Gas-exchange and fluorescence measurement best practices, and response curve models and data analysis

Hupp, J., Vath, R., (2025). A Hitchhiker’s Guide to Leaf-Level Gas Exchange. LI-COR, Inc. https://www.licor.com/podcast/leaf-to-leaf

Busch, F.A., Ainsworth, E.A., Amtmann, A., Cavanagh, A.P., Driever, S.M., Ferguson, J.N., Johannes Kromdijk, Lawson, T., Andrew, Jack, Meacham‐Hensold, K., Vath, R.L., Silvere Vialet‐Chabrand, Walker, B.J. and Papanatsiou, M. (2024). A guide to photosynthetic gas exchange measurements: Fundamental principles, best practice and potential pitfalls. Plant, Cell & Environment, 47(9). https://doi.org/10.1111/pce.14815.

Dany Pascal Moualeu-Ngangue, Chen, T. and Hartmut Stützel (2016). A New Method to Estimate Photosynthetic Parameters through Net Assimilation Rate−Intercellular Space CO2 Concentration (A−Ci) Curve and Chlorophyll Fluorescence Measurements. New Phytologist, 213(3), pp.1543–1554. https://doi.org/10.1111/nph.14260.

Dubois, J.B., Fiscus, E.L., Booker, F.L., Flowers, M.D. and Reid, C.D. (2007). Optimizing the Statistical Estimation of the Parameters of the Farquhar–von Caemmerer–Berry Model of Photosynthesis. New Phytologist, 176(2), pp.402–414. https://doi.org/10.1111/j.1469- 8137.2007.02182.x.

Farquhar, G.D., von Caemmerer, S. and Berry, J.A. (1980). A Biochemical Model of Photosynthetic CO2 Assimilation in Leaves of C3 Species. Planta, 149(1), pp.78–90. https://doi.org/10.1007/bf00386231.

Garen, J.C. and Michaletz, S.T. (2023). Fast Assimilation‐Temperature Response: a FAsTeR method for measuring the temperature dependence of leaf‐level photosynthesis. New Phytologist, 241(3), pp.1361–1372. https://doi.org/10.1111/nph.19405.

Long, S.P. and Bernacchi, C.J. (2003). Gas exchange measurements, what can they tell us about the underlying limitations to photosynthesis? Procedures and sources of error. Journal of Experimental Botany, 54(392), pp. 2393–2401. https://doi.org/10.1093/jxb/erg262.

Saathoff, A.J. and Welles, J. (2021). Gas exchange measurements in the unsteady state. Plant, Cell & Environment, 44(11), pp.3509–3523. https://doi.org/10.1111/pce.14178.

Sharkey, T.D. (2015). What Gas Exchange Data can Tell Us about Photosynthesis. Plant, Cell & Environment, 39(6), pp.1161–1163. https://doi.org/10.1111/pce.12641.

von Caemmerer, S. (2021). Updating the Steady State Model of C4 Photosynthesis. Journal of Experimental Botany, 72(17). https://doi.org/10.1093/jxb/erab266.

General data analysis

Tholen, D. (2024). GasanalyzeR: Advancing Reproducible Research Using a new R Package for Photosynthesis Data Workflows. AoB Plants, 16(4). https://doi.org/10.1093/aobpla/plae035.
Code: https://gitlab.com/plantphys/gasanalyzer

Curve fitting tools

Bellasio, C., Beerling, D. J., and Griffiths, H. (2016). An Excel Tool for Deriving Key Photosynthetic Parameters from Combined Gas Exchange and Chlorophyll Fluorescence: Theory and Practice. Plant, Cell & Environment, 39: 1180–1197. https://doi.org/10.1111/pce.12560.

de Lobo, F.A., de Barros, M.P., Dalmagro, H.J., Dalmolin, Â.C., Pereira, W.E., de Souza, É.C., Vourlitis, G.L. and Ortíz, C.E. (2013). Fitting Net Photosynthetic Light-response Curves with Microsoft Excel - a Critical Look at the Models. Photosynthetica, 51(3), pp.445–456. https://doi.org/10.1007/s11099-013-0045-y.

Duursma, R.A. (2015). Plantecophys - An R Package for Analysing and Modelling Leaf Gas Exchange Data. PLOS ONE, 10(11), p.e0143346. https://doi.org/10.1371/journal.pone.0143346.
Code: https://bitbucket.org/remkoduursma/plantecophys/src/master/

Gu, L., S.G. Pallardy, K. Tu, B.E. Law, S.D. Wullschleger (2010) Reliable estimation of biochemical parameters from C3 leaf photosynthesis-intercellular carbon dioxide response curves. Plant, Cell and Environment 33, 1852-1874. https://doi.org/10.1111/j.1365-3040.2010.02192.x

Automated web tool for structurally-optimized CO₂ response curve analysis: https://leafweb.org

Lei, T., Rizzo, K.T. and Bailey, B.N. (2025). PhoTorch: A Robust and Generalized Biochemical Photosynthesis Model Fitting Package Based on PyTorch. Photosynthesis Research, 163(2). https://doi.org/10.1007/s11120-025-01136-7.

Lochocki, E.B., Salesse-Smith, C.E. and McGrath, J.M. (2025). PhotoGEA: An R Package for Closer Fitting of Photosynthetic Gas Exchange Data With Non-Gaussian Confidence Interval Estimation. Plant, Cell & Environment. https://doi.org/10.1111/pce.15501.
Code: https://eloch216.github.io/PhotoGEA/

R modeling tools for C3 photosynthesis and ecophysiology response curve fitting tools

Stinziano J.R., Roback C., Gamble D., Murphy B., Hudson P., Muir C.D. (2023). photosynthesis: tools for plant ecophysiology & modeling. R package version 2.1.4.
Code: https://CRAN.R-project.org/package=photosynthesis; https://github.com/cdmuir/photosynthesis

Other resources

Dynamic Assimilation and curve-fitting: Considerations for fitting DAT CO₂ response curves. Application Note. LI-COR, Inc. licor.com/support/LI-6800/topics/dynamic-assimilation-and-curve-fitting.html.

FlashAnalysis, a tool for displaying and optimizing PAM chlorophyll fluorescence data from the LI-6400XT and LI-6800 Photosynthesis Systems and LI-600/N Porometer/Fluorometer: Flash Analysis Application Note. LI-COR, Inc. licor.com/support/Photosynthesis/topics/flash-analysis-application.html

A collection of code and resources for leaf functional trait experiments and leaf-level response curves: https://www.fridleylab.org/protocols.

Excel-based CO₂ and light response curve fitting tools: https://landfluxorg.godaddysites.com/tools.

Fitting A/Ci curves with simple R scripts and a shiny interface: https://github.com/poales/msuRACiFit.