# References

#### Pubic Data on Dryad

LeBauer, D.S., Burnette, M.A., Demieville, J., Fahlgren, N., French, A.N., Garnett, R., Hu, Z., Huynh, K., Kooper, R., Li, Z., Maimaitijiang, M., Mao, J., Mockler, T.C., Morris, G.P., Newcomb, M., Ottman, M., Ozersky, P., Paheding, S., Pauli, D., Pless, R., Qin, W., Riemer, K., Rohde, G.S., Rooney, W.L., Sagan, V., Shakoor, N., Stylianou, A., Thorp, K., Ward, R., White, J.W., Willis, C., and Zender C.S. (2020). TERRA-REF, An Open Reference Data Set From High Resolution Genomics, Phenomics, and Imaging Sensors. Dryad Digital Repository. [http://doi.org/10.5061/dryad.4b8gtht99](http://doi.org/10.5061/dryad.4b8gtht99)

AZMet Weather Data available on Dryad should be cited as

Brown, P. W., and B. Russell. 1996. “AZMET, the Arizona Meteorological Network. Arizona Cooperative Extension.” [https://cals.arizona.edu/AZMET/](https://cals.arizona.edu/AZMET/).&#x20;

#### Software

Burnette, Max, David LeBauer, Solmaz Hajmohammadi, Zongyang Li, Craig Willis, Wei Qin, Patrick, and JD Maloney. 2019. _terraref/extractors-multispectral: Season 6 Data Publication (2019)_ (version S6\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3406311](https://doi.org/10.5281/zenodo.3406311).

Burnette, Max, David LeBauer, Zongyang Li, Wei Qin, Solmaz Hajmohammadi, Craig Willis, Sidke Paheding, and Nick Heyek. 2019. _terraref/extractors-stereo-rgb: Season 6 Data Publication (2019)_ (version S6\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3406304](https://doi.org/10.5281/zenodo.3406304).

Burnette, Max, David LeBauer, Wei Qin, and Yan Liu. 2019. _terraref/extractors-metadata: Season 6 Data Publication (2019)_ (version S6\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3406329](https://doi.org/10.5281/zenodo.3406329).

Burnette, Max, Jerome Mao, David LeBauer, Charlie Zender, and Harsh Agrawal. 2019. _terraref/extractors-environmental: Season 6 Data Publication (2019)_ (version S6\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3406318](https://doi.org/10.5281/zenodo.3406318).

Burnette, Maxwell, Gareth S. Rohde, Noah Fahlgren, Vasit Sagan, Paheding Sidike, Rob Kooper, Jeffrey A. Terstriep, et al. 2018. “TERRA-REF data processing infrastructure.” In _ACM International Conference Proceeding Series_. [https://doi.org/10.1145/3219104.3219152](https://doi.org/10.1145/3219104.3219152).

Burnette, Max, Craig Willis, Chris Schnaufer, David LeBauer, Nick Heyek, Wei Qin, Solmaz Hajmohammadi, and Kristina Riemer. 2019. _terraref/terrautils: Season 6 Data Publication (2019)_ (version S6\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3406335](https://doi.org/10.5281/zenodo.3406335).

Burnette, Max, Charlie Zender, JeromeMao, David LeBauer, Rachel Shekar, Noah Fahlgren, Craig Willis, et al. 2020. _terraref/computing-pipeline: Season 4 & 6 Data Publication (2019)_ (version S46\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3635849](https://doi.org/10.5281/zenodo.3635849).

Burnette, Max, ZongyangLi, Solmaz Hajmohammadi, David LeBauer, Nick Heyek, and Craig Willis. 2019. _terraref/extractors-3dscanner: Season 6 Data Publication (2019)_ (version S6\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3406332](https://doi.org/10.5281/zenodo.3406332).

Chamberlain, Scott, Zachary Foster, Ignasi Bartomeus, David LeBauer, Chris Black, and David Harris. 2019. _Traits: Species Trait Data from Around the Web_. [https://CRAN.R-project.org/package=traits](https://cran.r-project.org/package=traits).

LeBauer, David, Nick Heyek, Rachel Shekar, Katrin Leinweber, JD Maloney, and Tino Dornbusch. 2020. _terraref/reference-data: Season 4 & 6 Data Publication (2019)_ (version S46\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3635863](https://doi.org/10.5281/zenodo.3635863).

LeBauer, David, Craig Willis, Rachel Shekar, Max Burnette, Ting Li, Scott Rohde, Yan Liu, et al. 2020. _terraref/documentation: Season 6 Data Publication (2019)_ (version v0.9). Zenodo. [https://doi.org/10.5281/zenodo.3661373](https://doi.org/10.5281/zenodo.3661373).

Mao, Jerome, Max Burnette, Henry Butowsky, Charlie Zender, David LeBauer, and Sidke Paheding. 2019. _terraref/extractors-hyperspectral: Season 6 Data Publication (2019)_ (version S6\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3406312](https://doi.org/10.5281/zenodo.3406312).

Marini, Luigi, Rob Kooper, Indira Gutierrez, Constantinos Sophocleous, Max Burnette, Todd Nicholson, Michal Ondrejcek, et al. 2019. _Clowder: Open Source Data Management for Long Tail Data_ (version v1.7.1). Zenodo. [https://doi.org/10.5281/zenodo.3300953](https://doi.org/10.5281/zenodo.3300953).

Rohde, Scott, Carl Crott, Patrick Mulroony, Jeremy Kemball, David LeBauer, Rob Kooper, Jimmy Chen, et al. 2016. _Bety: BETYdb 4.6_. Zenodo. [https://doi.org/10.5281/zenodo.48661](https://doi.org/10.5281/zenodo.48661).

Selby, Peter, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar E Benites-Alfaro, Clay Birkett, et al. 2019. “BrAPI—an application programming interface for plant breeding applications.” _Bioinformatics_ 35 (20): 4147–55. [https://doi.org/10.1093/bioinformatics/btz190](https://doi.org/10.1093/bioinformatics/btz190).

Willis, Craig, David LeBauer, Max Burnette, and Rachel Shekar. 2020. _terraref/sensor-metadata: Season 4 & 6 Data Publication (2019)_ (version S46\_Pub\_2019). Zenodo. [https://doi.org/10.5281/zenodo.3635853](https://doi.org/10.5281/zenodo.3635853).\


#### Sorghum Biomass Association Panel

Brenton, Zachary W., Elizabeth A. Cooper, Mathew T. Myers, Richard E. Boyles, Nadia Shakoor, Kelsey J. Zielinski, Bradley L. Rauh, William C. Bridges, Geoffrey P. Morris, and Stephen Kresovich. 2016. “A genomic resource for the development, improvement, and exploitation of sorghum for bioenergy.” _Genetics_. [https://doi.org/10.1534/genetics.115.183947](https://doi.org/10.1534/genetics.115.183947).

#### Soil Data

Babaeian, Ebrahim, Juan R. Gonzalez-Cena, Mohammad Gohardoust, Xiaobo Hou, Scott A. White, and Markus Tuller. 2020. “Physicochemical and Hydrologic Characterization Terra-Ref South Field.” _In Prep_.

#### **Genomics**

Morris, Geoffrey P., Davina H. Rhodes, Zachary Brenton, Punna Ramu, Vinayan Madhumal Thayil, Santosh Deshpande, C. Thomas Hash et al. "Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits." G3: Genes, Genomes, Genetics 3, no. 11 (2013): 2085-2094. [https://doi.org/10.1534/g3.113.008417](https://doi.org/10.1534/g3.113.008417)

#### **Reflectance Indices**

_Henrich, V., Krauss, G., Götze, C., Sandow, C._ (2012): **IDB - www.indexdatabase.de, Entwicklung einer Datenbank für Fernerkundungsindizes.** AK Fernerkundung, Bochum, 4.-5. 10. 2012. ([PDF](http://www.lap.uni-bonn.de/publikationen/posterordner/henrich_et_al_2012))

_Henrich, V., Jung, A., Götze, C., Sandow, C., Thürkow, D., Gläßer, C._ (2009): **Development of an online indices database: Motivation, concept and implementation.** 6th EARSeL Imaging Spectroscopy SIG Workshop Innovative Tool for Scientific and Commercial Environment Applications Tel Aviv, Israel, March 16-18, 2009

Apan, Armando; Held, Alex; Phinn, Stuart; Markley, John Formulation and assessment of narrow-band vegetation indices from EO-1 hyperion imagery for discriminating sugarcane disease 2003 2003 Spatial Sciences Institute Conference: Spatial Knowledge Without Boundaries (SSC2003)

Bannari, A.; Morin, D.; Bonn, F.; Huete, A. R. A review of vegetation indices 1995 Remote Sensing Reviews

Barnes, E.M.; Clarke, T.R.; Richards, S.E.; Colaizzi, P.D.; Haberland, J.; Kostrzewski, M.; Waller, P.; Choi, C., Riley, E.; Thompson, T.; Lascano, R.J.; Li, H.; Moran, M.S. Coincident detection of crop water stress, nitrogen status and canopy density using ground based multispectral data 2000 Proc. 5th Int. Conf. Precis Agric

Barnes, J. D.; Balaguer, L.; Manrique, E.; Elvira, S.; Davison, A. W. A Reappraisal of the Use of Dmso for the Extraction and Determination of Chlorophylls-a and Chlorophylls-B in Lichens and Higher-Plants 1992 Environmental and Experimental Botany

Blackburn, G. A. Spectral indices for estimating photosynthetic pigment concentrations: A test using senescent tree leaves 1998 International Journal of Remote Sensing

Carter, Gregory A. Ratios of leaf reflectances in narrow wavebands as indicators of plant stress 1994 International Journal of Remote Sensing

Carter, Gregory A.; Cibula, William G.; Miller, Richard L. Narrow-band Reflectance Imagery Compared with ThermalImagery for Early Detection of Plant Stress 1996 Journal of Plant Physiology

Chappelle, E.W.; Kim, M.S.; McMurtrey, J.E. Ratio analysis of reflectance spectra (RARS): an algorithm for the remote estimation of the concentrations of chlorophyll a, chlorophyll b, and carotenoids in soybean leaves 1992 Remote Sensing of Environment

Chen, J.M. Evaluation of vegetation indices and a modified simple ratio for boreal applications 1996 Canadian Journal of Remote Sensing

Daughtry, C. S. T.; Walthall, C. L.; Kim, M. S.; de Colstoun, E. Brown; McMurtrey Iii, J. E. Estimating Corn Leaf Chlorophyll Concentration from Leaf and Canopy Reflectance 2000 Remote Sensing of Environment

Daughtry, C.; Hunt, E. R.; Walthall, C. L.; Gish, T. J.; Liang, Shunlin; Kramer, E.J. Assessing the Spatial Distribution of Plant Litter  2001 Proceedings of the Tenth JPL Airborne Earth Science Workshop

Dobrowski, S. Z., Pushnik, J. C., Zarco-Tejada, P. J., & Ustin, S. L. (2005). Simple reflectance indices track heat and water stress-induced changes in steady-state chlorophyll fluorescence at the canopy scale. Remote Sensing of Environment, 97(3), 403-414.  &#x20;

Gamon, J. A.; Peñuelas, J.; Field, C. B. A narrow-waveband spectral index that tracks diurnal changes in photosynthetic efficiency 1992 Remote Sensing of Environment

Gamon, J. A.; Surfus, J. S. Assessing leaf pigment content and activity with a reflectometer 1999 New Phytologist

Gitelson, A. A.; Kaufman, Y. J.; Stark, R.; Rundquist, D. Novel algorithms for remote estimation of vegetation fraction 2002 Remote Sensing of Environment

Gitelson, A. A.; Merzlyak, M. N. Remote estimation of chlorophyll content in higher plant leaves 1997 International Journal of Remote Sensing

Gitelson, Anatoly A.; Kaufman, Yoram J.; Merzlyak, Mark N. Use of a green channel in remote sensing of global vegetation from EOS-MODIS 1996 Remote Sensing of Environment

Gitelson, Anatoly A.; Keydan, Galina P.; Merzlyak, Mark N. Three-band model for noninvasive estimation of chlorophyll, carotenoids, and anthocyanin contents in higher plant leaves 2006 Geophys. Res. Lett.

Gitelson, Anatoly A.; Merzlyak, Mark N.; Zur, Y.; Stark, R.; Gritz, U. Non-destructive and remote sensing techniques for estimation of vegetation status 2001 Third European Conference on Precision Agriculture

Gitelson, Anatoly A.; Viña, Andrés; Arkebauer, Timothy J.; Rundquist, Donald C.; Keydan, Galina: Leavitt, Bryan Remote estimation of leaf area index and green leaf biomass in maize canopies 2003 Geophys. Res. Lett.

Goel, Narendra S.; Qin, Wenhan Influences of canopy architecture on relationships between various vegetation indices and LAI and Fpar: A computer simulation 1994 Remote Sensing Reviews

Guyot, G.; Baret, F.; Major, D. J. High spectral resolution: Determination of specral shifts between the red and the near infrared 1988 International Archives of Photogrammetry and Remote Sensing

Haboudane, Driss; Miller, John R.; Pattey, Elizabeth; Zarco-Tejada, Pablo J.; Strachan, Ian B. Hyperspectral vegetation indices and novel algorithms for predicting green LAI of crop canopies: Modeling and validation in the context of precision agriculture 2004 Remote Sensing of Environment

Haboudane, Driss; Miller, John R.; Tremblay, Nicolas; Zarco-Tejada, Pablo J.; Dextraze, Louise Integrated narrow-band vegetation indices for prediction of crop chlorophyll content for application to precision agriculture 2002 Remote Sensing of Environment

Hardinsky, M. A.; Lemas, V. The influence of soil salinity, growth form, and leaf moisture on the spectral reflectance of Spartina alternifolia canopies 1983 Photogrammetric Engineering and Remote Sensing

Hernández-Clemente, R., Navarro-Cerrillo, R. M., Suárez, L., Morales, F., & Zarco-Tejada, P. J. (2011). Assessing structural effects on PRI for stress detection in conifer forests. Remote Sensing of Environment, 115(9), 2360-2375.  &#x20;

Herrmann, I.; Karnieli, A.; Bonfil, D. J.; Cohen, Y.; Alchanatis, V. SWIR-based spectral indices for assessing nitrogen content in potato fields 2010 International Journal of Remote Sensing

Huete, A. R. A soil-adjusted vegetation index (SAVI) 1988 Remote Sensing of Environment

Huete, A. R.; Liu, H. Q.; Batchily, K.; van Leeuwen, W. A comparison of vegetation indices over a global set of TM images for EOS-MODIS 1997 Remote Sensing of Environment

Hunt Jr, E. Raymond; Rock, Barrett N. Detection of changes in leaf water content using Near- and Middle-Infrared reflectances 1989 Remote Sensing of Environment

Kaufman, Y. J.;Tanre, D. Atmospherically resistant vegetation index (ARVI) for EOS-MODIS 1992 Geoscience and Remote Sensing, IEEE Transactions on

Lichtenthaler, Hartmut K. Vegetation Stress: an Introduction to the Stress Concept in Plants 1996 Journal of Plant Physiology

Merzlyak, Mark N.; Gitelson, Anatoly A.; Chivkunova, Olga B.; Rakitin, Victor Y. U. Non-destructive optical detection of pigment changes during leaf senescence and fruit ripening 1999 Physiologia Plantarum

Penuelas J., Baret F., Filella I. Semi-empirical indices to assess carotenoids/chlorophyll a ratio from leaf spectral reflectance 1995 Photosynthetica

Penuelas, J.; Filella, I.; Biel, C.; Serrano, L.; Save, R. The reflectance at the 950970 nm region as an indicator of plant water status 1993 International Journal of Remote Sensing

Peñuelas, J.; Gamon, J. A.; Fredeen, A. L.; Merino, J.; Field, C. B. Reflectance indices associated with physiological changes in nitrogen- and water-limited sunflower leaves 1994 Remote Sensing of Environment

Penuelas, Josep; Filella, Iolanda; Gamon, John A. Assessment of photosynthetic radiation-use efficiency with spectral reflectance 1995 New Phytologist

Pinty, B.; Verstraete, M. M. GEMI: a non-linear index to monitor global vegetation from satellites 1992 Plant Ecology

Rondeaux, Geneviève; Steven, Michael; Baret, Frédéric Optimization of soil-adjusted vegetation indices 1996 Remote Sensing of Environment

Roujean, Jean-Louis; Breon, François-Marie Estimating PAR absorbed by vegetation from bidirectional reflectance measurements 1995 Remote Sensing of Environment

Rouse, J.W., Jr.; Haas,R.H.; Schell, J.A.; Deering, D.W.  Monitoring the vernal advancement and retrogradation (green wave effect) of natural vegetation 1973 Prog. Rep. RSC 1978-1

Sims, Daniel A.; Gamon, John A. Relationships between leaf pigment content and spectral reflectance across a wide range of species, leaf structures and developmental stages 2002 Remote Sensing of Environment

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Vogelmann, J.E.; Rock, B.N.; Moss, D.M.  Red Edge Spectral Measurements from Sugar Maple Leaves 1993 International Journal of Remote Sensing

Zarco-Tejada, P. J.; Miller, J. R.; Noland, T. L.; Mohammed, G. H.; Sampson, P. H.  Scaling-up and model inversion methods with narrow-band optical indices for chlorophyll content estimation in closed forest canopies with hyperspectral data 2001 IEEE Transactions on Geoscience and Remote Sensing

Zarco-Tejada, Pablo J., Alberto Berjón, Raúl López-Lozano, John R. Miller, P. Martín, Victoria Cachorro, M. R. González, and A. De Frutos. "Assessing vineyard condition with hyperspectral indices: Leaf and canopy reflectance simulation in a row-structured discontinuous canopy." Remote Sensing of Environment 99, no. 3 (2005): 271-287.  &#x20;
