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LI-600 porometry

Why the LI-600 overestimates conductance

The LI-600 porometer assumes the air in its chamber stays at one temperature as it flows past the leaf. In fact, water evaporating from the leaf cools the air (psychrometric cooling). The instrument ignores this, so it overestimates stomatal conductance. The error grows at high conductance and low humidity.

The correction

pk li600 correct applies the correction of Rizzo & Bailey (2025). For each reading it restores the energy balance by solving three equations for three unknowns: the outlet air temperature, transpiration E and stomatal conductance gsw.

  1. Diffusion: transpiration driven by the leaf-to-chamber vapour gradient, through the stomatal and boundary-layer conductances in series.
  2. Water balance: transpiration from the change in water vapour between inlet and outlet air.
  3. Enthalpy balance: the energy carried by the air, including heat the instrument adds, \(C\,(T_{in} - T_{chamber})\).

The instrument's own boundary-layer conductance (2.921 mol m⁻² s⁻¹) and aperture area are built in. Two settings depend on your setup:

Option Default Meaning
--sidedness 1 1 for leaves with stomata on one side, 2 for both sides. Conductance and transpiration are multiplied by it.
--thermal-conductance 0.007 W °C⁻¹ Heat exchange between the instrument and the chamber air

overestimate_pct is \(100\,(g_{measured} - g_{corrected})/g_{corrected}\). Readings where the solve doesn't converge are left blank.

The correction adds these columns:

  • gsw_corrected
  • E_corrected, in mmol m⁻² s⁻¹ like the LI-600's E_apparent
  • the corrected chamber and outlet temperatures
  • the chamber water mole fraction
  • the sidedness used

Estimating A from conductance

pk li600 estimate solves net assimilation for each porometer reading. It uses the reading's conductance, light and leaf temperature, together with a photosynthesis parameter set.

  1. CO₂ conductance: \(g_{sc} = g_{sw}/1.6\).
  2. Absorbed light: Qamb × absorptance (default 0.85).
  3. Solve for Ci: find the CO₂ concentration where the photosynthesis model's A equals the diffusion supply, \(g_{sc}\,(C_a - C_i)\), with \(C_a\) = 420 µmol mol⁻¹ by default. The search covers 0.01–2000 µmol mol⁻¹.
  4. Mesophyll conductance: if the parameter set has a gm between 0 and 99, the solve uses stomatal and mesophyll conductance in series, and reports both Ci and Cc. Otherwise Cc = Ci.

If the file has a gsw_corrected column, it's used in place of gsw, so run the correction first for the most accurate A.

Very low or negative readings (the LI-600 reports negative gsw when the outlet is drier than the inlet) are raised to --min-gsw (default 0.001) and flagged clamped. With --min-gsw 0, they're left unsolved instead.

The parameter set can come from:

  • the model's defaults,
  • a --params file: a pk fit JSON result, a CSV of fitted parameters (the last row is used), a two-column Parameter/Value table, or name = value lines,
  • --set name=value.

Later sources win. Parameters the model doesn't use are listed in ignoredParams.

See Correct LI-600 conductance and Estimate A from porometry.