clicking this button opens the Exe Manual Mode window Now the user can configure two groups of digital outputs Out A and Out B set voltages at DACO and or DAC1 define Reference
22. Requirements This chapter describes the hardware and software requirements for using CellWorks CellWorks is a stand alone executable software package for the complete control of the experimental setup and data recording during electrophysiological investigations It is programmed in LabVIEW a high level programming environment developed by National Instruments Therefore CellWorks is available in native code both for IBM compatible PCs with Windows 95 98 or Windows NT 4 0 2000 XP and Apple Power Macintosh Power PC computers and can be used with a large variety of interface boards from National Instruments CellWorks runs on Notebooks as well Generally the hardware determines the performance specifications Thus performance depends on the hardware that is used 3 1 Recommended computer systems The following tables list the recommended minimum computer specifications required for Cell Works IBM compatible computer CPU Pentium 233 MHz RAM 64 MB hard disk 200 MB free disk space graphic board VGA 800 x 600 pixel resolution small fonts operating system Windows 9X ME or Windows NT 4 0 2000 XP Note If you select running a high screen resolution e g 1280x1024 large screen fonts in Windows the display of CellWorks may be corrupted Apple Power Macintosh computers CPU G3 Power Mac 200MHz RAM 64 MB hard disk 200 MB free disk space graphic board VGA 800 x 600 pixe
23. This chapter briefly describes the structure and some basic concepts of CellWorks CW like the subeditor technique and shows how to operate the modules of CellWorks using the CW Manager For a complete description of the basics of the user interface refer to CW 4 0 Manual which is on the CellWorks CD as well As mentioned above the software package CellWorks consists of two programs CellWorks that we distribute at the moment in three versions CellWorks Lite 5 5 CellWorks Lite E 5 5 and CellWorks Demo 5 5 and CellWorks Reader 3 6 that is designed to view and export data recorded with CellWorks mainly CHART data PULSE data should be exported using the Online analysis modules see chapter 5 8 CellWorks Demo and CellWorks Reader are not protected by a dongle and can be copied and given to any other person A fundamental concept of the CellWorks user interface is the use of subeditors which open after double clicking the corresponding editor field or table In many cases an editor window is opened where additional settings can be carried out You will find subeditors in many CellWorks modules and you can identify them by a small red line that surrounds the subeditorial field CellWorks is a modular structured program The central module is the CellWorks Manager CW Manager which is automatically launched when CW is started The CW Manager can call all other modules which are divided into three different categories a Adaptation to the ex
24. an UN curve in Graph 4 How to Use CellWorks 48 Pi Online Sweep Analysis P SUTIOnline1 File Edit Operate Help Exporting Off Switch A Number Last File Next 2002a18npi amp 0D t t File Cus i453 Jd i gt PI 200 0 400 0 500 0 800 0 soqoo msecongs DS A d 10 00 10 Figure 23 Online Sweep Analysis P window Graph 0 shows the pulse protocol A10 black with history gray on Ail blue The protocol consists of 10 sweeps incrementing one channel Ail Graph 1 tracks A10 at Cursor 0 Graph 2 shows the voltage of Ail at cursor 1 Graph 3 plots a histogram of A10 Min 0 Max 4 Bins 5 and Graph 4 shows a X Y Graph with X Ail and Y Ai0 Note that the export function is set to OFF If set to ONT the filename will be created with the default options in Export settings see field Next File The File menu of the menu bar offers commands to handle the configuration file of the Online module Load Save Delete to configure the module Options see above Export settings see below to call the standard windows printing dialog and to Close or Quit the module If the user wants to save axes scaling as well he first has to create new default settings see below with the new axes scaling and then save the configuration file The Operate menu contains commands to set the operation mode
25. are described in detail in the User manual Ver 4 0 Before you start to work please read the Safety Regulations chapter 1 and the Software License Agreement chapter 2 The software package CellWorks consists of two main programs the CellWorks program itself and the Cell Works Reader to view and export data mainly CHART data recorded with CellWorks As a consequence of new data acquisition technologies we have adapted the CellWorks program to new hardware and now distribute three versions CellWorks Lite 5 5 is designed to be used with the data acquisition board series 1200 from National Instruments in conjunction with the npi breakout box INT 10 or with the npi CellWorks amplifier TEC 03X CW Note National Instruments stops the production of PCI 1200 end of 2003 Therefore CWL 5 5 will be the last version of Cell Works which supports the PCI 1200 CellWorks Lite E 5 5 is designed to be used with the Low cost E series data acquisition boards from National Instruments in conjunction with the npi breakout box INT 20X or npi CellWorks amplifier TEC 03X CW CellWorks Demo 5 5 is not only a simple demo version It can be used to replay experiments recorded with CellWorks for offline analysis of and to export data to other programs Since CellWorks Demo is not protected by a dongle it can be copied to any computer Thus further data analysis and replay of experiments can be performed offline at any place and by anyone CellWorks
26. configurations and experiment settings under different USER names This has the following advantage the DEF user has its own directory which contains pre set configuration files e g for CHARTS and PULSES as well as folders for data and export files If you make further changes of CW configurations i e if you change CHART PULSE or EXPERIMENT parameters and you are logged in as DEF your default configuration files are overridden by the new settings But if a new USER is created the actual configuration files from DEET are copied to the new USER Thus if you are logged in as this new user all changes you make refer only to this user and the default configurations are kept It is possible to create up to 12 USERS all with their own individual configurations e g solutions CHART and PULSE protocols Only the first three letters of the username are displayed in the status window of the CW manager Figure 4 and are used to code filenames in the data and export directories Therefore we recommend you use only three letters as username oY Create a new USER a Open the CW User module by clicking the User button in the CW Manager window and then click the Change User button a Double click a user name in the left field with the red frame to enable the buttons at the right a Click the Add new user button and follow the instructions the first three letters of the USER folder name are used as USER initials
27. eeceeseceteceeeceeeeeenseceteeeees 69 date Le EE digital output digital output control essere 26 digital output Ines 21 23 doneledrtver dee deed EES ses 10 E Exe Record 4 eee eee ene entente eibi 43 Execution module 35 Experiment Editor eure et hers 30 EXPERIMENTS neige d e P eet 31 EXPO S557 export channels nl export fil riaime eb eee ed dele 51 Appendix export TE 68 export TOLMALE eee eres e fetten potete EEN senken 51 F fast voltage protocols sseeeeeeee 28 file formm t ich erede b e de eh ceo eno 25 file structure 67 filter are dette eO AERE 35 folder structure eere eet ciem 67 G Bet nee see ie Re aep 35 galt TaCtOrgx i eee stoves itk teer eterne ds 22 graph functions 68 H hardware 2 2 2 nenne hardware configuration file Hardware module I Installation SORS ERES RI installation procedure INSTRUCTIONS INT 10 INT 20X INT 20X Interface boards orai an MR 7 L TabVTEW EE 7 low cost board configuration 62 Low cost E series boards ccccccssscessceesecseceseeesseeesaees 7 LOWPASS eet eet eb iet d eet ie ba ded 35 M imamnual mode 5 2no coh eo hee 39 menu bar 68 minimum computer gu stem eee eeeeseeeeceteetseteeeeeeees 7 monitor settings enne enne 40 N NLEDAQ 5 neni eon EIER 10 O of
28. in the HASP Dongle Driver Folder only necessary for IBM compatible version to install the dongle driver Next run setup exe located in the NI DAQ Installer folder and follow the instructions Shut down and switch off your computer system and install the PCI board s For detailed information about the installation and configuration of the PCI board s please read the user manual shipped with the board s Installation 9 After the installation of the data acquisition board you have to check the board configuration in the Measurement amp Automation Explorer MAX located in the desktop folder Start MAX and select the PCI E series board e g PCI 6024E or PCI 1200 board from the device folder and make the following settings PCI 1200 AI 5 0V 5 0V Non referenced single ended AO bipolar all other settings default values E series AI 10 0V 10 0V Non referenced single ended AO bipolar all other settings default values In MAX you can select Test Panels for checking the data acquisition board Please do so and perform as much tests as possible No error must occur If you get an error please uninstall all NI related soft and hardware and go through the installation routines again If you still get an error contact npi electronic Note opt highly recommends the use of NI DAQ 6 9 3 for all Windows versions For MAC OS the NI DAQ 6 14 or higher must be installed Note We recommend ins
29. menu and set the parameters as desired CellWorks gets the date directly from the computer clock and it cannot be changed manually within the program How to Use CellWorks 24 Note If there are major problems please log in as Default USER DEF and rebuild your user environment step by step Even better create a backup copy of a working Default USER configuration for convenient restoration of a running system GY Select an Online module for a user a Open the CW User module by clicking the User button in the CW Manager window open the pull down menu and select Online Modules a You see a list with four available online modules a Select one of them When the Online module is opened the next time the selected module is displayed Note You cannot load external modules in this version of CellWorks 5 5 Edit CHART sequences in the Chart Editor This chapter briefly describes how to create and modify CHARTS continuous analog input recordings slow analog output signals and digital lines in the CW Chart Editor CHARTS are used to perform continuous analog input Ai recordings while writing slow analog output Ao signals controlling pump speed and or digital TTL output lines e g to apply solutions via valves or control stepper motors Manipulation i e editing changing creating saving etc of CHARTS and their parameters are carried out in the CW Chart Editor Figure 14
30. of the CHART That means if Gain is changed during a CHART the Ai values may be incorrect for 1s The same is true for all other settings of the amplifier i e Amp Mode and Filter Therefore we strongly recommend that you do not to change these settings during a CHART or PULSE neither at the amplifier nor in CellWorks If you want to change these settings via INSTRUCTIONS be sure to add a Wait command for at least 1s The middle of the CW Execution window shows a list containing all predefined protocols of the selected category you can select one of the categories CHART PULSE SNAPSHOTS or EXPERIMENT in the popup menu on top of the list To execute a protocol double click the corresponding name in the list Execution begins immediately Below the list of available protocols four status buttons indicate whether the executed CHART C PULSE P SNAPSHOT S is written to file button is red or not button is gray The button B indicates whether data between two CHART sweeps are written to disk Click to the Info button to get detailed information e g Time Base Number of Sweeps Markers DAC values about the marked protocol in the list Click the Options button to set several Options of execution including management of recording to the hard disk see next paragraph Options subeditor Clicking to the Options button opens the Options su
31. only in a Read only mode i e the user can check the settings of parameters but cannot alter them The next figure shows the common procedure for planning and executing an experiment using the CW modules First the hard and software is configured and adapted to the experimental setup Next a user is created and for this particular user an individual environment is defined Then the CHART and PULSE protocols for this user are assembled and experiments are planned Finally an experiment is carried out with the options of monitoring data acquisition using online analysis or exporting data How to Use Cell Works C Start the CellWorks program Y Define and configure the hardware used with CellWorks in the Hardware module select and configure the data acquisition board the analog inputs and outputs the digital output lines amplifier communication pumps and Till monochromator system Y Configure the hardware to the experimental setup in the Setup module Scale and name anaolg input and output lines define the used and stored analog input channels define solutions and link them to digital outputs USER 1 i CHARTI CHART2 PULSE2 PULSE 5 Define individual user environments in the EXPERIMENT 1 User module USER 2 define up to twelve user environments and set CHARTS CHART3 the hardware configuration source the 4 PULSE1 PULSE 4 used Online module configuratio
32. resulted from modification accident abuse or misapplication IN NO EVENT WILL LICENSOR BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY LOSS OF PROFITS LOST SAVINGS OR OTHER INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF YOUR USE OR INABILITY TO USE THE SOFTWARE Because some countries or states do not allow the exclusion or limitation of liability for consequential or incidental damages the above limitation may not apply to you If you have any question concerning this Agreement or wish to contact Licensor for any reason please write to npi electronic Hauptstrasse 96 71732 Tamm Germany Warning Regarding Medical and Clinical Use of the Software This software is not designed with components and testing for a level of reliability suitable for use in the diagnosis and treatment of humans or as critical components in any life support systems whose failure to perform can reasonably be expected to cause significant injury to a human Npi electronic expressly disclaims any warranties not stated herein Copyright Under the copyright laws this publication may not be reproduced or transmitted in any form electronic or mechanical including photocopying recording storing in an information retrieval system or translating in whole or in part O Ralf Schoepfer and npi electronic Trademarks All product names are trademarks or registered trademarks of their respective companies Hard and Software Requirements 7 3 Hard and Software
33. the Execution Module and select Record File The Exe Record subeditor opens a Select Load Data in the File menu and open the desired data file be sure that the data file is not write protected That is for instance the case if you try to read data files from CD a All CHARTS PULSES SNAPSHOTS and EXPERIMENTS stored in this file are displayed in the recording list To replay an item double click the desired protocol The stored data will be displayed in the appropriate monitors and or Online modules The speed of the CHART replay can be set in the menu bar group Timing The INSTRUCTIONS in an EXPERIMENT would be repeated as well if they have been written to file Note Because Online Modules can be active during replay it is possible to create and execute new data analysis procedures e g I V curves if one recognizes that the first online analysis was not appropriate 5 9 Online analysis and data export with the Online modules This chapter describes the selection and the use of Online modules for online analysis and PULSE data export These Online modules can be used only for PULSE data but not for CHART data While the CW Chart Monitor and CW Pulse Monitors just plot the recorded data the CW Online modules can be used to perform some data analysis The current CellWorks version has four built in Online modules How to Use CellWorks 45 Online Sweep Analysis P Online X Y Monitor P Online XY Mo
34. the pull down menus top right of the window in this manual called display options In the File menu an Option command is added where the user can select the Ai channels for storage operations Display options There are two pull down menus each for one trace with several options to select what is displayed Data the raw data are monitored Stored the stored data are displayed In the Operate menu the user sets which data are stored Data Stored the stored data are subtracted from the current data and the result is shown Data Stored the stored data are added to the current data and the result is shown Operate menu Store Ist sweep the first sweep of a protocol is stored Store Sum of Sweeps sweep by sweep the data are added up and the actual sum is stored Store Mean of Sweeps sweep by sweep the data are added up and the actual mean is stored Online Leak Subtraction P The Online Leak Subtraction P module is similar to the Online XY Monitor II P and is programmed to perform a simple leak subtraction of the current data The idea is to run an experiment to get and store the actual leak data Afterwards the user can display the raw current data and the data that are subtracted by the stored leak current Note In this module it is not possible to plot one Ai channel against the other 55 Reading Monitoring and Exporting Stored Data Files with the
35. to Execution window Figure 20 Exe Record window 43 How to Use CellWorks In the following we give some examples of how to operate the Execution module GU Start a PULSE in the CW Execution module First test whether the analog inputs and outputs work properly a Connect the analog input 0 A10 to the analog output 0 Ao0 and the analog input 1 Ail to the analog output 1 Aol at the front panel of the breakout box with BNC cables If you have a TEC 03X CW amplifier with the optional integrated I O unit connect Aol with Ai2 at the rear panel of the amplifier make sure that input channels A10 and Ai2 are configured in the Hardware module Note In TEC 03X CW Ao0 is already connected internally to A10 a Start the CW Execution module with the corresponding button in the CW Manager and open the Chart and the Pulse Monitor a Ifyou use a TEC 03X CW amplifier select the analog input 2 as trace B in the Pulse and Chart Monitor a Select Pulse in the popup menu of the Execution module and double click Simple Ramp A triangle pulse with increasing amplitude for each sweep trace A corresponding to A10 and a square pulse trace B corresponding to Ail or Ai2 for TEC 03X CW respectively should be displayed in the Pulse Monitor Figure 21 In the Chart Monitor you should see all sweeps E Pulse Monitor Point Interval 1 000 ms Operate Edi Layout Help IA rg Sit Cosa Dec JOE u ee E 100
36. 0 uA xc Jl Cursor in De CBR 150 0 100 0 50 0 00 50 0 100 0 150 0 1 00 Figure 21 Pulse Monitor with the default PULSE protocol Simple Ramp Important If you have configured the scaling of Au to show pA in TEC or nA in SEC amplifiers Gain factor 0 001 in Setup Module set the magnification factors for Channel Current to 1000 in order to see the signal If you are successful i e if your pulse monitor looks like Figure 21 connect your amplifier to the breakout box and the cell model and test the pulse protocol again 44 How to Use CellWorks Note It s a good idea first to run a configuration EXPERIMENT that sets up the execution environment to get familiar with the configuration of the execution environment try the settings of these parameters in the Options subeditor of the CW Execution module eo Open and close the current record file a Open the Execution module and select Record File in the menu Operate The Exe Record window opens a Increment the Record Number CellWorks creates a new record file with index 01 or loads this file if this file is already created The maximum Record Number is 99 that means a limit of 100 files a day per user a Decrement the Record Number to load an existing file with a lower index GY Load recorded data files and replay CHARTS PULSES SNAPSHOTS and EXPERIMENTS 4 Go to the Operate menu in
37. 5 that begins at t 100 ms in the pulse protocol the monitor shows the whole pulse calls the standard Windows printer setup dialog calls the standard printer dialog to print the pulse monitor window closes the pulse monitor but doesn t release it from memory closes the pulse monitor and releases it from memory Note The printing feature of CW is for an overview only It is not intended to be used for publications etc For data processing and printing please export data to an appropriate program like IGOR Sigma Plot etc 41 How to Use CellWorks The Exe Record subeditor for file management Record File located in the Execution menu Operate opens the Exe Record window where the user can perform several file related actions e g edit the actual recording list load already recorded data files create new recording files and edit the file parameters displayed in the upper part of the Execution module file information In the default configuration one part of the Exe Record window is hidden It can be shown by pressing lt Ctrl Shift D gt or selecting Toggle Size in the Display menu of the menu bar In the following we assume the Exe Record window to be fully displayed see Figure 20 In the upper left part of the window the actual recording list is displayed Above the list the owner of the list is shown i e User today for the actual experimenter or if a previously recorded d
38. B all buttons off if available Control off Read on Manual off npi TEC SEC analog input channel 4 If not available all buttons off Attenuation of Ai signals 1 1 Digital Write to Amp PCI 6024E Port A B PCI 6024E Port A B Digital Read from Amp none none Setup module subeditor Software Gain factors etc Ai a Channel 00 Gain Factor 0 001 Sensed Gain Gain A Units uA Long Names current Q Channel 01 Gain Factor 0 1 Sensed Gain none Units mV Long Names Voltage a Channel 00 Gain Factor 0 001 Sensed Gain Gain A Units nA Long Names current a Channel 01 Gain Factor 0 1 Sensed Gain none Units mV Long Names Voltage 62 Appendix a Channel 00 Gain Factor 10 Long Name Voltage out Short Name Vo a Channel 01 usually not used in this configuration Channel 00 Gain Factor 10 Long Name Voltage out Short Name Vo Channel 01 usually not used in this configuration Professional interface PCI 6052E with external breakout box INT 20X additional digital I O board PCI 6503 and additional INFA interface board inside the amplifier 68 pole 1 1 cable with SCSI female connectors computer ellWork S pi electronic PCI 6052E PCI 6503 50 pole ribbon cable connection breakout box amplifier INT 20X TEC 03 05 10 SEC 05 10 read write analog lines INFA interface board read
39. CW Reader Program 6 Reading Monitoring and Exporting Data with the CW Reader Program The next chapter shortly describes how to load CellWorks data files into the CellWorks Reader program how to monitor single sweeps of CHARTS and PULSES and how to export files or parts of files in ASCII or Igor format A more detailed description can be found in CW Manual 4 0 Offline analysis and export of CW CHART data is not possible with the modules explained in chapter 5 For this purpose you have to use the stand alone application CW Reader Figure 28 which is part of the CW program package After starting the CW Reader the user can load read data files which were saved during a CellWorks CHART PULSE SNAPSHOT or EXPERIMENT Note CW Reader cannot load data files in ASCII or Igor format Basically the CW Reader follows the same concept of the user interface as the modules of CW itself i e window manipulations and selection of options are performed in the same way as in CellWorks To load CW Data click the New Record button in the upper left corner of the CW Reader window A file menu appears where the data files can be selected for loading After loading the file all sweeps of the recorded data are displayed on the left side Select a sweep by clicking it Select and superimpose several sweeps by clicking while holding down the Shift key Various display and scaling parameters are available in the middle area above t
40. ES without analog output Ao signal generation SNAPSHOTS can be used for discontinuous pulsed Ai recordings perhaps in combination with an external stimulus generator The order of execution of CHARTS PULSES SNAPSHOTS and INSTRUCTIONS is explained later in this chapter Note When scheduling CHARTS PULSES and SNAPSHOTS CellWorks refers to list items by their position in the list and not by their name INSTRUCTIONS are powerful tools to program many aspects of an individual experiment Every parameter that can be set interactively in the Execution module or in the corresponding monitor menu bar chapter 5 8 can also be preprogrammed by an INSTRUCTION We recommend the user first learns the interactive settings before using INSTRUCTIONS The following categories can be selected from the popup menu of the INSTRUCTION subeditor in the EXPERIMENT module see below a NPI amplifier settings Amp Mode Gain and Filter frequency a Refs voltage reference settings Reference Voltage Offset Voltage a File file preferences e g Write Pulse to File Write Instructions to File a Sweeps CHART and PULSE settings e g First sweep in Chart number of Sweeps in Chart a Timing timing settings e g Pulse Trigger Mode Wait time to next command a Chart Buffer I chart buffer handling e g Buffer size Data reduction include
41. Factors etc and set the parameters according to the settings shown in the screenshot below link the actual amplifier gain to the Ai channel in order to scale the Ai defined in set multiplication signal due to define units names the Hardware factors to scale Ai the gain setting and short names for Module each Ai M Ai used in the present Units 8 Long Name 12 Shot ead Ri Name Sou t e experimental setup Channel 00 p Curent cog D d I Channel 01 mM Moltage E01 1 LI p Channel 02 1 000000 n C filtered E02 z Bm mu Channel 03 1 000000 nd Hoss Eua 3 B mu mu Channel 04 1 000000 Channel 04 E04 41 TIR Channel 05 1 000000 2 Channel 05 Kl 5j mu Channel 06 1 000000 F Channel 06 Kr E Channel 07 1 000000 2 Channel OF cor 7 p mu Channel 08 1 000000 2 Channel 08 Kl 8j Channel 03 1 000000 Channel 08 209 3 Channel 10 1 000000 id Channel 10 cid q pu 1 Channel 11 10000001 Channel 11 ci 1 p mu Channel 12 1 065080 Channel 12 E12 z jm mu Channel 13 1 000000 Channel 13 C13 3 mu mu Channel 14 1 000000 Channel 14 CA 4j pu pu V 1annnnnl T Channel 15 1 065080 Channel 15 cis s IB m k onfigure the
42. Kallbration parameters cannot be ermined here nown calibration paramerts cann be en here to the ADC and current ameters can be read from the ADC Figure 10 T I L L monochromator subeditor Note You have to open the Till monochromator subeditor even if this device is not installed at all Please close the subeditor by clicking OK How to Use CellWorks 20 5 3 Configure the experimental setup in the Setup module This chapter describes how to adapt the existing hardware to the experimental setup using the CW Setup module Figure 11 In this module Software gain factors are defined to adapt the scaling of diagrams monitors etc to the connected hardware This is important for correct saving and exporting of data as well In addition in the CW Setup module you define analog and digital outputs The user can assign outputs to solutions and group them in lists to define a complete sequence of solution changes in an experiment define names and link the double click here to scale names to the appropriate and name the analog inputs outputs e g solutionO1 defne a group of Ai and the analog outputs Ao shutter01 stepper motor01 outputs to lists E Setup DEFISetup ee re E File Edit Help Solutions Lists of Solutions Software Gain Factors etc Bi by channel Log Dez 0 Torr 90 Liston a GE DI Salut es Dutput l OL Listol S OZ Solution02 Output OZ 0Z Listdz Qe E 03 Selution02 O
43. Lite and CellWorks Lite E differ only in the application of different data acquisition boards PCI 1200 series or Low cost E series and the corresponding breakout box INT 10 or INT 20X The additional hardware like digital I O valve drivers pumps amplifier communication etc that compatible with CellWorks Lite is also compatible with CellWorks Lite E npi electronic 2003 Hauptstrasse 96 D 71732 Tamm email support npielectronic com Table of Contents l Safety Re CUA EE 4 2 Software License AXDTGOmetito EE 5 3c Hard and Software Requirements EE 7 3 1 Recommended computer eege EE 7 32 7 Interface DOSES EE 7 4 Installatio Eege te per i Deed Geer 8 2 Eege ee eet 14 5 1 Wastes amd CW Manager sn esse 14 5 2 Configure the hardware in the Hardware module sess 17 5 3 Configure the experimental setup in the Setup module ssssssss 20 5 4 Define the users in the User module make im t Re Rai 22 5 5 Edit CHART sequences in the Chart Editor use an 24 5 6 Edit PULSE sequences in the Pulse Editor esses 26 5 7 Linking CHARTS PULSES SNAPSHOTS and INSTRUCTIONS to EXPERIMENTS EE 28 5 8 Execute CHARTS PULSES and EXPERIMENTS monitor data online and offline 33 5 9 Online analysis and data export with the Online modules 44 6 Reading Monitoring and Exporting Data with the CW Reader Program s ss sse00s0000 55 Ts AppendiX OO 44 dil EE EE 58 7 2 Additional hardware compone
44. are License Agreement 5 2 Software License Agreement NPI ELECTRONIC LICENSOR IS WILLING TO LICENSE THE ENCLOSED SOFTWARE TO YOU ONLY IF YOU ACCEPT ALL OF THE TERMS IN THIS LICENSE AGREEMENT PLEASE READ THE TERMS CAREFULLY BEFORE YOU OPEN THIS PACKAGE BECAUSE BY OPENING THIS SEALED DISK PACKAGE YOU ARE AGREEING TO BE BOUND BY THE TERMS OF THIS AGREEMENT IF YOU DO NOT AGREE TO THESE TERMS LICENSOR WILL NOT LICENSE THIS SOFTWARE TO YOU AND IN THAT CASE YOU SHOULD RETURN THIS PRODUCT PROMPTLY INCLUDING THE PACKAGING THIS UNOPENED DISK PACKAGE AND ALL WRITTEN MATERIALS TO THE PLACE OF PURCHASE PROMPTLY FOR A FULL REFUND The enclosed Licensor software program Software and the accompanying written materials are owned by Licensor s supplier and are protected by copyright laws of Germany and the United States by laws of other nations and by international treaties Licensor grants you the right to use one copy of the Software on a single computer at one time You may permanently transfer the Software and accompanying written materials including the most recent update and all prior versions if you retain no copies and the transferee agrees to be bound by the terms of this Agreement Such a transfer terminates your license You may not rent or lease the Software or otherwise transfer or assign the right to use the Software except as stated in this paragraph You may not reverse engineer decompile or disassemble the Software
45. ase read manuals and instructions carefully The device is to be operated only at 115 230 Volt 60 50 Hz AC Please check for appropriate line voltage before connecting any system to mains Always use a three wire line cord and a mains power plug with a protection contact connected to ground protective earth Before opening the cabinet unplug the instrument Unplug the instrument when replacing the fuse or changing line voltage Replace fuse only with an appropriate specified type STATIC ELECTRICITY Electronic equipment is sensitive to static discharges Some input devices such as the analog inputs Ai of the PCI Low cost E series boards National Instruments are equipped with very sensitive FET amplifiers which can be damaged by electrostatic charge and therefore must be handled with care Static discharges can be avoided by touching a grounded metal surface when connecting or disconnecting such analog inputs Always turn power off when connecting or disconnecting electronic components TEMPERATURE DRIFT WARM UP TIME The system must be used only in a warmed up condition ca 15 30 minutes after turning on the power All analog electronic systems are sensitive to temperature changes Therefore all electronic instruments containing analog circuits shall be used for recordings only in a warmed up condition i e after internal temperature has reached steady state values In most cases a warm up period of 15 30 min is sufficient Softw
46. ata file is loaded the name of that file Further there is a field Record number and a box containing a number that can be changed Initially the box contains 0 which means that all CHARTS PULSES or SNAPSHOTS are saved in the D and F files with E00 D and E00 F respectively If the user increments the number in the box to 1 the following protocols are saved as E01 D and E01 F respectively see data storage conventions earlier in this chapter and chapter 7 4 Note Only CHARTS PULSES or SNAPSHOTS that are saved to disk are listed in the recording list To replay a CHART PULSE or SNAPSHOT simply double click the corresponding name in the list The protocols are replayed in the corresponding monitors i e CHART PULSE or Online monitor Click to the corresponding button below the recording list in order to delete the last entry from the data file The lower left part of the Exe Records window shows the execution parameters and is identical to the corresponding part in the Execute window In the right part of the Exe Records window the user can increment the Sample Identifier of the current record give a short max 16 letters Description that is display beneath the Rech in the Execute window and give Comments max 160 letters to the current record If the this part is no longer used it can be closed by pressing lt Ctrl Shift D gt again Timi
47. beditor which is divided into four subclasses of parameters General Chart Buffer Pulse Buffer and Till Photonic General subeditor The General subeditor window is divided into three groups of parameters File With the setting of the File parameters the user can specify whether the recorded data are saved to disc In addition you can specify the amount of free disk space in Megabyte at which CellWorks gives a warning to the experimenter when the recording is started Trigger With the setting of the Trigger parameters the user can specify whether CellWorks waits for trigger pulses to execute CHART PULSE or SNAPSHOTS experiments 36 How to Use CellWorks Sweeps The Sweeps parameters are related to the execution of CHART PULSE and SNAPSHOTS Sweeps In most cases Sweeps in Chart or Sweeps in Pulse are set to All i e all Sweeps of this protocol are executed However the other settings of these parameters allow the user to skip certain Sweeps of CHARTS or PULSES or to execute them in a particular order The settings for PULSE also applies to SNAPSHOTS Chart Buffer subeditor Clicking the Chart Buffer button opens the Chart Buffer subeditor The button name changes to Chart Monitor indicating that the settings are related only to the chart monitor Buffer Siz
48. ccording to the configuration file a Online II direct Online module settings Export on off saving options menu commands to be executed These Instructions are used to set module options directely Remember that CellWorks starts counting with zero Note The configuration file is loaded once and stored within CellWorks If the user changes a configuration file that is used in an Online I INSTRUCTION this configuration file has to be reloaded into the INSTRUCTION in the EXPERIMENT editor Otherwise the configuration is not updated INSTRUCTIONS which influence the execution of CHARTS PULSES or SNAPSHOTS will be executed when the EXPERIMENT schedule list reaches the corresponding command line The settings then become active for the remaining elements of the schedule list The execution of CHARTS PULSES or SNAPSHOTS does not wait for completion of INSTRUCTIONS which do not influence CHARTS PULSES or SNAPSHOTS e g monitor settings We therefore recommend to include a Wait command e g 1s if you want an INSTRUCTION to be executed before the next PULSE or CHART starts 31 EXPERIMENT table lists all available EXPERIMENTS double click here to delete rename and How to Use CellWorks this table views the EXPERIMENT command lines The commands will be interpreted beginnig from line 0 and sucsessive processed buttons to delete and a double click in this field opens a create EXPERIMENTS c
49. cht Einf gen Format Qxtras Daten Fenster Data Names Data Names data channel 0 second sweep data channel 1 second sweep bems rlkserlg Bern Autom LE ln o oo P Arial ur ERU ooo 18 8 F6616 Data Trailer Data Mame HeaderName Prefix TimeName Infix 01 name suffix Data Mame Trailert1 D0 2200 0 Name Prefix COO rName Infix O1name suffix Name Prefix CO1_rName Infix Oiname suffix 0 1 0 0 2 0 KH 2001c16pulseA00 Y data Monitor 1 Notes Y data Monitor 2 X Microsoft Excel 2001c16pulseAOO_txt IS Datei Barbeiten Ansicht Elhf gen Format Extras Daten Fenster 2 P ZA X data Y data X data Y data Monitor 3 Monitor3 Monitor A Monitor 4 histogram histogram XY plot XY plot Calc_Qata_HeaderCW_CalcO0 Calc data Traler CW Channel D CW Mode Pulse ame Simple Ramp Segment 1 OW QutA Def Off OW OutB Daf Off CW Channel amp iShart C01 CW ChannelAiLong Voltage CW Uniti mv CwW_DACO 0 00 CW DAC 0 00 CW FlowRate ml min CW Segment 1 CW ChannelAiLon CW Uniti n CW DACO 0 00 CW DACT 0 00 CW FlowRate Or CW Mame Simple Ramp CW Qui DefzOff Cw Ou Def Off CW ChannelAiShort COO CW Cal 295 47 350 07 418 63 185 23 219 45 52 44 100
50. d type the Y value e g 0 The cursor appears at 0 0 in the monitor display For the second cursor perform the same procedure in the second row The control elements marked with a crosshair and a padlock are used for further configuration of the cursor style and cursor behavior respectively The cursors are moved by dragging or by using the right field of the cursor control elements The commands in the menu bars of CHART and PULSE monitor are almost the same There are some differences only in the Operate menu which will be described separately for CHART and PULSE monitor Edit menu standard windows menu for copying cutting pasting Layout menu Clear Cursors immediately removes the cursor s from the graph Background black white sets the background to the corresponding color Don t show grid immediately removes the grid from the graph show grid shows a grid in the graph Size Xxx sets the size of the monitor module window to xxx 40 Operate menu Chart Monitor Operate menu Pulse Monitor Don t update Monitor Replay Printer Setup Print Window Close Quit Don t update Monitor Marker 1 Marker 2 t0 0 t0 real Full Pulse Printer Setup Print Window Close Quit How to Use CellWorks freezes the monitor i e the monit
51. des the information which available analog input channels are exported to file a File Name field Figure 25 and chapter 7 4 Here the user can set file name preferences e g whether the name includes the date set suffix or prefix letters or numbers and whether one file per PULSE or one file per PULSE sweep is written to hard disk 66 99 Note If you want to set a file extension via the field Suffix be sure to include a e g txt for Ascii columns for import in Excel a Data Header sets header information within the data file a Data Names in this field the user can decide whether the data names should include the date the channel information time The fields Data Header and Data names are normally used to organize the data within the file to facilitate automatic analysis a Data field to select which data are exported The user can select the data range Full Pulse or Markers see chapter 5 6 how to set markers the data format Exponential or Floating Point and the precision Furthermore it is possible to exclude data from exporting Set raw data to Export raw Data and calculated data to Don t export calc data if you want to export only the raw data Set the parameters the other way around to export only data that are calculated in the analyze windows Figure 26 illustrates the structure of the resulting Ascii file using the settings in Figure 24 A
52. e sets the amount of Bytes for the Chart Buffer Data reduction sets the factor for data reduction e g 5 means every fifth data point is shown on the chart monitor display Reset can be set to avoid i e buffer data are never cleared Thus if the end of the buffer size is reached CellWorks starts at the beginning and overwrites existing data The buffer data can also be deleted every Chart or every Sweep Pulse sets whether or not PULSE data are included in the chart monitor Clear Buffer Data immediately clears the CHART buffer and erases all traces on the CHART monitor for included Pulses if the user has decided to plot PULSE data in the chart monitor the setting of this popup menu specifies the Time base ms for Chart Buffer Time base ms for Chart Buffer allows the user to force a Point Interval for the buffer with Point Interval Time Base Reduction factor Pulse Buffer subeditor Clicking to the Pulse Buffer button opens the Pulse Buffer subeditor The button name changes to Pulse Monitor indicating that the settings are related only to the pulse monitor In this subeditor the user sets the factor for data reduction of the pulse buffer e g 5 means every fifth data point is shown on the pulse monitor display Till Photonic subeditor If a T I L L Photonics Polychrom II monochromator and or FDU ratiometr
53. e Electronic DI for the Life Sciences C ell Work npi electronic The Turnkey Software Solution for Experimental Control and Data Acquisition voToic22 Record Number sl o Edit Operate H SE Ge 0 84 06 A Exporting Off i Switch A 0 4 I Number 0 0 2 H Last Doing 02 Nest P SynCurl_ Rev i File actual max D 4 7 Es as owe mog L 3L 3 ET am faa Yd x KN 0 1 2 Tg 18 PI ER 00 200 0 400 0 600 0 800 0 1oco o frSeconds all 04 i3 1000 1500 2000 50 3000 3500 4000 4500 5000 Please read these notes before you start Short Manual for CellWorks Demo 5 5 CellWorks Lite 5 5 CellWorks Lite E 5 5 August 2003 Introduction This short manual should help to install the CellWorks software package and to connect external devices to your data acquisition computer It includes short descriptions of the several software modules and describes how to set the parameters for data acquisition and controls Important Since some parts of CellWorks didn t change with relation to version 4 0 they are described only very shortly in the Short Manual 5 5 This refers to Adaptation to the experimental environment CW Hardware CW Setup and CW User module and Configuration of individual experiments CW Chart CW Pulse and CW Experiment editor modules These modules
54. e module ecke ein 18 Figure 7 board configuration subeditor a 18 Figure 8 digital output lines E EE 19 Figure 9 amplifier subeditor u sehe tp ker tiet ENEE EEN 19 Figure 10 T I L L monochromator subeditor essere 19 Figure RE Setup modble use oe S Dh et REDE 20 Figure 12 CW Setup module basic settings for a npi TEC amplifier sssss 21 Figure 13 C W User EE 23 Figure 14 CW Chart Editor size 26 Figure 15 CW Pulse Editor after adding a segment in the example above 28 Figure 19 CW Experment E 31 Figure 17 subeditor to edit the file INSTRUCTIONS sese 32 Figure 18 C W Execution mod le na 34 Figure 19 6 W Pulse MOT Ob Ee 39 Figure 20 Exe Record E 42 Figure 21 Pulse Monitor with the default PULSE protocol Simple Ramp 43 Figure 22 Online Sweep Analysis P Options wmdow eene 47 Figure 23 Online Sweep Analysis P window eese eee enne tn eene entente 48 Figure 24 export configuration wIndOW s c acoso cae viet pt tad ue D y aed en lecce 50 Figure 25 filenames gege 50 Figure 26 structure of an Ascii export file au diari bag et ERE ERREUR erha PERRA AS en RAS 51 Figure 27 the Oriline XY Monitor P ue 53 Figure 28 de 56 72 Figure 29 Figure 30 Figure 31 Figure 32 Figure 33 Figure 34 Figure 35 Appendix CW Reader settings Eleng deed SEENEN dee eege 57 folder structur
55. e ofa USER 2 a ae ee 64 commonly used graph finetonsu nee 66 Cell Works data flow str cture aussen en 67 Cell Works Lite hardware connection ua 68 INT 10 breakout box front panel elements eececsceeseeeteceteeeeeeeeaeeesaeeeaeenes 69 CellWorks Lite analog in and out subeditor sse 70 73 7 11 Index A Giel amplifier gain amplifier Settings sss 31 amplifier subeditor sse 21 analog input 22 60 analog output essent 22 60 Ascii export format 54 assembling of hardware sess 12 B basic software settings using npi hardware 62 bidirectional communication 8 board configuration 20 BPS 8 RM 20 61 C CellWorks Demo 2 GCellWorks Lite s coto uneneen 2 70 Cell Works Lite E 2 CellWorks Lite hardware connection Tl Cell Works Reader aod Chart Editor 26 Chart Editor 5st e HEURES 28 Chart Monitor 35 40 Chart Monitor butter 31 CHARTS 26 57 Common user interface elements suse 68 concurrent modules 69 config Dies configuration files continuous analog input recordings sss 26 create a new CHARTS ceecccccsecesteceeeteeecnenseeeeeeee 26 create a new USER ross reference oed hd eres CW Malden iit aso er E E GERE GUI D d t analysis nce La eie ak o ARS EISE 46 data OxPort MC 46 51 data flow data interchange cee
56. e or markers of the sweep should be monitored and how they are displayed e g color interpolation style history a Layout sets which analyze graphs are displayed and at which positions and in which size they occur a Cursor Windows Here the user decides which data are taken for calculations in the Analysis monitors The cursors are counted from 0 to 3 and are referred in the Graph 1 4 fields as VO to V3 For each cursor two parameters are available to define a Cursor Window a popup menu with and items and a value field which gives the delta X range of the Cursor Window The items in the popup menu give the direction relative to the cursor position The default setting is and 10 which means that if Units are set to mSec the delta X range of the Cursor Window is 20 ms wide Derived Values This popup menu has the items min minimum max maximum mean peak over baseline and valley under baseline and is related to the Cursor Window ie its setting defines whether CellWorks searches within the Cursor Window for the lowest or highest value or calculates the mean of the data in the Cursor Window For peak over valley under baseline first the baseline is calculated from the first and How to Use CellWorks 46 last 10 of the cursor window by fitting a mean line to the data Then this baseline is subtract
57. ed from the original data and maximum peak or minimum valley are determined The result of this search or calculation is called Derived Value and can be used for further calculations a Graph 1 Graph 2 are used to show time based diagrams In the easiest case just the time course of the data calculated in the Cursor Window s the Derived Value s are shown Value A is determined by two settings first V0 to V3 which Cursor should collect the data and second the Ai channel which analog input line should provide the data Additionally the user can perform further calculations with a second value Value B which is determined analog to Value A and display this result in the graph As operators and 1 Value A are selectable The other parameters are used to format the display a Graph 3 This is the histogram graph to plot the specified type of cursor measurement as bars at the graph The user can define a value range and divide the range into a certain number of sections CellWorks calls these sections Bins The result of the calculation is a distribution histogram a Graph 4 is the x y display where Value A is plotted against Value B Like in the other analyze windows the user can set interpolation mode and point style as well as the Y axis mode Decimal Scientific or Engineering labeling and number of digits af
58. el by segment By Channel By Segment N 0 By Sweep EE NS o B Indicate PI Current Display Igor Wave Name Data Format Setting as Prefs Prefix s Displayed Don t incl Info Page Setup For Printing export Don t incl Date Ascii Columns opuons Include Number Exponential Sufix Precision 2 File KWRPref Append Igor Notes _ Load from File Save to Fie Figure 29 CW Reader settings window preference file handling 58 7 Appendix 7 1 Specifications For low cost E series boards Appendix analog input Number of channels in single ended mode maximal 16 Number of channels in differential mode maximal 8 input resistance IMQ with breakout box INT 20X max input range bipolar 10V 5V 1V software selectable max input range unipolar 0 10V number of channels transfer characteristics and resolution depend on the board that is used Please read the appropriate user manual from National Instruments shipped with the board analog output number of channels 2 voltage range 10V transfer characteristics and resolution depend on the board type which is used Please read the appropriate user manual from National Instruments shipped with the board digital output number of lines up to 96 digital output lines grouped as ports of 8 lines More information a
59. ervoirs tubes valves etc configuration for fast PCI 6070E and PCI PCI 6070E max analog input sampling PULSE recording and npij 6503 amplifier with rate 1 25 MS s max analog output bidirectional amplifier additional standard update rate 1MS s 12 bit resolution communication interface interface board PCI 6503 24 digital I O lines grouped to 3 ports 4 Installation This chapter describes the installation procedure for the software package CellWorks Lite E Only the CellWorks Demo version can be executed directly from the CD see the Read Me file for further details All other versions have to be installed to the computer hard disk Before you start installing the hard and software for CellWorks the following parts must be available Low cost E series board from National Instruments cable with SCSI female 68 pole connectors hardware dongle breakout box INT 20X or TEC 03 with additional I O unit and the CellWorks CD Optionally npi amplifiers can be supplied with a digital bidirectional communication unit In order to use this unit a further digital I O board with at least 16 digital I O lines e g PCI 6503 or PCI DIO 96 National Instruments is required For a complete hardware list see appendix chapter 7 2 Copy the a CellWorks Lite E Folder a Dongle driver Folder only necessary for IBM compatible computers a NI DAQ Installer Folder to your hard disk and run the hdd32 exe program located
60. ete buttons at the top of the window ER How to Use CellWorks LI Modify a command line LI Double click the command line in the right editor field The subeditor is opened LI Select a category CHART PULSE or SNAPSHOTS in the upper pull down menu If you release the mouse button all items of the category previously defined by the user are listed e g all PULSE protocols LI Select one of the available protocols e g for PULSE Simple Ramp or select an INSTRUCTION If you release the mouse button an instruction appears at the command line Double click the instruction to open the subeditor where you can select one of the INSTRUCTION categories described earlier in this chapter A window opens and you can set the parameters of the category e g for npi Amp Mode Gain and Filter Note A command line can hold only one CHART PULSE SNAPSHOT or INSTRUCTION LI Write recorded PULSE data to file using an INSTRUCTION LIGenerate a new command line with Duplicate button at the desired experiment position LI Double click the new command line and select INSTRUCTIONS in the popup menu Double click the INSTRUCTION command line LI Select the command group File in the popup menu of the subeditor and set Write Pulse to File to yes Figure 17 and OK all subeditors After passing this command line the recorded data during a pulse protocol will be written to file File
61. field and the appearance of the error message Error 99010 Possible reasons In this case you have to launch the CW Hardware module and select valid settings The hardware settings should be set to DEF default user Starting CellWorks the first time a Log in as user DEF default An error dialog box will appear after login see above Read the instruction and OK the dialog box a Click the Hardw button of the CW Manager to open the CW Hardware module The Board Interface Configuration text field contains four subeditors divided by dashed lines You must open each of these subeditors by double clicking into the text fields even if you do not change anything and select valid settings You will find basic settings for a variety of npi hardware in the appendix a At this time after the hardware configuration we recommend a first test to check whether the software and the DAQ board are working fine In chapter 5 8 1s an example of how to start a PULSE The right half of the module window contains parameter settings e g for adjusting the speed flow of external Pumps via the serial ports of the computer Mac Modem or Printer port PC COM 1 COM 8 and the configuration of digital TTL Output lines to control further external devices like valves to apply solutions automatically Figure 6 If the external devices require more than one digital line for complete software control the user can define
62. fline analysis 57 online analysis 46 Online Module 35 online module select 26 Online modules 46 Online Sweep Analysis 547 Online XY Monitor 439 Online XY Monitor II eese 56 options subeditor sesseeeeeee 37 74 P Polychrom II monochromator sss 61 professional interface 64 Pulse buffer 31 Pulse ER 28 Pulse Monitor 35 40 PULSES 28 57 PUMPS EE 19 S Safety Regulations eesenneneesensesnennesnennenennnne nenne 4 EE WE EE nde eee REP aier 22 35 Setup module 19 22 24 SNAPSHOTS 30 Software gain factors nun nee 22 software gain factors etc 62 64 65 Software License Agreement sss 5 software requirements UU M subedutors nennen 16 68 synchronous Ai recording sssssseeee 28 T TEC 03 seen tee er et hs NEGO CE ubl E Till monochromator subeditor timing settings U user folder ree 67 User module 3 BE TO 24 user related files een 67 V MD324 s ceo nti E ies 60
63. g IK above sample rate 1KHz Ao Channels Daco DACI m Number of Ai Channels 4 Pulse E Ao Channels DACH DACI EN Ca Figure 35 CellWorks Lite analog in and out subeditor 7 8 Keyboard shortcuts keys description ctrl o load config file in a module and load data file in the Exe Record module ctrl p print window ctrl q quit module ctrl s save the module config file ctrl w close module ctrl shift d toggle size of the Exe Record window ctrl shift e export settings opens the export settings window in the online module ctrl shift o options opens the options window in the Online module ctrl shift r record file opens the Exe Record window in the Execution module 71 Appendix 7 9 Abbreviations used in this manual ADC Analog Digital conversation Ai Analog input Ao Analog output Ch channel DAC Digital Analog conversation DAQ Data Acquisition CW CellWorks CWL CellWorks Lite CWR CellWorks Reader fig Figure NI National Instruments npi npi electronic Pref s Preference s Ref V Reference Voltage Trig Trigger TTL digital lines high corresponds to 5V and low to 0V 7 10 Figures Figure 1 assembling the hardware eee eee tiec te pe i de EGRE REIR 10 Figure 2 IN1 20X Font panels EE 11 Figure 3 time course of trigger out sismals ae 13 Figure4 OW EE 15 Figure 5 Flow chart of using the CW modules sese 14 Figure 6 CW Hardwar
64. g input channel 1 Ail front panel breakout box INT 20X to connector POTENTIAL OUTPUT front panel SEC TEC a BNC cable from analog input channel 2 A12 front panel breakout box INT 20X to connector CURRENT SENSITIVITY front or rear panel SEC TEC 4 BNC cable from analog input channel 3 A13 front panel breakout box INT 20X to connector FREQ MON front or rear panel SEC TEC For some SEC only a BNC cable from analog input channel 4 Ai4 front panel breakout box INT 20X to connector MONITOR OUTPUTS FILTER POTENTIAL rear panel SEC Software settings parameter amplifier Hardware module subeditor Amplifier TEC 03 05 10 SEC 05 10 Interface Digital Lines TTL Control Ai telegraph reading Digital Lines TTL Control Ai telegraph reading Mode Control on button is red Control on button is red Read Read off button is gray off button is gray Manual on Manual on op T S 05 old npi T S 05 old Gain A Control off Read on Control off Read on Manual Manual off TEC 1 47 off SEC 1 7 see the range see the range written on written on the amplifier front the amplifier front panel panel analog input channel 2 analog input channel 2 Gain B all buttons off all buttons off Filter A Control off Read on Control off Read on Manual Manual off op TEC SEC off op TEC SEC analog input analog input channel 3 channel 3 Filter
65. haracters and the following number indicates the Sample Identifier a number that can be used to organize the data These file parameters can be changed in the Exe Record subeditor as shown in Figure 20 Below the file information field are amplifier interface popup menus where the user can read or define the desired amplifier settings Amp Mode Gain and lowpass Filter The values of Sensed Gain settings defined in the Hardware module chapter 5 2 and linked to Ai in the Setup module chapter 5 3 are displayed and can be set via the popup menu under certain conditions see below Depending on the configuration of the CW Hardware module Amplifier subeditor these values can be read and or controlled via digital or telegraph lines or set manually If CellWorks has been configured to read the amplifier settings the corresponding popup menus appear in the window and actual settings of the amplifier are shown But the settings can only be changed within CellWorks if it is configured to control the amplifier in the CW Hardware module When the CW Hardware editor is configured to manually set these parameters the menu first show but they can be set to other values However the same settings should also be made at the amplifier to get correct values for the acquired data 34 How to Use CellWorks P Execution Operate Edit Help Rect 0 Sample file information Amp Made Gain Filter V clamp 0128v n amp
66. he interval between two sweeps and two markers The markers are used to mark a subset of segments e g segments 1 3 A value of 1 means disabled In the CellWorks Reader see chapter 6 and or in Online modules see chapter 5 9 these markers are used to show and or export only parts of sweeps For a more detailed description of the parameters of CHARTS see CW Manual 4 0 How to Use CellWorks 26 CHART table lists all in this segment time base user configuration parameter move and update available charts names buttons segments rate Chart Editor zditor DEFIChart ra Timing a OI l Time Base ms yi OutA Type Single Definition Single Definition Single Definition No of Sweeps T 1 Sweep List Value Solution Solution SolutionD1 Sweep Int s 1 0 Fast Chart OutB Type Single Definition Single Definition Single Definition Marker1 14 Value Def Off Def O ff Def O ff Make2 47 100 00 E 0 00 Add 10 00 Ext 5 00 Ext Display 0 00 0 00 0 00 1 50 SC nn Sweep No 0 T Update Interval ms 100 Scale Birken min mas S5 ant 213 Scale X to largest __ Window is editor field _ RefVelage mv e 0 00 IBIBI show OA sl 10 IB Dent show Flow Rate_ I ShowDaco Dont Sen DACI Show Segment Limits Don t Autoscale Y DACO Value 0 00 Add Time s 5 00 Ext Delta V mv F act 0 00 0 00 DEE T ass 0 00 0 00 i D DACI Value LD
67. he monitor field Figure 28 Many of these parameters follow the standard display and cursor control elements of CellWorks The two columns of text fields in the upper right area of the CW Reader window display the solutions which were applied at Out A left column or Out B right column To export data first click the Settings button to open the CWR Settings window In the lower left field of the window called Export you can set the export parameters according to your needs Figure 29 Close the window with OK and click the Export button at the top of the CW Reader window You are prompted to enter a filename Do so and click the Save button By default all data that are displayed are exported to that file Note File extensions were not automatically generated In the CWR Settings window the user can beside changing export parameters set several display parameters for CHARTS and PULSES e g display color and style interpolation set the option to include information in the printout and save or load settings from disk To format the display first decide in the upper left field Styles where the defined style should come from Default A or B By channel By segment or By sweep The selection possibilities in the pull down menus refer to the fields on the right Figure 29 These are configured by clicking in the field to open a pull down menu w
68. he physical Reference voltage output at DACO has to be set in the Manual mode subeditor in the Execution module For DACI you only can set delay value and length DACI is preferable for generating trigger pulses How to Use CellWorks 27 In the Timing subwindow the Time Base value defines the sampling rate In contrast to CHARTS no oversampling can be performed As in CHARTS a PULSE can consist of more than one sweep and in the Timing subwindow the user can set the number of sweeps and the interval between two sweeps Markers can be set as well They are used in the Pulse Monitor to display only parts of sweeps and in the Online Modules to display and or export only parts of sweeps For a more detailed description of the parameters of PULSES see CW Manual 4 0 To edit create change or delete list items open the subeditor by a double click to one of the PULSE names in the list CellWorks comes with several predefined PULSES which should be used to create your own versions The basic procedure is the same as in the CW Chart Editor First take an existing pulse duplicate the pulse in the subeditor and then modify the pulse parameters according to your needs GY How to add a new segment to a PULSE sweep a Open the Pulse Editor with the corresponding button in the CW Manager a Select one of the available PULSES e g Simple Ramp a Click the button at the segment 2 A popup menu appears
69. ic system is connected to CellWorks this subeditor is used to set various data acquisition parameters See documentation supplied by T I L L Photonics for a detailed description 37 How to Use CellWorks Data storage conventions CellWorks creates for every user a DATA directory where recorded data are saved For each day a new subdirectory folder is created The name of the subdirectory is composed of the user name 3 letters the current year 2 or 4 numbers the actual month 1 letter coded as a for January b for February and so on Note that i is not used and day 2 numbers Each daily folder contains 4 files for each experiment The first part of the filename is built by the same rules as the daily folder L the Nme name file contains all the names of Solutions Charts Pulses etc L the D data file has accumulated all the data values of this experiment the E in the filename stands for Experiment and the following two numbers are the number of this experiment now called record LI the F format file links to the D file to distinguish later the solitary recordings of the D data file and more information e g which Ao channels time base Sweep numbers etc were used LI the E Experiment file is a leftover from an earlier CellWorks version see also chapter 7 4 Important It is important to mention that ALL
70. ile per Pulse _ Figure 25 file names Export calculated Data Append Notes Data Flle Header Selection Include Date Pie Header Prefix Mame Prefix Full Pulse Bord Date Format exported data lata Name Header Floating Point f d Include Chanel Preci He ormat an recision 7 ace Data Name Trailer Timing Time precision Data Name Trailer Regular Stored Export raw Data Data Traler TncludeTiming Das Trailer Include stored Data a Include stored Data exported data translation of settings in the File Name field of the export settings window into filenames How to Use CellWorks File name Data header time data first sweep N Microsoft Excel 2001cTopulseAUU txt m Datei Bearbeiten Ansicht Einf gen Format xtras Daten Fenster 51 Data Names data channel 1 first sweep Data Names data channel 0 first sweep D c mem vs ms SERA wir al vio ip E nl IE SS 76 um 5d ES Za Data_Narne_TrailerO 00 File_HeaderData_Name_HeaderName Prefix TimeName Infix DOname suffix Name Prefix C00 rName Infix Q name suffix Name Prefix CO Mame Infix OUname suffix D n 1 D 2 D U 3 0 0 pih 2001ci amp pulseAQD Ak Bereit Data header time data second sweep Microsoft Excel 2001c16pulseA00 txt Ka Datei Bearbeiten Ansi
71. iles Configuration files Hardware Setup Pulses Charts etc are saved by default in USER Config folder 7 5 Common user interface elements This chapter describes the elements and methods commonly used in several modules Menu bar Every module header includes a menu bar similar to other Windows or Mac programs with commands e g to load configuration files to close the module or to print Shortcuts are available for most of the menu commands e g to close a module press control w Subeditors A fundamental concept of the CellWorks user interface are subeditors which open after double clicking to the corresponding editor field or table You will find subeditors in many CellWorks modules and they are indicated by a small red line surrounding the subeditorial field or button Graph functions If you want to change the scaling of any graph axis click to the corresponding value type a new value and press Return This can be also done in the Options menu of the Execution module or with an INSTRUCTION command line in the Experiment Editor The control elements in the upper left corner of a monitor set autoscaling for either X or Y axis ON or OFF specify the scale format and can be used to activate a zoom in or out function 66 Appendix auto scale scale zooming button format tool cursor control elements auto scale lock shift gt Us 3 OF Cursor b be CR Mre egi M t Cursor Dt De 1D panning too
72. ith several format options 56 Reading Monitoring and Exporting Stored Data Files with the CW Reader Program Note The Prefs button in the CWR main window does not function in this version Note The current version 3 6 differs only slightly from version 3 5 which is described in more detail in the CW 4 0 manual zooming and Out B group autoscaling of digital outputs load data Ai channel Out A group button sweep list selection susor of digital outputs Info selection button Cellworks Reader File Edit Help Use GFE pate 51 59 Rec v9 Ente Senke Le 14 47 P pretet 18 119 18 113 SIS 19711 i n Ch Show Full_ Superimp Sw P JShow Full Buperimp Sw x 1 19 x 1 14 48 P pretet 217119 217119 E 1 14 48 P pretet 22 119 22 119 1 14 49 P pretet 23 119 23 113 14 49 P pretet 24 113 24 113 14 49 P pretet 25 119 25 113 A 14 49 P pretet 26 119 26 113 ki rt EFT 14 0 00 250 500 750 1000 1250 1500 1750 2000 2250 250 0 2750 3000 3250 3500 3750 4000 4250 4500 4750 5000 Figure 28 CW Reader window 37 style selection For Chart For Pulse Point Style by Default A Default B Line Style by Defaut A Defaut B nterpolation by Default A Default B Color by Default A Default B Export Appendix style definition style definition style definition style definition for default by sweep by chann
73. iting for trigger LED PWR indicates that an external power supply is plugged in 11 WAIT Wait for Trigger signal LOW 0 V by default Gets GPCTRI OUT HIGH 5 V if CellWorks waits for a trigger and remains high until STARTSCAN has been started see Figure 3 Note GPCTRI1 OUT is set by software and therefore not very precise a few ms 12 Installation 13 Start Start Data Acquisition Data Acquisition Begin of Begin of Wait for Trigger Wait for Trigger 5V WAIT E 4 BM 5V SYNC OV Figure 3 time course of trigger out signals CellWorks provides a variety of possibilities of controlling amplifiers Some examples of how to connect npi amplifiers and of basic software parameter settings are described in the appendix of this manual chapter 7 3 How to Use CellWorks 14 5 How to Use CellWorks The following chapters describe the structure of CellWorks CW and give an overview of the main parts The idea is to provide enough information for the user to get started with CellWorks and to perform first experiments While reading this chapters we recommend the user s to sit in front of a suitable computer system and follow the instructions directly in CellWorks Before you start CellWorks make sure that the installation and configuration procedures have been completed see chapter 4 5 1 Basics and CW Manager
74. l leave zoom mode Figure 31 commonly used graph functions 7 6 Server client structure Concurrent modules When multiple modules are opened concurrently it could happen that conflicting parameters are created by the user To avoid such problems the concurrent opening of modules which are dependent on each other is restricted For example when the CW Execution module is open the CW Chart Editor can be opened only in a Read only mode i e the user can check the settings of parameters but cannot alter them Cross reference The cross reference i e the data exchange between modules e g the PULSE configuration data between the Pulse Editor and the Experiment Editor is done by element position and not by element name Thus elements are always referred by their position in a list and not by their name Data interchange The Execution module is the core module of CW and it s relationship to monitors and Online modules that can be open in parallel can be explained as a server client structure The Execution writes predefined protocols and works as server The Online modules and monitors are the clients of the Execution module The server is not necessarily synchronized with the clients and does not wait until the clients have done their job The next figure shows the data flow structure of CellWorks 67 Appendix Settings by Settings by Setup Editor Selection of actual protocol by Execution Module Hardware Editor excep
75. l resolution operating system Mac OS 8 1 8 6 9 0 Note MAC OS X is not supported 3 2 Interface boards CellWorks Lite E was developed to run in conjunction with the National Instruments Low cost E series boards A variety of board types with different resolutions as well as sampling and update rates are available For operating the bidirectional communication of npi amplifiers an additional digital I O board e g PCI 6503 with 24 digital I O lines is necessary The next table gives three examples for system configurations Hard and Software Requirements application board type and additional hardware important specifications minimal configuration low cost E series board PCI 6024E max analog input sampling rate 200 kS s max analog output update rate 10 kS s 12 bit resolution enhanced configuration for predominantly recording CHARTS with high resolution and enhanced solution exchange management up to 96 valves PCI 6036E and PCI DIO 96 npi VD 24 valve controller valve drivers for up to 24 valves per controller ALA BPS 8 solution system for 8 valves per system PCI 6036E max sampling rate 200 kS s max analog output update rate 10 kS s 16 bit resolution PCI DIO 96 96 digital I O lines grouped to 12 ports VD 24 valve driver for up to 24 valves low noise and avoiding valve heating up technology BPS 8 solution system with 8 channels including res
76. lder contains the initial file CWInit with basic configuration settings As all other user folders CWE default contains three sub folders a Config contains all module configuration files a Data contains all data files For each day CW creates a new sub folder the daily folder where all data of this day are saved a Export contains the export data files generated in the Online modules or in the CW Reader The structure of this folder is similar to the Data folder structure User Folder Config Folder configuration folder contains all module configuration files Data Day Folders CellWorks generates a new data day folder automatically each day with the follwing Data Folder format contains all data folders files gt 0 7 9 characters from this user DIE 0 h 1 4 0 2 first 3 characters of the user folder 3 4 dependes whether the year format is set to 4 or 2 characters 5 6 year 7 month whereas a correspondes to January b to Februrary 8 9 day Export Folder Export Day Folders contains all exported data and config CellWorks generates a new export day folder files from this user CellWorks auto amp 3 automatically each day in the same way as matically creates for each day the a data day folder export function is used a new folder Figure 30 folder structure of a USER Within the daily folder Ce
77. llWorks generates four different file types that are all used for reloading data in CellWorks or CellWorks Reader 65 Appendix a D file e g 2000h11E00 D contains raw data of an experiment a F file e g file 2000h11E00 F contains the format information of an experiment e g which Ao channels time base sweep numbers etc have been used a E file e g DEF2000h11 E00 does no longer hold information a Nme file e g 2000h11Nme contains all the names of Solutions CHARTS PULSES There is one E F and D file for each experiment and only one Nme file for all experiments of one USER during one day The data files are created only if a CHART PULSE sweep or SNAPSHOT sweep is running in the Execution module and the proper options or INSTRUCTIONS e g Write Pulse to File have been set After finishing the current CHART or PULSE sweep the data file will be closed That means the data files are not automatically opened if the Execution or any other module is launched i e by default data are not saved Export files PULSE data recorded in CellWorks can be exported to ASCH Igor Text Autes or Axon Binary format in the Online modules chapter 5 9 The export data file type is configured in the Online modules CellWorks opens the same export or a new export file according to the export settings when starting the next sweep Currently CHART data can only be exported offline in the CellWorks Reader program chapter 6 Config f
78. monitored in the lower half of the window To the left of the status fields are several buttons which influence execution The user can Pause or abort execution of CHARTS PULSES SNAPSHOTS or INSTRUCTIONS Abort C P S I or cancel the whole EXPERIMENT Abort Exp Furthermore it is possible to skip the running segment or sweep and continue with the next segment or sweep Next Seg Next Sweep see Figure 18 During execution the acquired data are immediately displayed in the graphic field of the corresponding monitor module or in the selected Online module CHART data are plotted in the CW Chart Monitor whereas PULSE data can be displayed in the CW Pulse Monitor CW Online modules and with some limitations in the CW Chart Monitor in the latter case you have to set the PULSE popup menu in the Chart buffer subeditor of the Options menu to include Chart and Pulse Monitor The elements and menus are almost identical for both Chart and Pulse Monitor Therefore we describe both modules in one chapter Note Many monitor settings can be preset by programming corresponding INSTRUCTIONS in the experiment editor see chapter 5 7 It is a good idea to run a configuration experiment prior to experiments containing pulses charts or snapshots in order to have the correct configuration of the monitors The main part of the monitor modules is a large graphic field monitor display where the acquired da
79. n data format EXPERIMENT 2 and date format USER 3 CHARTI CHART3 PULSE3 PULSE 8 EXPERIMENT 1 Parameter settings Preprogram Preprogram CHART protocols in PULSE protocols in the the Chart Editor to Pulse Edit or the mode perform continous for pulsed synchronized analog input recording analog output and input while executing prepro grammed analog voltage steps solution changing and pump settings INSTRUCTIONS set of commands that can be used to control peripheral devices or CellWorks program parameter like amplifier settings Figure 5 Used for fast acquisition Chart and Pulse Mostly used in of data with synchronized Monitor size pharmacological analog input and output file operations experiments Preprogram OPTIONS EXPERIMENTS in the Experiment Editor to A part of the INSTRUC link CHARTS PULSES and INSTRUCTIONS TIONS setable in the together to perform an automatically executable EXPERIMENT editor experiment protocol like the Chart and Pulse buffer size file and Till can be monochromator settings the EXECUTION module set manually in Y 4 Execute and store data in the Execution module the preprogrammed CHARTS PULSES SNAP SHOTS and EXPERIMENTS Set CellWorks and peripheral parameters 4 manually Operate in the Execution Recorded module with the recorded data files open and close files
80. nd specifications can be found at the National Instruments homepage www ni com 7 2 Additional hardware components component company short description INT 10 npi Breakout box for CellWorks Lite and the being www npielectronic com 1200 data acquisition board series from discontinued National Instruments with multiple trigger possibilities additional digital power output for up to 8 valves and connector for the digital bidirectional communication of npi amplifiers INT 20X npi Breakout box for CellWorks Lite E and the Lowcost E series data acquisition boards VD 24 npi Universal valve controller for up to 24 valves low noise and valve heat up reduction technology 59 Appendix BPS 8 4 ALA www alascience com Bath perfusion system for 8 or 4 valves controlled by one of the breakout boxes or the VD 24 valve driver also available with a stand alone controller TEC 03 05 CW npi Voltage clamp amplifier with build in I O unit for Low cost E series data acquisition boards from National Instruments optional with digital standard interface INFA TEC and SEC npi All TEC or SEC amplifiers can be supplied amplifiers optionally with the digital standard interface INFA Pumps ISMATEC Pumps controlled by the serial port COMI COMS PCs or modem printer port Mac Polychrom II T LL L PHOTONICS Controlled by the serial port COMI COMS8 monochromator PCs or modem printer p
81. ng menu The Timing menu of the menu bar contains several commands to set the speed of replay of CHARTS and PULSES For CHARTS the user can set display speed factors and for PULSES the interval time between single sweeps A delay can be set for instructions to ensure execution immediately File Menu The File menu contains some commands for loading recorded data into the Exe Record subeditor The name of the loaded file is shown at the top of the right part of the Exe Record window User Today and Selected Folder lets the user toggle between the records of the 42 How to Use CellWorks current user today and the file loaded via Load Data command Printer Setup and Print Window call the standard windows dialog boxes To leave the Exe Record window and go back to the Execution window simply click to the OK button at the bottom of the window close the current file and open that field with Toggle Size create a new record by in the menu Display incrementingt this number lis iE Exe Records file source recorded i CHARTS PULSES Simple Jump Sample Identifier 0 SNAPSHOTS and Pulse series EXPERIMENTS 44 P Simple Ramp Fast Snapshot Short Description 16 Doing actual max Comments 160 xample similar to Execution module field Solutiond1 Def Off Actual Sampling Hz Flow ml min 1000 00 back
82. nitor II P Online Leak Subtraction CE O O O amp How to select an Online modules a Open the CW User module with the corresponding button in the CW Manager a Select Online Modules in the popup menu left a Select one of the four Online modules in the list and close the User module a The selected Online module is now available and can be launched with the Online A button in the CW Manager a Start the Execution and the Online module and activate a PULSE protocol to see how the Online modules work Online Sweep Analysis P This module is the most used in CellWorks It is supplied to show and analyze data to get a quick survey of the running experiment The acquired data of up to sixteen Ai channels are plotted online in the large upper left graphic field of the Online Sweep Analysis module Figure 23 This is the Online monitor that contains four cursors as well The other four graphs are Analysis monitors that display the results of various calculations which are performed with the data points measured by the four cursors of the Online monitor see below The submenu Options in the File menu is used to determine how data are displayed and what kind of calculation is performed in the analyze windows It contains the following fields see Figure 22 a Graph 0 Here the user can select which data are displayed on the Online monitor i e which Ai channels and which part full puls
83. nts sss 58 7 3 Basic software settings using npi hardware sese 59 7 4 File and directory structure and management 64 7 5 Common user interface elements u a Reken ema aria eee Re at 64 1 0 SCEVERCHENESUUCUUNE EE 66 7 7 CellWorks Lite for 1200 board Series cceeccesceeeceesceesceceeeceeeeeeeeeaeecaecnaeeneeeenseees 67 Ju8 e ENT ur CN 66 7 9 Abbreviations used in this manmal un uen n een 71 7 10 E 71 SIE a G8 cp EE 73 Safety Regulations 4 1 Safety Regulations VERY IMPORTANT Instruments and components supplied by npi electronic are NOT intended for clinical use or medical purposes e g for diagnosis or treatment of humans or for any other life supporting system npi electronic disclaims any warranties for such purpose Equipment supplied by npi electronic must be operated only by selected trained and adequately instructed personnel For details please consult the GENERAL TERMS OF DELIVERY AND CONDITIONS OF BUSINESS of npi electronic D 71732 Tamm Germany This system is designed for use in scientific laboratories and must to be operated by trained staff only General safety regulations for operating electrical devices should be followed Please protect the device s from moisture heat radiation and aggressive chemicals AC MAINS CONNECTION While working with the npi systems always adhere to the appropriate safety measures for handling electronic devices Before using any device ple
84. opy command lines subeditor where the command can be edited Experiment Editor DEF Expmnt File Edit Default Ca z Online h Esperimenti Inzert before Duplicate Duplicate ONLINE Il Module Sweep Analysis F Autoesport Off Switch A Number 00 ONLINE Leak Subtraction P DEF Online 09 08 00 set Options set Export set Menu set Traces set Scales set Fror ONLINE Il Module Leak Subtraction P amp utaespart OFF Swatch A Number OD ONLINE I Se Monitor Il D EFIO nline3 09 08 00 set Options set Export set Menu set Traces set Scales set Front Pat ONLINE II Module Y Monitor II P amp utaexport CIF Switch A Number 00 Figure 16 CW Experiment Editor Co How to create a simple EXPERIMENT LI Open the CW Experiment Editor by the corresponding button in the CW Manager LI Create a new EXPERIMENT d m m d d Double click a name of an experiment in the EXPERIMENT list left to open the subeditor Click the button Order Locked if it appears red Select an EXPERIMENT in the EXPERIMENT list left and click the button Duplicate Rename the duplicated EXPERIMENT in the small upper name editor field and move it to the desired location in the EXPERIMENT list OK the subeditor to close it LI Select the new generated experiment L Similar to the CHART or PULSE editor it is possible to duplicate or delete command lines using the Duplicate and Del
85. or is not updated when CellWorks acquires further data the monitor is updated when new data are acquired after setting the monitor mode to Replay it is possible to replay certain parts of the chart For this purpose a and a button appears after the selection of Replay left to the popup menu Clicking one of these buttons leads to the replay of the next or previous part of data on the monitor calls the standard Windows printer setup dialog calls the standard printer dialog to print the chart monitor window closes the chart monitor but don t release it from memory closes the chart monitor and releases it from memory freezes the monitor Le the monitor is not updated when CellWorks acquires further data the monitor is updated when new data are acquired the monitor shows only the part of the pulse defined by Marker 1 see CW Pulse Editor chapter 5 6 the monitor shows only the part of the pulse defined by Marker 2 see CW Pulse Editor chapter 5 6 if the monitor is configured to show Markers the user can define the time for t0 at the display the beginning of the marked part of the pulse is set to 0 e g the shown trace begins at 0 ms even if the marker is set to for instance segment 5 that begins at t 100 ms in the pulse protocol the beginning of the marked part of the pulse leaves untouched e g the shown trace begins at 100 ms if the marker is set to segment
86. ort Mac and FDU ratiometric system to get information about the technical data hardware please contact npi For information how to combine peripheral 7 3 Basic software settings using npi hardware Low cost E series board PCI 6024E with TEC 03X CW computer 68 pole 1 1 cable with SCSI female connectors Sa S PCI 6024E Connection TEC 03X CW d unit name direction LL read write a NUNT gain filter C ad mode VC CC a 68 pole 1 1 cable with SCSI female connectors from the PCI board inside the computer to the rear panel connector TO DATA ACQUISITION BOARD TEC 03X Software settings parameters amplifier Hardware module subeditor Amplifier TEC 03 Interface Analog In Telegraph Lines Reading Only Mode all buttons OFF Gain A Control OFF Read ON Manual OFF npi TEC 1 7 see range written at the amplifier s front panel analog input channel 2 Gain B all buttons off 60 Appendix Filter A Control OFF Read ON Manual OFF npi TEC SEC analog input channel 3 Filter B all buttons off Attenuation of Ai Low cost E series 1 Signals Digital Write to Amp none Digital Read from none Amp Setup module subeditor Software Gain Factors etc Ai a Channel 00 Gain Factor 0 001 Sensed Gain Gain A Units uA Long Names current a Channel 01 Gain Factor
87. os 10v sngeended Oontuse Dont use Configuration wih two channels E apcos 10v singe ended Oontuse Dontwe ADCOS 10V single ended Dont use Dont use sc TC single ended Dontuse Dont use Abco TC argeended eet ue Oontuse ADC0B TC single ended Dontuse Dont use apcos 310v sngeended Dontuse Dont use apcio TC singeended oontuse Oontuse AC HL 10v singe ended Dontuse Dont use apciz TC Tee eded Oontuse Oontuse ADCI3 TC singe sde Dontuse Dont use apci4 sio angeended Oontuse Dont use ADCIS sj 10y_ singe ended eet vs Dont use Lol sl Figure 7 board configuration subeditor How to Use CellWorks 19 Digtal out Port Assignement Lines 00 07 pev 3 PCI 6024 Port A 8 EE e Weslbgs iene Lines 24 31 None Lines 32 39 lone lines4047 hee Lines 48 55 None Lines 56 63 None INN Lines 72 79 Lines 80 87 one i Wess ne _ 8 H Amplifier Digkal Lines NPI Bidirectional 3 PTECS IO af roisec ij 6 Tei TIS old npi SEC 5 10 noi LPBF roi 3x variable noi 3x variable i pi TEC 1 47 pi LPBF pi LPG npi TEC 03 EC 1 4 Axop 2006 Aichannels i o sl o sl o foi Ld Attenuation of ai signal 1 00 Dighal write to Ame Dev 2 PCI 6503 Port A Bichannel s 0 Digital Read from Amp Pev 2 Pc 6503 Port B ee m communication i Kg CS Figure 9 amplifier subeditor Communication with via Plone SC
88. perimental environment CW Hardware CW Setup and CW User module a Configuration of individual experiments CW Chart CW Pulse and CW Experiment editor modules a Execution of experiments CW Execution CW Chart and CW Pulse Monitor several CW Online modules The Quit button in the right lower corner of the CW Manager terminates the program if all other modules are closed The indicator above shows the status of the program and the name of the active user folder How to Use CellWorks 15 E CWE Manager Demo Eile Edit Help status indicator termination button adaption to the configuration of execution of experiments experimental individual experi environment ments Figure 4 CW Manager Modules can be launched by clicking their corresponding buttons Every module header includes a menu bar similar to other Windows or Mac programs with commands Short cuts are available for most of the menu commands for instance to close a module press control w Several modules can be loaded into memory at the same time An active module is marked by a red line surrounding the module button When multiple modules are opened concurrently it is possible that conflicting parameters are created by the user To avoid such problems the concurrent opening of modules which are dependent on each other is restricted For example when the CW Execution module is open the CW Chart Editor can be opened
89. pumps scale and name Ao Gain Factors Long Name 12 ee Pump max Flow for the experiment the Ao channels Channel 00 16000000 Channel 00 Kai No Pump Channel 01 1 000000 Channel UT oux Runs it Mark 0 Sec Figure 12 CW Setup module basic settings for a np TEC amplifier How to Use CellWorks 22 Note All signals are scaled to mV an input of 1V and a Gain of 1 will be indicated as 1000 mV The default scaling of the npi amplifier 10mV current output is pA for SEC 05 10 and nA forTEC 03 05 10 If you want to have the TEC current displayed in LA and the SEC current in nA the scaling factor must be 0 001 5 4 Define the users in the User module This chapter describes the multi user feature of CellWorks and how different users can be created or loaded in the User module When CellWorks is started the CW Manager always loads a user related configuration DEF is the default user configuration setting from a configuration file in the user directory It contains information of all individual parameters and configurations necessary to perform experiments Thus each user can have her his own set of preferences and configuration settings which is very helpful if the experimental setup is shared by several persons The initial hardware and software configuration should be done as DEF user However after finishing this initial configuration see above we strongly recommend creating a new USER i e to perform further
90. t for oversampling with averaging Settings by Instructions or within Monitors or within Online Analysis Chart NI e g 4 channels 3008 averaging Analog in board Chart e g 3 channels 10Hz Write to Harddisk Pulse e g 2 channels IK Pulse Software selection E 2 channels IKHz of channels Chart Buffer eg with 5 Hz 1 Telegraph Data reduction Chart Monitor lines Scaling of data NPI interface include Pulse eg 100Hz Pulse Monitor Pulse Buffer with Data reduction Online Analysis and Export built in or Plug In Figure 32 CellWorks data flow structure 7 7 CellWorks Lite for 1200 board series This chapter describes the differences between CellWorks Lite E and CellWorks Lite as well as the connection and the configuration of the CellWorks Lite hardware CellWorks Lite is designed to use the PCI 1200 data acquisition board series from National Instruments The installation procedure is similar to CellWorks Lite E chapter 4 The next figures show the hardware connection the elements of the breakout box INT 10 and a screenshot of the Analog Main Board subeditor in the Hardware module Note that the analog input range of the PCI 1200 data acquisition is restricted to 5V and that the attenuation of Ai Signals must be set to 0 5 in the Amplifier subeditor of the Hardware module Furthermore one has to take care
91. t of one or more sweeps that are build up by one or more segments Thus segments are the smallest components of a CHART that can be configured independently of each other the number of segments within a CHART is not limited The parameter settings of three CHART segments are shown in the window If the CHART consists of more than three segments the user can move them by the or segment mover buttons Segments are duplicated deleted or inserted using the button beneath the segment mover buttons The configuration of the CHART is visualized by a CHART trace on the graph in the lower part of the module window Various display parameters are available for suitable monitoring of CHARTS including a Play button for CHARTS with more than one sweep A very important CHART parameter is the Time Base which can be found in the Timing subwindow This parameter defines the temporal distance between the acquired voltage data points If Time Base calculated in ms is higher than the Target Ai Sampling Rate of the CW Hardware module calculated in Hz the latter value defines the real sample frequency If Time Base is lower CellWorks selects a suitable sampling rate close to Target Ai sampling rate and performs an averaging oversampling of the acquired voltage data points This leads to data reduction and improvement of the signal to noise ratio In the Timing subwindow the user can also set the number of sweeps per CHART t
92. ta are displayed 39 How to Use CellWorks m Pulse Monitor Point Interval 0 200 ms Operate Edit Layout Help Adr B m S in mSec A Current kum oltage ki Elm Cursor in De ORRE 70 0 50 0 25 0 0 0 25 0 50 0 80 071 0 0 Figure 19 CW pulse monitor The control fields in the upper right part of the window are used to configure basic monitoring parameters what is displayed The user can select two Ai channels e g voltage and current set magnification factors for each of the channels and set units and length of the X axis Clicking the field furthest to the right with the trace icon opens a pull down menu that allows the user to select graphical settings for each of the channels individually e g line and point style color interpolation mode The control elements in the upper left corner set autoscaling for X and or Y axis ON or OFF specify the scale format precision and mode and are used to activate zooming functions To change the scaling of a graph axis manually simply click the corresponding value type in a new value and press lt Return gt The control elements in the upper middle part above the monitor display are used for the control of two crosshair cursors After starting the monitor the cursors are not active To activate them click the first field labeled Inf and type the X value e g 0 Then click the second Inf field in the same row an
93. talling the PCI Low cost E series boards as far away as possible from the graphic board Switch off the system again and install all other hardware components dongle breakout box amplifiers Figure 1 Note The dongle types for PCs and Macs are different The PC dongle is connected to the parallel port the Mac dongle is connected to the ADB For use of CellWorks on Macs without an ADB port e g G4 an iMate adapter is required Please contact npi for details Before connecting or disconnecting the dongle switch off the computer Otherwise the computer or dongle could be damaged Installation 10 Typical installation with control of valves pump and the T I L L monochromator computer with I O boards and ports SCSI 50 pole ribbon cable DIO board e IO board SCSI 68 pole serial I O dongle cable cum a Z T LL L monochromator JA Ke BI D power supply Ws INT 20 rear panel Lui Qe EL 6 EE INF Adapter perfusion system parallel port cable AN Some npi decticnic GmbH TEC SEC ns om Term errem os E TM rear panel actos woo Keess xor MENNNNNES VEH aan MODE OF OPERATION TL sace O wea ono O
94. ter the decimal point In addition the mode of the X axis can be configured Note Most changes are only displayed correctly when the next pulse is executed How to Use CellWorks 47 position and displ jficati size of analyze Cursor windows isplay range magnification windows operation and units factor mode range mode history trace Derived Values Cursor Windows Graph 0 Display Full Pulse_ E Layout Units mer History om G A e Eeer a Graph 1 Jupper short CurserO f Mel i nd 2 L i x1 m Graph 2 Jower short Curser 1 Ea s 10 00 mean s06 REI E E 4 Li a ki 1 i Graph 3 fipper right Curser2 tf 10 00 mean pue s EH LG Graph 4 Jower right Curser 3 X 10 00 mean E s GJ 70 m g I Graph 1 Graph 2 Graph 3 Graph 4 x y display A A histogram Value A operato Value 4 operator Value B Value X Value Y ichannel display color Ces Fans GECE Dol Fe Ire vi display in T Channel D crei y eere E D ema monitor ER stepleft Interpol step left Min 200 00 Interpol none Point large dot Point largedot Max 600 00 Point small dot interpolation Color m Color Bins a Color M style Interpol step left_ Point small dot_ Decimal fY Decimal z 0 Color F1 x Decimal 1 axis mode x Dedma 1i Y Decimal 1 v Decimal slo v Decimal 1 Histor
95. that the for PCI 1200 Write to Amp is performed via Port A 68 Parallel Port Put the white Egg Works Dongle here 50 Pole SCSI Cable Breakout Box RS 9 Arrows must point at the red marked wire of the SCSI cable D type 1 1 Cable SEC TEC Figure 33 CellWorks Lite hardware connection Appendix Appendix DALE JO Ld LO LINH D PISMO St T TANNYHO Me wasis ay JO SALES JO AWOPX LOL NO aes juasard ayy aearpuy TFILNAL Od 9 pasamos amp udino TLL 10 M uon elek Alay PLOIAT Oy ay psal equis ns DO saaga amp pawon anya jndur 3 agnd T L1 eura we q spauweys mamno Sopewy a SEI paras3u aq wes uas on CH parau Waals ara JAZZU 107 SUITE Dat See ed e apOL 19 2210 asooys asks EG a JO aassaenpu CAT Fr uor as jdjno aATea Jaz Od ayy 10 1938 AO argeirese st Land Jr ga OT 8 HAA Oc uoyug 138811 El amp penureur 0 gong end peyoauuo2 e aowa e aD xagrqdure durera ap Od eu eje UOTYELLLIOPUT AAT SAAT ENHE 69 Figure 34 INT 10 breakout box front panel elements 70 Appendix Input Range of 10V is not valid for L amp B 1200 E series boards Analog in and out Board Device pev 1 PCI 1200 Mode 5871 200 advanced Input Voltage Range OOOO 2 O Physical Channel Number 0 1 2 34 5 6 7 Aj Channel Software Mapping pep 2 3 8 IE 6 C7 to Target Channel Number of Ai Channels 2 4 Chart Target Ai Sampling Rate Hz Sf ann User Interface silencin
96. utput 02 pd Sie 04 Solutiond Output pa ann 05 Solutionds Output os 05 Channel 05 x1l 00E 0 regular Cos C P 08 dolusions Oupput 06 O6 Channel 06 x1 00E O regular COS C P u _ n_ Nee Replace O7 Channel 07 x1 00Et0 regular car c P 05 Channel 08 xl 00Et0 regular cos C P O9 Channel 03 xl O Et0 regular 2 co C P OL Solution l Channel 10 1l 00E 0 regalar 3 clo C P Of Solution 5 ll Channel ll x1 00E 0 regular 2 Cll C P 02 Solution lz Channel 12 xz1 00E 0 regular Cl2 C P 12 Channel 12 xl 00E 0 regular 3 C13 C P l4 Channel 14 x1 00Et0 regular Cla C P l5 Channel 15 xl O0Et0 regular cls C P o by channel 00 Channel 00 xl 0Etl Man Ol Channel Ol xl 00E 0 Vol Ho pump selected n Dutput l e Figure 11 CW Setup module the parameters listed in the Software Gain Factors etc table fit to a TEC amplifier In order to configure the analog input Ai and analog output Ao channels of the hardware environment that may change from experiment to experiment launch the CW Setup module and open the Software Gain Factors etc subeditor Here you can name the different Ai and Ao channels and more important select which of the physically available channels defined in the CW Hardware module will be used and stored to file on the hard disk Gain Factors and Sensed Gain telegraphing multiplication factors for the individual analog channels are defined as well Figure 12
97. v Write Chart to File No Change__ Write Pulse to File Yes __ Write Snaps to File No Change__ Record Chart Between Sweeps No Change__ Write Instructions to File Yes Warn if free Disk Space No Change__ is less than MB 5 Cancel OK Figure 17 subeditor to edit the file INSTRUCTIONS 33 How to Use CellWorks 5 8 Execute CHARTS PULSES and EXPERIMENTS monitor data online and offline This chapter describes how the preprogrammed CHART PULSE SNAPSHOT and EXPERIMENT protocols are executed and how parameters like the amplifier gain setting or the values of the analog outputs can be set manually in the CW Execution module Loading of data files in this module is explained in this chapter as well The acquired data can be monitored in the CW PULSE Monitor the CW CHART Monitor and in the CW Online Modules In contrast to all other modules and in order to display the acquired data immediately the CW Chart Monitor CW Pulse Monitor and CW Online modules can be active in parallel to the CW Execution module Thus we recommend opening CW Execution and at least one suitable monitor and or Online module at the same time The upper part of the window contains the file information indicator field Rech shows the file record number CW starts with record number 0 and it is possible to create or load other day files by changing that number see below Sample is the short description max 16 c
98. weep The X axis sweep number is not saved in a column The data of Monitors 3 histogram and 4 XY plot are listed in the following 4 columns The column labeled CW Calc02 contains the X data and the column labeled CW Calc03 contains the Y data of the histogram CW Calc04 and CW Calc05 contain the X and Y data of the XY plot monitor respectively The last part of the file contains the Notes with some information about the data and the experiment e g pulse name data acquisition rate solutions Ai channel names Note CellWorks uses a dot as decimal point whereas most of the internationalized programs use a comma and after importing the Ascii file these programs might interpret numbers as text Thus be sure that the program will recognize a point as decimal point An example of the various Export Settings as shown in Figure 24 is supplied in the CellWorks Demo folder CWE Default Demo XCONFIG To test these settings the user can load the Online module configuration file Online Export Settings Demo using the Load command in the File menu How to Use CellWorks 53 Online XY Monitor P This module is used 1 to monitor ONE Ai channel over time or data points respectively or 2 to show the data by plotting one Ai channel against the other Furthermore the user can export the data with the export function export filename Aichannel zooming control cursor control axis selection settings and display
99. write digital lines read BE BEE 15e write name E filter all mode VC CC a 68 pole 1 1 cable with SCSI female connectors from the PCI board inside the computer to the front panel connector PCI E SERIES BOARD INT20X a 50 pole 1 1 cable with SCSII female connectors from the PCI board inside the computer to 50 pole SCSII female connector rear panel amplifier a BNC cable from analog input channel 0 A10 front panel breakout box INT 20X to connector CURRENT OUTPUT front panel SEC TEC a BNC cable from analog input channel 1 Ail front panel breakout box INT 20X to connector POTENTIAL OUTPUT front panel SEC TEC software settings Parameters amplifier Hardware module TEC 03 TEC 05 and TEC 10 SEC 05 and SEC 10 subeditor Amplifier Interface Digital Lines npi Bidirectional Digital Lines npi Bidirectional Mode Control on button is red Control on button is red Read on Manual off button is Read on Manual off button is gray npi TEC 5 10 gray npi SEC 5 10 Gain A Control on Read on Manual Control on Read on Manual off TEC 1 77 see the range off SEC 1 77 see the range written on the amplifier front written on the amplifier front panel panel Gain B all buttons off all buttons off Filter A Control on Read on Manual Control on Read on Manual off opt TEC SEC off opt TEC SEC 63 Appendix Filter
100. y Color Grid Don t show Grid Dont show Grid pont show Grid Dontshow Grid Dont show Number of History Traces 10 lost changes are only displayed correctly when the next Pulse is executed Background White Grid Color a alue from T HD values for B channel number value at operator cursor number Figure 22 Online Sweep Analysis P Options window To change the X or Y scaling of the graphs manually click to the highest or lowest scaling value change the value via the keyboard and either press Return or click with the mouse to any other point outside the graph but within the module window For both graph axes there is an auto scale function available as well It is accessible in the Cursor display and scaling field right to the Online monitor A click to the two auto scale graph buttons automatically scales the corresponding axis of the online graph so that all of the recorded data are visible with an appropriate magnification While the sweeps of a PULSE experiment are executed and the sweep data are plotted at the upper Online graph the cursor calculations are performed online for each sweep and the four lower analyze graphs are updated immediately while the calculated data of the former sweep are still kept Thus it is possible to visualize various changes of the recorded voltage or current responses that occur from sweep to sweep and to perform simple operations e g to calculate

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CellWorks© Short Manual - NPI Electronic Instruments