Software for photosynthesis data analysis

Many LI-6800 and LI-6400XT operators seek tools for data post-processing, analysis, and response curve model fitting. A variety of non-commercial software packages are available for these tasks, based on popular statistical data analysis programs and published photosynthetic models. Several of these publications and packages are listed below. LI-COR does not test or formally endorse these tools.

General data analysis

1

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

A/C_i, CO₂, light, and combined gas-exchange and fluorescence analysis

2

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.

3

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.

4

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.

5

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.

6

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.

7

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/Plant, cell and environment, 47(9). https://doi.org/10.1111/pce.14815.

8

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.

9

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.

Curve fitting tools

10

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/

11

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.

12

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.

13

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/

14

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.

Other resources

Flash Analysis (a LI-COR application): Flash Analysis.

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

Web-based Exhaustive Dual Optimization (EDO) approach from Gu et al., 2010 at https://leafweb.org.

Excel spreadsheet: https://www.life.illinois.edu/bernacchi/links.html.

Excel spreadsheet: https://landflux.org/tools.

Code and resources: https://www.fridleylab.org/protocols.

Code with modeling tools for C3 photosynthesis and analytic tools for curve-fitting plant ecophysiology responses: https://github.com/cdmuir/photosynthesis.