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 Tanr√© (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)

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)

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)

Greenness Index

R554 / R677

Summary

Hyperspectral Algorithm and pipeline

Data Access

Raw Data

Level 1 data access

Level 2 data access

Level 3 data access

Hyperspectral Indices

See also