Software for Fitting Photosynthetic CO2 or Light Response Curves

Software for Fitting Photosynthetic CO2 or Light Response Curves

A frequent question from LI-COR LI-6400XT users is a request for software resources for fitting the Farquhar, von Caemmerer and Berry (FvCB) model of photosynthesis (Farquhar, von Caemmerer & Berry 1980).  There is a wealth of literature on this topic and a variety of methods developed to fit the model.  There are currently no commercial software packages available for this purpose. Several software packages are, however, freely available for fitting the FvCB model of photosynthesis. Some approaches use only gas exchange data, while others combine gas exchange with chlorophyll fluorescence.  LI-COR does not endorse or validate any of these approaches, but leaves it up to the user to choose the best model fit for their data.

Fitting the FvCB model to CO2 Response Curves 

Peer-reviewed literature

1. Microsoft Excel spreadsheet from Sharkey, 2015:

http://onlinelibrary.wiley.com/doi/10.1111/pce.12641/full

2.  SAS program from Dubois et al., 2007:

http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02182.x/full

3. Web-based Exhaustive Dual Optimization (EDO) approach from Gu et al., 2010:

http://leafweb.ornl.gov

Combined Gas Exchange and Chlorophyll Fluorescence Data

1. Excel spreadsheet from Bellasio et al., 2015:

http://onlinelibrary.wiley.com/doi/10.1111/pce.12560/full

2. Excel spreadsheet from Mouleau-Ngangue et al., 2017:

http://onlinelibrary.wiley.com/doi/10.1111/nph.14260/full

Other software resources available

1. Excel spreadsheet – http://www.life.illinois.edu/bernacchi/links.html

2. Excel spreadsheet http://landflux.org/Tools.php

3. R code – https://sites.google.com/site/fridleylab/home/protocols

Fitting Models to Light Response Curves

Peer-reviewed literature

1. Microsoft Excel spreadsheet from Lobo et al., 2013:

http://link.springer.com/article/10.1007%2Fs11099-013-0045-y

Other software resources available

1. R code – https://sites.google.com/site/fridleylab/home/protocols

2. Excel spreadsheet – http://landflux.org/Tools.php

Reference

Farquhar G.D., Von Caemmerer S. & Berry J.A. (1980) A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149, 78–90.

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