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

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:
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
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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

Last modified 1yr ago