Photosynthetic, Internal and Stomatal Conductance Analyses of Leaves (PISCAL) Instruction for setting up the input file for PISCAL -----Mentioning a brand name in this document does not constitute support for the brand------- General instruction - Variables with labels started with '!' must be provided in order for PISCAL to do any analysis. For other variables, fill in with -9999 if unavailable. - Each input file must contain only data from a single curve. Separate curves may be stored in separate input data files and submitted at the same time. - Save data in comma separated value format (.csv) Line 1 to Line 10: Space provided for descriptive information about the investigator, contact information, the site,the sample leaf and its general environmental condition Line 11: Complementary data not used by PISCAL but needed for properly interpreting the A/Ci data and for synthesis SiteID - (Dimensionless), Site identifier (do not leave blank between letters) Latitude(Degrees) - Site latitude, northern hermisphere positive Longitude(Degrees) - Site longitude, east positive Elevation - (m), site elevation SampleYear - (year), the year when the A/Ci data is taken SampleDayOfYear - (day), the day of year (since 1 Jan) when the A/Ci data is taken GrowSeasonStart - (day), the approximate start day (since 1 Jan) of growing season GrowSeasonEnd - (day), the approximate end day (since 1 Jan) of growing season StandAge - (year), stand age since the last disturbance CanopyHeight - (m), the height of the canopy LeafAreaIndex - (m2/m2), the leaf area index in the middle of growing season SpeciesSampled - (dimensionless), the species of the leaf sample (don't leave blank between letters) AveTimeResolution - (minutes), the average time interval between two consecutive A/Ci data points SampleHeight - (m), the height at which the leaf is located LeafAge - (day), the age of the leaf SpecificLeafArea - (cm2/g), specific leaf area of the sample LfNitrogenContent - (%), dry leaf nitrogen content of the sample LfCarbonContent - (%), dry leaf carbon content of the sample LfPhosphContent - (%), dry leaf phosphorus content of the sample Line 12: The units of corresponding variables in Line 11 Line 13: The values of corresponding variables in Line 11 Line 14: The photosysnthetic model parameters you want to keep constant at the values you provide, fill in -9999 if you want to let PISCAL decide Gamma* - (Pa), chloroplastic CO2 photocompensation point (must be positive if provided) Kc - (Pa), Michaelis-Menten constant for RuBP carboxylation (must be positive if provided) Ko - (Pa), Michaelis-Menten constant for RuBP oxygenation (must be positive if provided) Alpha - (Dimensionless), the fraction of glycolate carbon not returned to the chloroplast (must be between 0~1 if provided) Rd - (umol/m2/s), dark respiration (must be positive if provided) gi - (umol/m2/s/Pa), internal (also known as mesophyll) conductance Line 15: The units of corresponding variables in Line 14 Line 16: The values of corresponding variables in Line 14 Line 17: A/Ci data for a variety of analyses, including photosynthesis, stomatal conductance, internal conductance, water use efficiency. At this stage, we only provide to users parameters from A/Ci curve analysis. Results from other analyses will be provided to users once they are thoroughly tested. The format used here represents a typical output from a Licor-6400 except for the last two columns (PhiPS2 and OxygenPress). Most variables have the same label as those in the Licor-6400 guidebook with the same definition. Not all variables are used by PISCAL. By using this format, however, Licor-6400 users don't have to do a lot of data organization in order to use PISCAL. Users of other instruments could ignore columns that are not needed for A/Ci analyses (fill in those columns with -9999) and just provide the essential variables. Again, essential variables have labels started with '!'. Obs: (dimensionless), the data point No. HHMMSS - (hh:mm:ss), clock time FTime - (seconds), number of seconds since file opened Photo - (umol/m2/s), photosynthetic rate !AdjPhoto - (umol/m2/s), adjusted photosynthetic rate (leakage corrected), must provide !StomCond - (mol/m2/s), stomatal conductance, must provide !Ci - (umol/mol), intercellular CO2 concentration (umol CO2 / mol moist air), must provide !Trmmol - (mmol/m2/s), transpiration rate, must provide !VpdL - (KPa), water vapor pressure deficit based on leaf temperature, must provide Area - (cm2), leaf area StmRat - (NA), estimate of the ratio of stomatal conductances of one side of the leaf to the other BLCond - (mol/m2/s), total boundary layer conductance Tair - (oC), temperature in sample cell !Tleaf - (oC), temperature of leaf thermocouple, must provide TBlk - (oC), IRGA Block temperature CO2R - (umol/mol), reference CO2 concentration CO2S - (umol/mol), Sample CO2 concentration H2OR - (mmol/mol), reference cell water vapor concentration H2OS - (mmol/mol), sample cell water vapor concentration RH_R - (%), Reference cell relative humidity RH_S - (%), sample cell relative humidity Flow - (umol/s), molar flow rate of air entering the leaf chamber !PARi - (umol/m2/s), PAR measured by the in-chamber quantum sensor, must provide PARo - (umol/m2/s), PAR measured by the external quantum sensor Press - (KPa), atmospheric pressure CsMch - (umol/mol), sample CO2 offset HsMch - (mmol/mol), sample H2O offset StableF - (NA), a stability indicator as a decimal value Status -(NA), status flag PhiPS2 - (NA), DeltaF/Fm, the fraction of absorbed PSII photons that are used in photochemistry OxygenPress - (Pa), atmospheric O2 partial pressure Line 18: The units of corresponding variables in Line 17 Line 19 and below: The actual data body of the A/Ci curve