Hyperspectral imaging data

Summary

Hyperspectral imaging data is collected using the Headwall VNIR and SWIR sensors. In the Nov 2017 Beta Release only VNIR data is provided because we do not have the measurements of downwelling spectral radiation required by the pipeline.

Please see the README hyperspectral pipeline README for more information about how the data are generated and known issues.

Hyperspectral Algorithm and pipeline

See Hyperspectral extractor

Data Access

Raw Data

Raw data is available in the filesystem, accessible via Globus in the following directories:

• VNIR: /sites/ua-mac/raw_data/VNIR

• SWIR: /sites/ua-mac/raw_data/SWIR

These files are uncalibrated; see the hyperspectral pipeline repository for information on how these can be processed.

Level 1 data access

Hyperspectral data is available via Clowder, Globus #Terraref endpoint, the TERRA REF Workbench, and our THREDDS server:

• Clowder:

  • VNIR Hyperspectral NetCDFs

  • SWIR Collection: Level 1 data not available

• Globus and Workbench:

  • VNIR: /sites/ua-mac/Level_1/vnir_netcdf

  • SWIR: Level 1 data not available

• Sensor information:

  • Headwall SWIR

  • Headwall VNIR

For details about using this data via Clowder or Globus, please see Data Access section.

Level 2 data access

Level 2 data are spectral indices computed at the same resolution as Level 1. These can be found in the same Level 1 directories as their parents, but the files are appended *_ind.nc.

To get a list of hyperspectral indices currently generated https://terraref.ncsa.illinois.edu/bety/api/v1/variables?type=Reflectance%20Index

traits::

Level 3 data access

Hyperspectral Indices

The following indices are computed and provided as both Level 2 data at full spatial resolution and as Level 3 (plot level) means.

Citations can be found 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.

Index	Label	Formula	Citation
DWSI1	Disease Water Stress Index 1	R800 / R1660	Apan, Held, Phinn and Markley (2003)
ND900_680	Normalized Difference 900/680	(R900 - R680)/(R900 + R680)	Rouse et al. (1973)
SR900_680	Simple ratio 900/680	R900/R680	Rouse et al. (1973)
DWSI2	Disease Water Stress Index 2	R1660 / R550	Apan, Held, Phinn and Markley (2003)
TCARI	Transformed Chlorophyll Absorption Ratio	3 ((R700 - R670) - 0.2 (R700 - R550) * (R700/R670))	Haboudane et al. (2002)
DWSI3	Disease Water Stress Index 3	R1660 / R680	Apan, Held, Phinn and Markley (2003)
DWSI4	Disease Water Stress Index 4	R550 / R680	Apan, Held, Phinn and Markley (2003)
DWSI5	Disease Water Stress Index 5	(R800 + R550) / (R1660 + R680)	Apan, Held, Phinn and Markley (2003)
SR700_670	Simple Ratio 700/670	R700/R670 Part of TCARI index
RDVI	Renormalized Difference Vegetation Index	(R800 - R670)/(R800 + R670)^0.5	Rougean and Breon (1995)
PRI531	Normalized Difference 531/570 Photochemical Reflectance Index 531/570	(R531 - R570)/(R531 + R570)	Gamon et al. (1992)
EVI	Enhanced Vegetation Index	2.5 (R800 - R680) / (R800 + 6.0f R680 - 7.5f * R450 + 1.0f)	Huete et al. (1997)
ARVI	Atmospherically Resistant Vegetation Index	(R800 - (2.0f R680 - R450)) / (R800 + (2.0f R680 - R450))	Kaufman and Tanré (1996)
REIP1	Red-Edge Inflection Point 1	700 + 40 * {[(R670 + R780)/2 - R700] /(R740 - R700)}	Guyot and Baret, 1988
TVI	Triangular Vegetation Index	0.5 (120 (R750 - R550) - 200 * (R670 - R550))	Haboudaneet al. (2004)
GEMI	Global Environmental Monitoring Index	((2 (pow(R800) - pow(R680)) + 1.5 800 + 0.5 680) / (800 + 680 + 0.5) (1.0 - 0.25 (2.0f (pow(800) - pow(680)) + 1.5 800 + 0.5 680) / (800 + 680 + 0.5))) - ((680 - 0.125) / (1.0 - 680))	Pinty and Verstraete (1992)
GARI	Green Atmospherically Resistant Index	(R800 - (R550 - 1.7 (R450 - R680))) / (R800 + (R550 - 1.7 (R450 - R680)))	Gitelson et al. (1996)
DVI	Difference Vegetation Index	R800 - R680	Tucker et al. (1979)
GDVI	Green Difference Vegetation Index	R800 - R550	Sripada et al. (2006)
GNDVI	Green Normalized Difference Vegetation Index	(R800 - R550) / (R800 + R550)	Gitelson and Merzlyak (1998)
GRVI	Green Ratio Vegetation Index	R800 / R550	Sripada et al. (2006)
SR750_710	Simple Ratio 750/710 Zarco-Tejada & Miller 2001	R750/R710	Zarco-Tejada et al. (2001)
MSR705_445	Modified simple ratio 705/445	(R750 - R445)/(R705 - R445)	Sims and Gamon (2002)
WI	Water index	R900 - R970	Penuelas. et al. (1993)
Chl index	Chlorophyll index	R750/R550	Gitelson and Merzlyak (1994)
NDVI705	Normalized Difference 750/705 Chl NDI	(R750 - R705)/(R750 + R705)	Gitelson and Merzlyak (1994)
ChlDela	Chlorophyll content	(R540 - R590)/(R540 + R590)	Delaieux et al. (2014)
FRI2	Fluorescence ratio indices 2	R740/R800	Dobrowski et al. (2005)
NDVI1	Normalized Difference Vegetation Index1	(R800 - R670)/( R800 + R670)	Rouse et al. (1973)
FRI1	Fluorescence ratio index1	R690/R600	Dobrowski et al. (2005)
OSAVI	Optimized Soil Adjusted Vegetation Index	(1 + 0.16) * (R800 - R670)/(R800 + R670 + 0.16)	Rondeaux et al. (1996)
NDRE	Normalized Difference 790/720 Normalized difference red edge index	(R790 - R720)/(R790 + R720)	Barnes et al. (2000)
Car1Black	Carotenoid index from Blackburn 1998	R800/R470	Blackburn (1998)
SIPI	Structure intensive pigment index	(R800 - R450)/(R800 + R650)	Penuelas. et al. (1995)
AntGitelson	Anthocyanin (Gitelson)	(1/R550 - 1/R700) * R780	Gitelson et al.(2003,2006)
Car2Black	Carotenoid index 2 from Blackburn 1998	(R800 - R470)/(R800 + R470)	Blackburn (1998)
PRI586	Photochemical reflectance index from Panigada et al 2014	(R531 - R586)/(R531 + R586)	Panigada et al. (2014)
AntGamon	Anthocyanin from Gamon and Surfus 1999	R650/R550	Gamon and Surfus (1999)
CarChap	Carotenoid index (Chappelle)	R760/R500	Chappelle et al. (1992)
PRI512	Photochemical reflectance index from Hernandez-Clemente et al 2011	(R531- R512)/(R531 + R512)	Hern√°ndez-Clemente et al. (2011)
TCARI_OSAVI	Transformed Chlorophyll Absorption in Reflectance Index/Optimized Soil-Adjusted Vegetation Index: TCARI/OSAVI	TCARI/OSAVI	Haboudane et al. (2002)
IPVI	Infrared Percentage Vegetation Index	R800 / (R800 + R680)	Crippen et al. (1990)
NLI	Non-Linear Index	(pow(R800, 2) - R680) / (pow(R800, 2) + R680)	Goel and Qin (1994)
MNLI	Modified Non-Linear Index	((pow(R800, 2) - R680) * 1.5f) / (pow(R800, 2) + R680 + 0.5f)	Yang et al. (2008)
SAVI	Soil Adjusted Vegetation Index	(1.5f * (R800 - R680)) / (R800 + R680 + 0.5f)	Huete et al. (1988)
TDVI	Transformed Difference Vegetation Index	sqrt(0.5f + ((R800 - R680) / (R800 + R680)))	Bannari et al. (2002)
VARI	Visible Atmospherically Resistant Index	(R550 - R680) / (R550 + R680 - R450)	Gitelson et al. (2002)
RENDVI	Red Edge Normalized Difference Vegetation Index	(R750 - R705) / (R750 + R705)	Gitelson and Merzlyak (1994)
mRESR	Modified Red Edge Simple Ratio Index	(R750 - R445) / (R750 + R445)	Sims and Gamon (2002)
mRENDVI	Modified Red Edge Normalized Difference Vegetation Index	(R750 - R705) / (R750 + R705 - 2.0f * R445)	Sims and Gamon (2002)
VOG1	Vogelmann Red Edge Index 1	R740 / R720	Vogelmann et al. (1993)
VOG2	Vogelmann Red Edge Index 2	(R734 - R747) / (R715 + R726)	Vogelmann et al. (1993)
VOG3	Vogelmann Red Edge Index 3	(R734 - R747) / (R715 + R720)	Vogelmann et al. (1993)
MCARI	Modified Chlorophyll Absorption Reflectance Index	((R700 - R670) - 0.2f (R700 - R550)) (R700 / R670)	Daughtry et al. (2000)
MCARI1	Modified Chlorophyll Absorption Reflectance Index Improved 1	1.2f (2.5f (R790 - R670) - 1.3f * (R790 - R550))	Haboudane et al. (2004)
MCARI2	Modified Chlorophyll Absorption Reflectance Index Improved 2	(1.5f (2.5f (R800 - R670) - 1.3f (R800 - R550))) / sqrt(pow(2.0f R800 + 1.0f, 2) - 6.0f R800 - 5.0f sqrt(R670) - 0.5f)	Haboudane et al. (2004)
MTVI	Modified Triangular Vegetation Index	1.2f (1.2f (R800 - R550) - 2.5f * (R670 - R550))	Haboudane et al. (2004)
MTVI2	Modified Triangular Vegetation Index Improved	1.5f (1.2f (R800 - R550) - 2.5f (R670 - R550)) / sqrt(pow(2.0f R800 + 1.0f ,2) - (6.0f R800 - 5.0f sqrt(R670)) - 0.5f)	Haboudane et al. (2004)
GMI1	Gitelson and Merzlak Index 1	R750 / R550	Gitelson and Merzlak (1997)
GMI2	Gitelson and Merzlak Index 2	R750 / R700	Gitelson and Merzlak (1997)
Lic1	Lichtenthaler Index 1	(R790 - R680) / (R790 + R680)	Lichtenthaler et al. 1996
Lic2	Lichtenthaler Index 2	R440 / R690	Lichtenthaler et al. 1996
Lic3	Lichtenthaler Index 3	R440 / R740	Lichtenthaler et al. 1996
NDNI	Normalized Difference Nitrogen Index	(log(1.0f / R1510) - log(1.0f / R1680)) / (log(1.0f / R1510) + log(1.0f / R1680))	Fourty et al. (1996)
MSR	Modified Simple Ratio	((R800 / R680) - 1.0f) / (sqrt(R800 / R680) + 1)	Chen et al. (1996)
LAI	Leaf Area Index	3.618f ((2.5.0f (R800 - R680)) / (R800 + 6.0f R680 - 7.5.0f R450 + 1.0f)) - 0.118f	Boegh et al. (2002)
NRI1510	Nitrogen Related Index NRI1510	(R1510 - R660) / (R1510 + R660)	Herrmann et al. (2009)
NRI850	Nitrogen Related Index NRI850	(R850 - R660) / (R850 + R660)	Behrens et al. (2006)
NDLI	Normalized Difference Lignin Index	(log(1.0f / R1754) - log(1.0f / R1680)) / (log(1.0f / R1754) + log(1.0f / R1680))	Melillo et al. (1982)
CAI	Cellulose Absorption Index	(0.5 * (R2000 - R2200)) / R2100	Daughtry et al. (2001)
PSRI	Plant Senescence Reflectance Index	(R680 - R500) / R750	Merzlyak et al. (1999)
CRI1	Carotenoid Reflectance Index 1	1.0f / R510 - 1.0f / R550	Gitelson et al. (2002)
CRI2	Carotenoid Reflectance Index 2	1.0f / R510 - 1.0f / R700	Gitelson et al. (2002)
ARI1	Anthocyanin Reflectance Index 1	1.0f / R550 - 1.0f / R700	Gitelson et al. (2001)
ARI2	Anthocyanin Reflectance Index 2	R800 * ((1.0f / R550) - (1.0f / R700))	Gitelson et al. (2001)
SRPI	Simple Ration Pigment Index	R430 / R680	Penuelas et al. (1995)
NPQI	Normalized Phaeophytinization Index	(R415 - R435) / (R415 + R435)	Barnes et al. (1992)
NPCI	Normalized Pigment Chlorophyll Index	(R680 - R430) / (R680 + R430)	Penuelas et al. (1994)
WBI	Water Band Index	R900 / R970	Penuelas et al. (1995)
NDWI	Normalized Difference Water Index	(R857 - R1241) / ( R700 + R1241)	Gao et al. (1995)
MSI	Moisture Stress Index	R819 / R1599	Hunt and Rock (1989)
NDII	Normalized Difference Infrared Index	(R857 - R1241) / ( R700 + R1241)	Hardisky et al. (1983)
NMDI	Normalized Multiband Drought Index	(R819 - R1649) / (R819 + R1649)	Wang and Qu (2007)
HI	Healthy Index	((R534 - R698) / (R534 + R698)) - (R704 / 2.0f)	Mahlein et al. (2013)
CLSI	Cercospora Leaf Spot Index	((R698 - R570) / (R698 + R570)) - R734	Mahlein et al. (2013)
SBRI	Sugar Beet Rust Index	((R570 - R513) / (R570 + R513)) + (R704 / 2.0f)	Mahlein et al. (2013)
PMI	Powdery Mildew Index	((R520 - R584) / (R520 + R584)) + R724	Mahlein et al. (2013)
Crt1	Carter Index 1	R695 / R420	Carter (1994)
Crt2	Carter Index 2	R695 / R760	Carter (1996)
BIG2	Blue/Green Index	R450 / R550	Zarco-Tejada et al. (2005)
LSI	Leaf Structure Index	R1110 / R810	Maruthi Sridhar et al. (2007)
BRI	Browning Reflectance Index	((1.0f / R550) - (1.0f / R700)) / R800	Chivkunova et al. (2001)
G	Greenness Index	R554 / R677

See also

• Sensor calibration

• Hyperspectral data pipeline

• Geospatial information