This documentation file was generated on 2020-10-19 by Marja Haagsma ------------------- # GENERAL INFORMATION ------------------- 1. Hyperspectral imagery of Pinus strobiformis infected with fungal pathogen 2. Creator Information Name: Marja Haagsma Institution: Oregon State University College, School or Department: Biological and Ecological Engineering Address: 124 SW 26th St, Corvallis, OR 97331, USA Email: haagsmam@oregonstate.edu Name:Gerald F. M. Page Institution: Oregon State University College, School or Department: Department of Forest Ecosystems and Society Address: 3100 SW Jefferson Way, Corvallis, OR 97333, USA Email: pageg83@gmail.com Name:Jeremy S. Johnson Institution 1: USDA Forest Service College, School or Department 1: Dorena Genetic Resource Center Address 1: 34963 Shoreview Dr, Cottage Grove, OR 97424, USA Institution 2: Northern Arizona University College, School or Department 2: School of Forestry Address 2: 200 E Pine Knoll Dr, Flagstaff, AZ 86011, USA Institution 3: Prescott College College, School or Department 3: Department of environmental studies Address 3: 220 Grove Ave, Prescott, AZ 86301, USA Email: jeremy.johnson@prescott.edu 3. Contributor information Name: Christopher Still Institution: Oregon State University College, School or Department: Department of Forest Ecosystems and Society Address: 3100 SW Jefferson Way, Corvallis, OR 97333, USA Email: chris.still@oregonstate.edu Name: Kristen M. Waring Institution: Northern Arizona University College, School or Department: School of Forestry Address: 200 E Pine Knoll Dr, Flagstaff, AZ 86011, USA Email: Kristen.Waring@nau.edu Name: Richard A. Sniezko Institution: USDA Forest Service College, School or Department: Dorena Genetic Resource Center Address: 34963 Shoreview Dr, Cottage Grove, OR 97424, USA Email: richard.sniezko@usda.gov Name: John S. Selker Institution: Oregon State University College, School or Department: Biological and Ecological Engineering Address: 124 SW 26th St, Corvallis, OR 97331, USA Email: John.Selker@oregonstate.edu 3. Contact Information Name: Marja Haagsma Institution: Oregon State University College, School or Department: Biological and Ecological Engineering Address: 124 SW 26th St, Corvallis, OR 97331, USA Email: haagsmam@oregonstate.edu or marja_haagsma@hotmail.com ORCID: Role: ------------------- CONTEXTUAL INFORMATION ------------------- 1. Abstract for the dataset Hyperspectral images were taken from March till October, 2018, of southwestern white pine (Pinus strobiformis), SWWP, seedlings of ten different seed-source families. Half of the seedlings were inoculated with white pine blister rust (Cronartium ribicola). Visual assessments of vigor coincided with hyperspectral data acquisition. 2. Context of the research project that this dataset was collected for. The aim of the experiment was to use hyperspectral data to automaticaly and objectively identify infection and degree of infection in SWWP seedlings. Moreover, we developed and evaluated a feature importance algorithm to identify the most usefull hyperspectral features for classification tasks. 3. Date of data collection: Start: 2018-03-16 End: 2018-10-16 4. Geographic location of data collection: Oregon State University, East Greenhouse, 2801 SW Campus Way, Corvallis, OR 97331, USA 5. Funding sources that supported the collection of the data: National Science Foundation under grant nr. NSF-EAR 1440506 National Science Foundation under grant nr. NSF-DEB 1442456-1442597 National Science Foundation under grant nr. NSF-CCF 1521687 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ 2. Links to publications related to the dataset: Marja Haagsma, Gerald F. M. Page, Jeremy S. Johnson, Christopher Still, Kristen M. Waring, Richard A. Sniezko, John S. Selker. Using hyperspectral imagery to detect an invasive fungal pathogen and symptom severity in Pinus strobiformis seedlings of different genotypes. [in progress] 3. Recommended citation for the data: Haagsma, M.; Page, G.F.M., Johnson, J.S.(2020) Hyperspectral imagery of Pinus strobiformis infected with fungal pathogen (Version 1) [Dataset]. Oregon State University. https://doi.org/10.7267/pn89df234 4. Dataset Digital Object Identifier (DOI) https://doi.org/10.7267/pn89df234 -------------------------- VERSIONING AND PROVENANCE -------------------------- 1. Last modification date 2020-10-01 -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Hyperspectral images were taken using the VNIR Nano-Hyperspec Headwall (Photonics, MA, USA) camera. The camera was placed on a motion control system (hyper-rail). 2. Methods for processing the data: Raw data is converted to radiance using a dark reference and the sensor specific calibration files in SpectralView software (verson 5.5.1. Headwall). Radiance to reflectance conversion was performed using the empirical line method utilizing a 99%-reflectance panel. 3. Instrument- or software-specific information needed to interpret the data: The hypercubes are in ENVI format. This can be opened in for example Matlab (propietary) or Python (open source). --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: HyperCubes\[Date]_SWWP Short description: Hyperspectral image for that Date in ENVI format. It is a flat-binary raster file. B. Filename: HyperCube\[Date]_SWWP.hdr Short description: Header file (ASCII) associated with the hypercube of the same Date. C. Filename: MetaData\Pot_numbering.png Short description: Image with pot number convention. It has the same top view as the hypercubes. D. Filename: MetaData\Treatment_Family.csv Short description: CSV file with treatment and family labels per seedling position. E. Filename: MetaData\Vigor_assessment.csv Short description: CSV file with the experts vigor assessment of inoculated seedlings. 3. Formats ENVI (for hyperspectral images) png (for overview pot position image) csv (for metadata) ----------------------------------------- TABULAR DATA-SPECIFIC INFORMATION FOR: Treatment_Family.csv ----------------------------------------- 1. Number of variables: 3 2. Number of cases/rows: 170 3. Variable List A. Name: Position: Description: Pot position number. See Pot_numbering.png for relative spatial location. B. Name: Innoc. Description: Status of seedlings in terms of inoculation with white pine blister rust 0 = non-inoculated seedlings 1 = inoculated seedling C. Name: Family Description: Family number, Family identifier, Family name, Lat (of origin), Lon (of origin) 1, A, CUM105, 20.37, -104.99 2, B, RAN88, 34.40, -111.00 3, C, COO220, 33.06, -105.64 4, D, BRA08, 32.98, -105.72 5, E, SBI249, 32.41, -110.72 6, F, MUS127, 33.05, -105.65 7, G, PR1166, 27.03, -107.16 8, H, HAN99, 33.65, -109.33 9, I, SPE237, 32.42, -110.74 10, J, FRO142, 33.45, -108.65 ----------------------------------------- TABULAR DATA-SPECIFIC INFORMATION FOR: Vigor_assessment.csv ----------------------------------------- 1. Number of variables: 8 2. Number of cases/rows: 85 3. Variable List A. Name: Position: Description: Pot position number. See Pot_numbering.png for relative spatial location. B. Name: DOY 45 Description: Vigor Assesment at Day of year = 45 in year 2018 C. Name: DOY 89 Description: Vigor Assesment at Day of year = 89 in year 2018 D. Name: DOY 124 Description: Vigor Assesment at Day of year = 124 in year 2018 E. Name: DOY 130 Description: Vigor Assesment at Day of year = 130 in year 2018 F. Name: DOY 145 Description: Vigor Assesment at Day of year = 145 in year 2018 G. Name: DOY 235 Description: Vigor Assesment at Day of year = 235 in year 2018 H. Name: DOY 285 Description: Vigor Assesment at Day of year = 285 in year 2018 B-H. Name: Vigor labels 1 = Vigorous: Vigorous growth 2 = Moderately Vigor: Moderately vigorous growth 3 = Sickly: Sickly 4 = Dead: Dead from white pine blister rust