Spectral, Thermal, and Physiological Data for Plant Condition Assessment

Access this dataset on Dryad (Dataset DOI: 10.5061/dryad.4qrfj6qr3)

Summary Description

This dataset contains three complementary data types collected from native vegetation in Western Australia between September 2018 and December 2019. The data were acquired to investigate relationships between remotely sensed indicators (spectral reflectance and thermal imagery) and plant physiological traits under seasonal conditions. These data support research in plant ecophysiology, remote sensing calibration, and drought stress assessment.

The dataset includes:

Spectral reflectance measurements from ASD FieldSpec4 (350–2500 nm)

Thermal imagery for stomatal conductance estimation

Physiological measurements (e.g., leaf water potential, relative water content)

All data are anonymized and pertain to plant measurements only; no legal or ethical restrictions apply.

Description of the Data and File Structure

The dataset is provided as a compressed folder:

File: Tracking_plant_condition_Dryad.zip

This folder contains three subdirectories:

1. Physiological_for_dryad

Content: Excel spreadsheets summarizing physiological traits for each sampling campaign.

Variables and Units:

rwc – Relative Water Content (%)

lwc – Leaf Water Content (g g⁻¹)

lwp – Leaf Water Potential (MPa)

ewt – Equivalent Water Thickness (g cm⁻²)

plant - code of the plant sampled. Iincludes species (et (Eucalytpus todtiana)/bm (Banksia menziesii)/jf (Jacksonia floribunda)/hs (Hibbertia subavinata)/ po (Pattersonia occidentalis, as well as sampling round (first number) and replicated number (second round). For example, "et-1-1" is the first replicate sampled in the first round of sampling of a Eucalyptus todtiana plant).

fresh weight - weight (in g) of the leaf in the time of sampling.

full turgor weight - weight (in g) of the leaf after overnight petiole immersion in deionized water.

dry weight - weight (in g) of the leaf after 48 hours of drying at 70 degrees Celsius.

time of lwp - time of leaf water potential measure

stomatal conductance (ab) - stomatal conductance (in mmol water per square centimeter) in the abaxial side of the leaf

stomatal conductance (ad) - stomatal conductance (in mmol water per square centimeter) in the adaxial side of the leaf

total conductance - stomatal conductance (ab) + stomatal conductance (ad)

wind - wind speed (in m/s) right next to the leaf at the time of thermal image

reference T - temperature of a reference plate that was used as a sanity check of thermal images (not used in analysis)

time of thermal - time of thermal image (used to match the plant code with the thermal images in the "thermal_for_dryad" folder).

date - date of sampling

area - area (in square centimeters) of the sampled leaf

fv/fm - maximum quantum efficiency of Photosystem II (PSII) in dark-adapted sampled leaves

pi - measure of plant photosynthetic apparatus vitality and efficiency, which integrates information from several key stages of the photosynthetic energy flow. Provided by the fluorometer together with fv/fm, but not used for analysis.

Additional Information: Each row corresponds to a sampled plant. Columns include plant code, sampling date, and timestamp of associated thermal image.

2. Spectral_for_dryad

Content:

Raw ASD FieldSpec4 output files (.asd.sco) organized by sampling date.

Folder names correspond to the following sampling rounds (which can then be linked to the plant codes): 

  1- Sept2018  

  2- Nov2018

  3- Jan2019

  4- Mar2019 + Mar2019_2

  5- May2019

  6- Aug2019

  7-Oct2019

  8- Dec2019

Description: In each folder (all starting with name "Hanson", which corresponds to a uniformal site name), I stored the reflectance measures from the ASD FieldSpec4 spectroradiometer. Each file contains reflectance values for wavelengths from 350–2500 nm. There are 3 types of files in the "Hanson" folders: the original ASD reflectance files (with no extension, which can be opened and plotted only with ASD software RS3 or ViewSpec Pro), the splice-corrected ASD files (SCO Files, which are a post-processed version of the original ASD files in which small shifts in reflectance values in wavelengths that occur at transition between sensor types have been corrected, with extension asd.sco or *XXX.sco, *which can be opened and plotted only with ASD software RS3 or ViewSpec Pro), and a txt version of this latter file (Text File), which is ultimately what is used for analysis and read in R). If you don't have access to RS3 or ViewSpec Pro, that is not a problem, since the txt files contain exaclty the same data (reflectance value for each wavelength a 1 nm resolution), and you can open them in any text editor (notepad/word), as well as in R, which is what I used for this study and what I recommend if you want to use these data. In some folders, there are also PDF documents where the spectral signature of some of the measures was plotted and shown as an example (some correspond to plant level measures that were not used for the study).

The spectroradiometer takes 5 measures per sample (which need to be averaged). That was done by following the plant order outlined in the csv files provided in the same folder (eg "Sept2018"), named "plant_order" and a date. The date coincides with the folders with the spectral data (for instance, plant_order_18_sept_2018.csv has the plant order of measures that are stored in the folder "Hanson_18-09-18". This responds to the fact that the spectroradiometer interface doesn't allow to store a custom name for each measure (such as a plant code), so that match has to be done a posteriori). In these same folders there are also two types of R files: the R code that was used to create the spectral averages for each plant (R Files) and the output R tables (R Data Files). All analysis was done in R version 3.4.1.

Format: all spectral files in a text format that can be read with many open-source software, such as excel, notepad and R.

Software: all data was processed in R version 3.4.1.

3. Thermal_for_dryad

Content: Thermal images captured for stomatal conductance modeling. Folders in this section are named according to the date in which they were collected. But the most important thing here is to focus on the "Date modified" field for each one of the thermal image files (in IS2 format). This will tell you which sample that picture corresponds to, by matching it with the "date" and "time of thermal" fields in the "Physiological_for_dryad" excel spreadsheets. 

Format and software: all thermal images are in IS2 format and can be opened with the opensource and free software SmartView from the Fluke thermal camera maker (available here https://www.fluke.com/en/support/software-downloads/software-for-fluke-infrared-cameras#smartview-classic).

Missing Data Codes:

NA indicates missing measurements.

Sharing/Access Information

Other publicly accessible locations:

None

Data was derived from the following sources:

Original field measurements (no external sources).

Code/Software

Analysis Environment: R (version 3.4.1)