LI-600 Porometer Correction

PhyTorch provides a correction function for systematic bias in stomatal conductance measurements from the LI-COR LI-600 porometer/fluorometer.

Overview

The LI-600 porometer exhibits systematic positive bias in stomatal conductance measurements due to temperature variations in the instrument's flow path. This correction addresses these measurement errors, which are most significant at:

• High stomatal conductance values (>0.3 mol m⁻² s⁻¹)
• Low humidity conditions
• Large leaf-air temperature differences

The correction is based on solving a coupled system of thermodynamic equations accounting for heat transfer in the instrument's flow path (Rizzo & Bailey, 2025).

Basic Usage

from phytorch.utilities import correct_LI600

# Correct LI-600 measurements
corrected_data = correct_LI600('li600_data.csv', stomatal_sidedness=1)

# View original vs corrected values
print(corrected_data[['gsw', 'gsw_corrected']])

Parameters

correct_LI600(filepath, stomatal_sidedness=1.0, thermal_conductance=0.007, save_output=True, output_path=None)

Parameter	Type	Default	Description
filepath	str or DataFrame	-	Path to LI-600 CSV file or DataFrame with LI-600 data
stomatal_sidedness	float	1.0	Stomatal distribution factor (see below)
thermal_conductance	float	0.007	Thermal conductance C in W/°C
save_output	bool	True	Whether to save corrected data to CSV
output_path	str	None	Output file path (auto-generated if None)

Stomatal Sidedness

The stomatal_sidedness parameter accounts for stomatal distribution on the leaf:

Value	Description
1.0	Hypostomatous (stomata only on lower surface)
2.0	Amphistomatous (stomata on both surfaces equally)
1.0-2.0	Intermediate cases

Required Data Columns

The LI-600 CSV export must contain these columns:

• gsw - Stomatal conductance to water vapor (mol m⁻² s⁻¹)
• Tref - Reference temperature (°C)
• Tleaf - Leaf temperature (°C)
• rh_r - Reference relative humidity (%)
• rh_s - Sample relative humidity (%)
• flow - Flow rate (µmol s⁻¹)
• P_atm - Atmospheric pressure (kPa)
• E_apparent - Apparent transpiration rate (mmol m⁻² s⁻¹)

Output

The function returns a DataFrame with original data plus corrected columns:

Column	Description	Units
gsw_corrected	Corrected stomatal conductance	mol m⁻² s⁻¹
Ta_chamb_corrected	Corrected chamber temperature	°C
T_in_corrected	Inlet temperature	°C
T_out_corrected	Outlet temperature	°C
W_chamb_corrected	Corrected chamber water vapor mole fraction	mol/mol
stomatal_sidedness	Applied sidedness value	-

Examples

Hypostomatous Leaves

from phytorch.utilities import correct_LI600

# Correct measurements from leaves with stomata on lower surface only
data = correct_LI600('measurements.csv', stomatal_sidedness=1.0)

Amphistomatous Leaves

# Correct measurements from leaves with stomata on both surfaces
data = correct_LI600('measurements.csv', stomatal_sidedness=2.0)

Without Saving Output

# Process data without saving to file
data = correct_LI600('measurements.csv', save_output=False)

Using DataFrame Input

import pandas as pd
from phytorch.utilities import correct_LI600

# Read and correct data from DataFrame
df = pd.read_csv('measurements.csv')
corrected = correct_LI600(df, stomatal_sidedness=1.5, save_output=False)

Custom Thermal Conductance

# Use custom thermal conductance value (if calibrated for your instrument)
data = correct_LI600('measurements.csv', thermal_conductance=0.008)

Visualization

Plot the correction results to visualize the impact:

from phytorch.utilities import correct_LI600, plot_correction

# Apply correction
corrected_data = correct_LI600('measurements.csv')

# Create comparison plots
fig, axes = plot_correction(corrected_data, save_path='correction_plot.png')

The plot shows:

• Left panel: Original vs corrected stomatal conductance
• Right panel: Original vs corrected chamber water vapor mole fraction

Technical Details

Correction Method

The correction solves a system of three coupled equations:

1. Fick's Law for water vapor diffusion: $E = g_{tw}(W_{leaf} - W_{chamb})$

2. Mass Balance for water vapor: $E = \frac{u_{in}}{s} \frac{W_{out} - W_{in}}{1 - W_{out}}$

3. Energy Balance including latent and sensible heat: $E = \frac{1}{s}\left(\frac{Q + u_{in}h_{in}}{h_{out}} - u_{in}\right)$

where:

• $E$ = Transpiration rate (mol m⁻² s⁻¹)
• $g_{tw}$ = Total conductance (stomatal + boundary layer)
• $W$ = Water vapor mole fraction (mol/mol)
• $u_{in}$ = Inlet flow rate (mol/s)
• $s$ = Leaf area (m²)
• $Q$ = Heat transfer from air to chamber (W)
• $h$ = Moist air enthalpy (J/mol)

Convergence

The solver uses scipy.optimize.fsolve to find the corrected values. If convergence fails for a data point (residual > 10⁻⁶), that point is assigned zero values in corrected columns and a warning is issued.

Failed convergence typically indicates:

• Invalid or extreme input values
• Instrument malfunction during measurement
• Environmental conditions outside calibration range

Reference

Rizzo, K.T. & Bailey, B.N. (2025). A psychrometric temperature correction for porometer measurements of stomatal conductance. (In review)