DualPAM Software Version 1.19 Release Note

Transcription

1 DualPAM Software Version 1.19 Release Note Content 1 Software Installation 1.1 Download software from Walz homepage 1.2 Installation 1.3 Update Firmware Firmware check MEGA RISC processor TINY RISC processor 2 New features of Version Windows 8 compatibility established. 2.2 Triggered run error 2.3 Variable background color 3 New features of Version System Management Log File for improved user support Calibration PS I Fluorescence Light and temperature measurements USB connection Clock 3.2 New Experimental Options Sinus-shaped Actinic Illumination Maximum Illumination Width increased Actinic Light On after Fast Kinetics 3.3 Error Correction Fast Kinetics Trigger SP-Analysis Plot Flux Measurement Data export 3.4 Data handling Slow kinetics export Slow Kinetics Settings, Fast Kinetics Settings Flux Measurement Fo'/Fo 3.5 Script File Options New commands Repetition Blocks 4 New features of Version Major changes Light curves Triggered runs Fo mode Far red light intensity External trigger control Actinic light intensity setting P700 signal calibration Actinic light Single turn-over flash sequence New Script File Timing of script file command sequences Fast Kinetics 4.2 Minor changes Firmware update menu Fast kinetics file (*.DFK) Blue light checkbox Experimental time Greek characters 5 New features of Version New driver for USB serial port 5.2 New script file commands 5.3 Setting commands 5.4 Clock cycles 5.5 Slow kinetics 5.6 Maximum frequency of measuring light 5.7 Light curve 5.8 Curve difference and curve averaging 5.9 Interruption of USB communication 5.10 Clock 5.11 New clock-triggered events 5.12 Fast kinetics trigger 5.13 User settings 5.14 Actinic light intensities 5.15 Miscellaneous 6 DualPAM software Version 1.8 release note 6.1 General comments 6.2 Miscellaneous 6.3 Script files Heinz Walz GmbH Eichenring Effeltrich Germany DualPAM 1.19 Release Note Phone +49-(0)9133/ Telefax +49-(0)9133/5395 info@walz.com

2 DualPAM Software Version Software Installation 1.1 Download software from Walz homepage Installation Close all programs. Execute DualPAM setup.exe. Pass through installation process. Connect and switch on DUAL-PAM-100. Start DualPAM software. 1.3 Update Firmware Firmware check Note that from DualPAM version 1.16 on, firmware versions will be checked automatically. In case of outdated firmware, the user will be asked to update firmware MEGA RISC processor The current firmware version is displayed in the title bar of the DualPAM software window. The firmware version must be (Fw: ). To install firmware, proceed as described next: click <Firmware Update> and <Program MEGA RISC> click <Read Hex File> and <Download Hex File>, wait for completion of download click <Program RISC>, read and confirm warning during RISC programming, a status message is visible which is then replaced by a message box confirming instrument reset click <ok> to exit program modus prior to proceeding, establish computer to DUAL-PAM-100 communication by clicking on the red LED symbol in the upper left corner of the software window Successful firmware update can be checked by the command Read Firmware Version in the menu Firmware Update ; the title bar will display the current firmware version only after restart of the DualPAM software TINY RISC processor Note: before updating the TINY RISC, the MEGA RISC has to be updated. To update: click <Firmware Update> and <Program TINY RISC>, click <Read Hex File> and <Download Hex File>, wait for completion of download click <Program RISC>, read and confirm warning during RISC programming, a status message is visible which is then replaced by a message box confirming instrument reset click <ok> to exit program modus close and restart DualPAM program DualPAM 1.19 Release Note 2

3 2 New features of Version Windows 8 compatibility established. 2.2 Triggered run error Error in time scale (occurring when using triggered runs of previous DualPAM software) corrected. 2.3 Variable background color Variable background color in graphic windows (click Options Color Chart Background) 3 New features of Version System Management Log File for improved user support The behavior of DualPAM software during startup is recorded in the file DualPAM_COM.log which is located in the directory DualPAM. The Walz software team can use this log file to diagnose errors during program start Calibration During signal calibration, any active triggered run sequence is halted PS I Fluorescence The relative contribution of PS I to total Fo fluorescence is calculated online according to Pfündel et al. (2013) Photosynth Res: PRES2013a ( PSI Fluo display, bottom left corner of window) Light and temperature measurements Enhanced accuracy of light and temperature measurements by improved input calibration USB connection Reconnection after communication failure improved. USB 3.0 communication implemented Clock Accuracy of repetitive triggering (clock) improved by stopping online monitoring of fluorescence, P700, PAR and temperature inactivated 1 second prior to trigger time point. 3.2 New Experimental Options Sinus-shaped Actinic Illumination Actinic light (red, blue, far red) can be sine modulated with periods 1s Maximum Illumination Width increased Maximum time intervals for illumination by red, blue and far red light as well as for trigger output has been extended from 10 to 60 minutes (see window Actinic Light ) Actinic Light On after Fast Kinetics The option to reestablish previous actinic light conditions after fast kinetics has been introduced (Checkbox Keep AL after Kinetics in SP Trigger window. 3.3 Error Correction Fast Kinetics Trigger Error in Fast Kinetics trigger file Poly300ms.FTM corrected SP-Analysis Plot Ordinate scaling corrected. DualPAM 1.19 Release Note 3

4 3.3.3 Flux Measurement Calibration of flux signal corrected Data export Various errors related to formatting of numbers removed. 3.4 Data handling Slow kinetics export Several slow kinetics of Report can be selected and collectively exported as csv data Slow Kinetics Settings, Fast Kinetics Settings A list of all settings of Slow Kinetics and Fast Kinetics can be displayed by right click on button Copy Settings from Man. Rec Flux Measurement Flux rate is always given in ΔI I -1 msec -1. Therefore, the flux rate is independent from modulation frequency of actinic light. The Flux Multiplier applied during measurements is displayed in the offline mode. (For new information on DUAL-PAM-100 flux measurements see: Klughammer et al (PRES 2013b) Fo'/Fo Fo'/Fo can be displayed in the SP-Analysis und Light Curve graphical windows of DualPAM software. These ratios are entered in the Report file. Opening of old Report files missing Fo'/Fo switches software to offline. 3.5 Script File Options New commands If Temperature and Wait until Temperature permit triggering of commands depending on temperature. Else allows execution of one of two alternative commands depending on the state of a selected condition. are provided to control sinus modulation of actinic red and blue light as well as far red light Repetition Blocks Editing of repetition blocks improved: disabling the command Begin of Repetition Block automatically disabled the corresponding command End of Repetition Block and vice versa. End of Release Note for Version 1.18 (Next pages: notes to former versions) DualPAM 1.19 Release Note 4

5 4 New features of Version Major changes Light curves Export of light curve enabled Triggered runs In the earlier program versions, conflicts arose when the command Copy Triggered Run from Manual Record copied the commands used for Fo determination, that is, illumination by PS I light during an interval with actinic light switched off. Now, the Fo mode during measurements is not considered by the command Copy Triggered Run from Manual Record ; the Fo mode needs to be activated manually by checking the Fo box Fo mode In the Fo mode, 5 seconds of PS I illumination after saturation pulse is also applied under dark conditions (e.g. actinic light off for fluorescence recovery) Far red light intensity An error affecting correct display of far red light intensity is removed External trigger control The DUAL-PAM-100 is prepared for external triggering pressing the Ext. Trigger of the fast kinetics screen. The command Ext. Trigger is launching a window for external trigger control. When external triggering is primed, normal keyboard and mouse operation of the DUAL-PAM-100 is disabled Actinic light intensity setting Intensity setting 0 (zero) for blue and red actinic light is enabled. When automatic change of measuring light frequency is activated (Auto MF-High ON), and the level of actinic light intensity is 0, switching on the actinic light results only in an increase in measuring light frequency P700 signal calibration Signal calibration uses a fixed acquisition rate of 5 ms per data point. This means, calibration always requires 3 s and is independent of current slow kinetics acquisition rate. After calibration procedure the previous acquisition rate is restored Actinic light In addition to red actinic light, blue light, as well as blue and red light together, can be used as actinic illumination when the DualPAM routines Induction Curve and Light Curves are performed Single turn-over flash sequence Exactly timed sequences of single turn-over flashes can be delivered in the Fast Acquisition Mode. Single turn-over flash sequences can be defined in the window Pulse Widths which is available via the button Pulse Widths in the window Actinic Light, or directly by right-click on the ST button. Adjustable parameters are (1) numbers of flashes within a sequence, (2) time interval (width) between two flashes down to 10 ms, and (3) execution of fast kinetics measurement after the sequence. Pressing the ST button triggers a single turn-over flash sequence if the number of flashes in ST Pulse Sequence sequence is > 1. DualPAM 1.19 Release Note 5

6 New Script File Command TR Wait until Clock Counter Auto Fo' Select Act. Light ST sequence number ST sequence width Fast Kin. after ST sequence. GFS-3000 Command Group Actinic Light Condition General Settings Actinic Light Actinic Light GFS-3000 Action Applies 5V to TRIGGER OUT socket as defined in trigger settings. Continues script program depending on number of clock counter. Switches on or off the automatic Fo determination mode. Selects actinic light source (blue, red, or blue plus red) for automatic induction and light curves. Configures a series of exactly timed single turn-over flashes. To be active, the DualPAM software has to be in the in the Fast Kinetics Window of the Fast Acquisition Analysis Mode. This can be achieved by script file commands: Analysis Mode = Fast Acquisition Visible Page = SP Kinetics The script command SP triggers a series of flashes for ST sequence number > 1. A large number of commands designed to simultaneously operate the DUAL-PAM-100 and the GFS-3000 systems using the DUAL-PAM-100 Gas- Exchange Cuvette. A detailed description of these commands will be delivered with the DUAL-PAM-100 Gas-Exchange Cuvette Timing of script file command sequences During execution of a script command the execution of the succeeding command is automatically prevented; wait intervals to separate consecutive actions can be omitted Fast Kinetics Extended observation time for slow relaxation processes: By choosing acquisition points >32000 and checking Ext. time checkbox in the Fast Acquisition Settings menu, the total observation time can be extended by decreasing the acquisition rate at points >32000 and > This function requires MEGA RISC firmware version Minor changes Firmware update menu In the VIEW mode, the firmware update menu is disabled Fast kinetics file (*.DFK) Light intensity values (PAR, µmol m-2 s-1) of red and blue actinic light, saturation pulses and measuring light are saved together with fast kinetics data Blue light checkbox Removed in window for actinic light settings. DualPAM 1.19 Release Note 6

7 4.2.4 Experimental time On Slow Kinetics Settings window, the total experimental time resulting from number of points and rate is displayed Greek characters Greek characters are replaced by similar ASCII characters (e.g. µ u). 5 New features of Version New driver for USB serial port Adjustment of latency time to 1 ms is no longer required. 5.2 New script file commands P700 calibration: Automated routine for calibration of the scale of the P700 (or P515) difference signal. Measuring light MF Log: For measurements of fast fluorescence decay. The MF Log command decreases measuring light frequency logarithmically directly after maximum measuring light frequency (MF-max) is switched off. The MF log function can also be activated in the fast trigger window. Measuring light MF-M: Four levels of maximum frequency of measuring light are available (see below). Read with start conditions: Trigger files are saved together with the settings present at the trigger pattern s start. Load with start conditions: installs the trigger pattern selected and activates all start settings which influence the trigger-controlled fast kinetics. Display commands: A range of commands affecting the display of data has been added, for instance, automatic axis scaling and data averaging. 5.3 Setting commands New commands defining DUAL-PAM-100 settings have been added. Now, stored DUAL-PAM-100 settings can be activated (Open User Settings), detector heads can be defined and slow kinetic trigger files can be opened and executed. 5.4 Clock cycles The number of clocked events can be adjusted. 5.5 Slow kinetics Improved time management by coarse graphing of data in the presence of high rates of data acquisition (e.g. 1 point/ms) 5.6 Maximum frequency of measuring light The maximum measuring light frequency is adjustable at 4 different levels: 2000, 5000, and Hz. Note that these numbers correspond to frequencies of trains of 14 x 1.25 µs measuring pulses separated by 1.25 µs. The option of selecting among various maximum measuring light frequencies is not available when MF Log is selected. 5.7 Light curve A second model for analyzing light curve data has been implemented. DualPAM 1.19 Release Note 7

8 5.8 Curve difference and curve averaging Improved manual subtraction and manual averaging of slow and fast kinetics (see the <+> and <- > icons in the kinetics windows). 5.9 Interruption of USB communication Stable execution of DualPAM during interruption of USB connection Clock Clock stops when <Reset> or <New> is clicked during fast kinetics averaging New clock-triggered events Triggered run, actinic light on, and FR/BL switch Fast kinetics trigger Pretrigger conditions consistently used as starting conditions for main trigger pattern. <Clear All> sets all pretrigger and trigger signals to zero. The command <Synchronize ADC> can be activated by a checkbox. The <Synchronize ADC> is saved as part of the <Start Conditions> of a trigger file User settings Settings of country and format of numbers is saved with a user setting Actinic light intensities Actinic light intensities can be set to zero 5.15 Miscellaneous Error (EOF) during reading of report corrected. 6 DualPAM software Version 1.8 release note 6.1 General comments A software component has been implemented to operate the P515/535 module for measurements of electrochromic absorbance shift at 515 nm (P515) and absorbance changes at 535 nm (I 535). Expanded control of external PAR and temperature sensors are available via right-click on PAR and temperature display, respectively. Specifically: automatic dark offset adjustment for low and high PAR ranges, switching between external PAR and predefined internal PAR values, storage of sensor calibration data in the DualPAM.INI file. 6.2 Miscellaneous Improved memory management for long-term measurements. Removal of a bug which affected calculations of Φ(NO). A routine has been added to calculate the difference between two curves (Slow and fast kinetics. Available by clicking the dash button right of the <Save kinetics button>). DualPAM 1.19 Release Note 8

9 Improved performance of the functions <Copy Triggered Run from Manual Record> and <Pretrigger> in fast trigger settings. 6.3 Script files Script files are automatically placed into the DualPAM directory. The files adjust parameters and execute measuring routines of the Dual-PAM-100. A short description of the script files is given next. I1_Oszillation.prg Records 60 ms polyphasic rise kinetics interspaced by 60 seconds dark intervals. Prior to each polyphasic rise, various number of single turn-over flashes are given (ranging from zero to eight). Get_AL_Intensities.prg Writes photon flux densities as measured by a quantum sensor connected to the DUAL-C control unit into the internal list of actinic light intensities. Get_BL_Intensities.prg Writes photon flux densities as measured by a quantum sensor connected to the DUAL-C control unit into the internal list of blue light intensities. IC+LC.prg Runs a P700 + fluorescence induction curve and, subsequently, a light curve. P700 MT-Width.prg Records P700 kinetics for multiple turn-over flashes of increasing length. P700_FineAdjust.prg Automatically balances 830 sample and 875 reference beams. Pool+IC.prg Assesses intersystem electron carrier pool by P700 measurements and, subsequently, performs a P700 + fluorescence induction curve. Poly60ms.FTM Records 60 ms polyphasic rise. Poly300ms.FTM Records 300 ms polyphasic rise. Qa_Decay.FTM Measures decay kinetics after single turn-over flash. Kautsky01.STM Runs a Kautsky induction curve. DualPAM 1.19 Release Note 9