Hyperspectral imaging dataset of potato plants exposed to water-deficient and nematode induced stress

An experiment:

• Experiment Overview:

  • Conducted in a glasshouse at the Agricultural Institute of Slovenia, Ljubljana.
  • Duration: Early April to late June 2021.
  • Environment: Enclosed with controlled day/night illumination, average temperature of 19.8 ± 3.0°C, and relative humidity of 63.2 ± 12.7%.

• Key Milestones:

  • April 2: Planting of potato tubers.
  • April 15: Nematode inoculation.
  • April 26, May 25, and June 25: Evaluations (Evaluation 1, 2, and 3) with coinciding hyperspectral imaging sessions (IS).

• Hyperspectral Imaging Sessions (IS):

  • Conducted at three critical stages:
    • Day 10 (DAI 10): Early nematode infection, no visible symptoms.
    • Day 40 (DAI 40): High metabolic activity phase during nematode lifecycle.
    • Day 70 (DAI 70): Visible symptoms and cyst maturation.

• Experimental Setup:

  • Plant species: Potato (Solanum tuberosum), cultivar Désirée, susceptible to G. pallida and G. rostochiensis.
  • Substrate: Custom mix for balanced water retention and aeration.
    • Composition: MP4 coarse-grain, MP1/G fine-grain quartz sand, kaolin, lightweight expanded clay aggregate (Glinopor), and controlled-release fertilizer (Osmocote® Exact Standard).
  • Standardized growth: Limited to three stems per plant, supported by 1-meter stakes.

• Nematode Inoculation:

  • Inoculation date: 14 days post-planting (April 15).
  • Nematodes: G. pallida Pa3 (Chavornay) and G. rostochiensis Ro1 (Ecosse).
  • Preparation: Eggs and J2 released from cysts using potato root diffusate and rotary plunger.
  • Inoculum levels:
    • Low: 5 eggs + J2 per cm³ substrate.
    • High: 30 eggs + J2 per cm³ substrate.
  • Method: Nematodes introduced into moist substrate at a 10cm depth.

• Water Regimes:

  • Well-watered treatment: Consistent substrate moisture.
  • Water-deficient treatment: Watering halted 3–5 days before assessments or imaging to simulate drought stress.
  • Manual moisture maintenance: Weekly weighing and adjustments to 12-15% moisture (dry substrate weight).

• Experimental Design:

  • Randomized design with 7 replicates per treatment.
  • Total: 70 pots, rotated weekly to minimize positional effects.

• Data Collection:

  • Regular evaluations and hyperspectral imaging ensured comprehensive monitoring of plant responses.
  • Nematode infection effects were differentiated from drought stress.

Nematode extraction, plant physiology and plant morphology:

• Measurements During Experiment:

  • Shoot Height:
    • Measured at each evaluation (10, 40, and 70 days after inoculation, DAI).
  • Leaf Area:
    • Total leaf area measured at the end of the experiment using LI-3100C Area Meter (LI-COR Biosciences, USA).
  • Fresh Plant Weight:
    • Recorded at the end of the experiment.

• Nematode Assessment:

  • Cyst Extraction:
    • Mature G. pallida and G. rostochiensis cysts extracted after DAI 70 using the modified Fenwick can method.
    • Cleaned of plant debris via flotation in absolute ethanol.
  • Cyst Counting:
    • Cysts were aerially dried and counted using ImageJ image recognition software.
  • Reproduction Factor (Rf):
    • Calculated using the formula Rf=PfPiRf = \frac{Pf}{Pi}, where:
      • PfPf: Total number of nematode cysts after the experiment.
      • PiPi: Initial number of cysts in the inoculum.

• Plant Stress Assessment:

  • Conducted at all evaluations (DAI 10, 40, 70).
  • Parameters measured using LI-6400XT Portable Photosynthesis System (LI-COR Biosciences, USA):
    • Photosynthesis rate (Photo).
    • Stomatal conductance (gsw).
    • Effective quantum efficiency of Photosystem II (PhiPS2).
  • Measurement Conditions:
    • Ambient air temperature: 19.2°C – 25.5°C.
    • Air humidity: 54.6% – 78.8%.
    • Reference CO2 concentration: 400 μmol mol⁻¹.
    • Light intensity: 1000 μmol photons m⁻² s⁻¹ from internal LED source.
  • Measurements conducted between 9:30 AM and 1:00 PM.

Hyperspectral imaging:

• Hyperspectral Imaging Setup:

  • Cameras Used:
    • VNIR-1600 (Hyspex, Norsk Elektro Optikk): 400–988 nm, 160 bands, 3.6 nm bandwidth, resolution 2700×1600 px.
    • SWIR-384 (Hyspex, Norsk Elektro Optikk): 950–2500 nm, 288 bands, 5.4 nm bandwidth, resolution 900×384 px.
  • Mounting and Lighting:
    • Cameras positioned 3 meters above plants in a dark room.
    • Lighting provided by calibrated halogen light sources, turned on 15 minutes prior to imaging to reduce thermal drift.
  • Imaging Setup:
    • Each session imaged up to three potato plants.
    • Included a 20% gray calibrated reflectance panel (SphereOptics, Germany) on a black synthetic background (<5% reflectance).
  • Purpose: Monitor differences between infected and non-infected plants across growth stages.

• Pre-processing Workflow:

  1. Radiometric Calibration: Images converted to radiance units (W sr⁻¹m⁻²) using proprietary Hyspex software.
  2. Reflectance Conversion: VNIR and SWIR images normalized using the reference panel.
  3. Image Segmentation: Extracted leaf-area pixels from each image.
  4. Spectral Signature Calculation: Mean spectral signature calculated for VNIR and SWIR pixels.
  5. Channel Removal: Excluded the first and last five spectral channels from both VNIR and SWIR datasets, leaving 428 bands.
  6. Spectral Concatenation: VNIR and SWIR signatures combined into a single spectral signature for each plant.

• Software Used:

  • Steps (2) to (6) conducted using open-source SiaPy software.

• Dataset Overview:

  • Total spectral signatures per session: 70 (one per plant).
  • Number of imaging sessions: 3.
  • Total dataset: 210 spectral signatures.

Files:

📂 data
├── 📁 imaging1
│   ├── 📄labels.csv
│   ├── 📄signatures_swir.csv
│   └── 📄signatures_vnir.csv
├── 📁 imaging2
│   └── 📄 ...
├── 📁 imaging3
│    └── 📄 ...
├──📚measurements.xlsx
└── 📐 bands.json

This directory contains all the data generated and processed during the experiment.

imaging1,  imaging2 and  imaging3

The folders contain data from the hyperspectral imaging session (DAI 10, DAI 40, DAI 70).

•  labels.csv

  • Contains plant identifiers.

•  signatures_swir.csv

  • Spectral signatures in the short-wave infrared (SWIR) range (950–2500 nm).
  • Data includes reflectance values for 288 spectral bands after pre-processing.

• signatures_vnir.csv

  • Spectral signatures in the visible to near-infrared (VNIR) range (400–988 nm).
  • Data includes reflectance values for 160 spectral bands after pre-processing.

measurements.xlsx

• A consolidated spreadsheet with all plant growth, physiological, and nematode reproduction data collected during the experiment.
• Includes:
  • Shoot height measurements at DAI 10, 40, and 70.
  • Leaf area and fresh plant weight at the end of the experiment.
  • Plant stress indicators:
    • Photosynthesis rate (Photo).
    • Stomatal conductance (gsw).
    • Effective quantum efficiency of Photosystem II (PhiPS2).
  • Nematode reproduction factor (Rf) data derived from cyst counts.

bands.json

• A JSON file containing wavelength ranges for VNIR and SWIR bands used in the hyperspectral imaging.