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| license: cc-by-4.0 | |
| pretty_name: "PGP v2: A Multispecies Plant Phenotyping Dataset with RGB and Multispectral Images" | |
| tags: | |
| - plant-phenotyping | |
| - agriculture | |
| - agronomy | |
| - image-segmentation | |
| - object-detection | |
| - multispectral-imaging | |
| - computer-vision | |
| - remote-sensing | |
| - cold-stress | |
| task_categories: | |
| - image-segmentation | |
| - object-detection | |
| # PGP v2 Dataset — Release Package | |
| Companion dataset for: | |
| *A Data-Driven Image Extraction and Analysis Pipeline for Plant Phenotyping in Controlled Environments* | |
| Fahimeh Orvati Nia, Joshua Peeples, et al. — *The Plant Phenome Journal* | |
| This release contains the Plant Growth and Phenotyping version 2 (PGP v2) dataset collected in the | |
| Texas A&M AgriLife Automated Precision Phenotyping Greenhouse (APPG). PGP v2 expands the earlier | |
| PGP v1 release and includes longitudinal multispectral greenhouse imagery of maize, cotton, rice, | |
| and sorghum, together with processed pseudo-RGB images and annotation products used for | |
| computer-vision and plant-phenotyping analyses. It also includes an independent maize cold-stress | |
| RGB dataset (Case Study 2) used to evaluate the generalizability of the analysis pipeline beyond | |
| the APPG robotic imaging system. | |
| > **Release status:** the `core/` bundle (pseudo-RGB images, segmentation masks, and COCO | |
| > annotations for all four crops) is available now. The `raw_multispectral/` bundle and the | |
| > Case Study 2 (CERCA maize cold-stress) bundle are being added in follow-up updates — see the | |
| > Files table below for per-file status. | |
| See **`DATASET_MANIFEST.csv`** in this folder for the release-level inventory, package sizes, | |
| file counts, filename patterns, examples, and package-specific notes. | |
| ## Dataset at a glance | |
| The manuscript reports the following PGP v2 image collection: | |
| | Crop | Date range | Imaging sessions | Imaging frequency | Number of plants | Frames per plant | Total images | | |
| |---|---|---|---|---|---|---| | |
| | Maize | Dec 2023–Jul 2024 | 40 | 3–4×/week | 271 | 6–15 | 14,448 | | |
| | Cotton | Apr 2024–Jul 2024 | 66 | Daily | 12 | 5–10 | 27,660 | | |
| | Sorghum | Dec 2024–May 2025 | 17 | Weekly | 48 | 13 | 10,608 | | |
| | Rice | May 2024–Aug 2024 | 8 | Weekly | 8 | 10–26 | 1,376 | | |
| Total reported in the manuscript: **54,092 images**. | |
| ## What is in this dataset? | |
| PGP v2 contains repeated plant-imaging sessions collected in a controlled greenhouse. Plants were | |
| imaged on fixed benches using a robotic gantry. During an imaging run, the camera moved through the | |
| greenhouse and captured vertically stacked sequences of overlapping frames from the plant base | |
| toward the canopy apex. | |
| The dataset is intended to support tasks including: | |
| - plant detection and segmentation | |
| - semantic and instance segmentation | |
| - plant-instance tracking across vertically stacked frames | |
| - image stitching / plant mosaic reconstruction | |
| - vegetation-index analysis | |
| - texture analysis | |
| - morphological trait extraction | |
| - longitudinal plant phenotyping | |
| - development and evaluation of computer-vision and deep-learning methods | |
| The full analysis pipeline used in the companion manuscript is available at: | |
| https://github.com/Advanced-Vision-and-Learning-Lab/Plant_Analysis_Tool_Pipeline | |
| Project website: https://advanced-vision-and-learning-lab.github.io/PGP_Website/ | |
| ## Multispectral imaging system | |
| APPG multispectral images were collected using the MSISAGRI1A multispectral camera (Spectral | |
| Devices Inc.). The camera uses a 4-megapixel CMOS sensor and captures four spectral bands | |
| simultaneously: | |
| | Band | Center wavelength | Description in the manuscript | | |
| |---|---|---| | |
| | Yellow / yellow-green | 580 nm | Used as the surrogate visible/green channel in the analysis pipeline | | |
| | Red | 660 nm | Visible red band | | |
| | Red-edge | 735 nm | Red-edge spectral band | | |
| | Near-infrared (NIR) | 820 nm | Near-infrared spectral band | | |
| Each multispectral frame is stored as a 16-bit TIFF image at 512 × 512 pixels with the four | |
| spectral channels. | |
| The imaging system used synchronized LED illumination and AntiXTalk technology to reduce | |
| inter-band leakage. Exposure time and gain were held fixed at 1000 µs and 1.0, respectively, and | |
| LED illumination settings were held constant across imaging sessions. | |
| **Important spectral-data limitation:** the raw multispectral images were not converted to | |
| absolute reflectance. The manuscript states that no dark-reference correction, white-reference | |
| correction, sensor non-uniformity correction, or other radiometric calibration was applied before | |
| analysis. Therefore, spectral measurements in this release should be interpreted as image-derived | |
| spectral intensities, not absolute reflectance measurements. | |
| ## Pseudo-RGB images | |
| For compatibility with standard computer-vision models, the four-band multispectral images were | |
| converted to 8-bit pseudo-RGB composites. Each spectral band was independently min-max normalized | |
| to the 0–255 range and cast to unsigned 8-bit format. The pseudo-RGB composite uses: | |
| - 580 nm yellow/yellow-green band as the surrogate green channel | |
| - 735 nm red-edge band | |
| - 660 nm red band | |
| The 820 nm NIR band was retained separately for vegetation-index and spectral analysis. | |
| This normalization is a processing step for visualization and model compatibility and does not | |
| constitute radiometric or color calibration across imaging sessions. | |
| ## Case Study 2 — CERCA maize cold-stress dataset | |
| This release also includes RGB images from an independent maize cold-stress experiment conducted | |
| at the University of Nebraska–Lincoln CERCA facility, used to evaluate the generalizability of the | |
| analysis pipeline beyond the APPG robotic imaging system. The dataset contains 50 RGB images from | |
| 10 maize genotypes, with one image per genotype under five conditions: before treatment, after | |
| 10 °C treatment, after 4 °C treatment, recovery following 10 °C treatment, and recovery following | |
| 4 °C treatment. Images were acquired using a Canon EOS M10 camera and are provided in | |
| `Maize-CS-2-RGB-1.zip` and `Maize-CS-2-RGB-2.zip`. The companion manuscript uses these images to | |
| evaluate RGB-derived vegetation-index, texture, and morphological features for characterizing | |
| variation associated with cold stress and recovery. | |
| ## Image acquisition and sequence structure | |
| Each plant is represented by a vertical sequence of frames captured at successive robot positions | |
| along the Z-axis. Taller plants require more frames to cover the complete plant profile. | |
| For maize, cotton, and sorghum, the manuscript reports an approximate 50 mm vertical spacing | |
| between consecutive camera positions, with scans beginning near a robot Z-position of 925 mm. The | |
| upper scan position was selected according to crop and canopy height. | |
| Consecutive frames intentionally overlap spatially so that they can be used for: | |
| - plant-instance association | |
| - frame-to-frame matching | |
| - image stitching | |
| - full-plant reconstruction | |
| - trait aggregation across views | |
| A fixed numerical overlap percentage was not recorded in the acquisition metadata. | |
| ## Recorded acquisition metadata | |
| For each image acquisition, the APPG system records metadata including: species, room number, | |
| date, time, image index, row number, plant number, orientation, plant spatial coordinates, and | |
| robot spatial coordinates. These metadata support plant identification, spatial calibration, and | |
| longitudinal tracking. | |
| Treatment and genotype annotations are not uniformly available for every component of PGP v2. | |
| Where available, those annotations are included in the associated metadata. | |
| ## Release files | |
| The release is organized into three logical bundle types. | |
| ### Core bundles | |
| Core bundles contain processed imagery and annotation products intended for most computer-vision | |
| users. | |
| | File | Crop | Contents | Manifest item count | Approx. size | Status | | |
| |---|---|---|---|---|---| | |
| | `core/rice_core.zip` | Rice | pseudo-RGB images + semantic masks + instance masks + COCO annotations | 2,791 | 0.28 GB | ✅ available | | |
| | `core/sorghum_core.zip` | Sorghum | pseudo-RGB images + semantic masks + instance masks + COCO annotations | 17,609 | 3.85 GB | ✅ available | | |
| | `core/maize_core.zip` | Maize | pseudo-RGB images + semantic masks + instance masks + COCO annotations | 19,864 | 5.11 GB | ✅ available | | |
| | `core/cotton_core.zip` | Cotton | pseudo-RGB images + semantic masks + instance masks + COCO annotations | 71,648 | 10.08 GB | ✅ available | | |
| *Important: the core-bundle item count is the number of packaged files/items and should not be | |
| interpreted as the number of unique raw plant images, because each bundle can contain images, | |
| masks, and annotation files.* | |
| ### Raw multispectral bundles | |
| Raw multispectral bundles contain the original four-band 16-bit TIFF frames. | |
| | File | Crop | Contents | Raw frame count in release manifest | Approx. size | Status | | |
| |---|---|---|---|---|---| | |
| | `raw_multispectral/rice_multispectral.zip` | Rice | 4-band 16-bit TIFF frames | 1,376 | 1.31 GB | ✅ available | | |
| | `raw_multispectral/sorghum_multispectral.zip` | Sorghum | 4-band 16-bit TIFF frames | 10,607 | 10.40 GB | ✅ available | | |
| | `raw_multispectral/maize_multispectral.zip` | Maize | 4-band 16-bit TIFF frames | 14,448 | 16.22 GB | ✅ available | | |
| | `raw_multispectral/cotton_multispectral.zip` | Cotton | 4-band 16-bit TIFF frames | 27,660 | 31.62 GB | ✅ available | | |
| ### Case Study 2 bundle | |
| | File | Crop | Contents | Item count | Status | | |
| |---|---|---|---|---| | |
| | `case_study_2/Maize-CS-2-RGB-1.zip` | Maize (CERCA cold-stress) | RGB images, Canon EOS M10 | part of 50 total | ✅ available | | |
| | `case_study_2/Maize-CS-2-RGB-2.zip` | Maize (CERCA cold-stress) | RGB images, Canon EOS M10 | part of 50 total | ✅ available | | |
| **Core bundles total: 19.29 GB** | **Raw multispectral total: 59.55 GB** | | |
| **Grand total (core + raw multispectral): 78.83 GB** | **Case Study 2: to be added** | |
| ## Which files do I need? | |
| For most computer-vision and segmentation work, download the `core/` bundle for the crop(s) of | |
| interest. Use the `raw_multispectral/` bundle when you need the original four-band 16-bit TIFF | |
| data for spectral analysis, vegetation-index development, alternative pseudo-color construction, | |
| custom normalization or preprocessing, or methods that operate directly on multispectral channels. | |
| If you need both processed products and the original spectral data, download both the core and raw | |
| multispectral bundles for that crop. Use the `case_study_2/` bundle if you are evaluating | |
| pipeline generalizability on an independent RGB dataset with a cold-stress treatment design. | |
| ## Filename conventions | |
| Filename patterns differ slightly across crops. | |
| **Rice core:** `crop-date-plantN-frameN.ext` | |
| Example: `rice-2024-05-29-plant1-frame1.png` | |
| **Sorghum core and raw multispectral:** `crop-date-plantN-frameN.ext` | |
| Examples: `sorghum-2024-12-04-plant10-frame1.png`, `sorghum-2024-12-04-plant10-frame1.tif` | |
| **Maize and cotton:** `crop-date-rowN-cameraN-frameN.ext` | |
| Examples: `maize-2024-06-24-row1-camera2-frame21.png`, `maize-2024-06-24-row1-camera2-frame21.tif`, | |
| `cotton-2024-06-24-row1-camera2-frame21.png`, `cotton-2024-06-24-row1-camera2-frame21.tif` | |
| **Rice raw multispectral:** `crop-date-cameraN-plantN-frameN.ext` | |
| Example: `rice-2024-05-29-camera1-plant1-frame1.tif` | |
| ## Data organization and intended reuse | |
| PGP v2 was designed to support longitudinal and multi-crop controlled-environment phenotyping. | |
| Data are organized around crop identity, imaging date, plant identity, and frame position. | |
| Potential reuse includes: benchmarking plant segmentation algorithms, training segmentation and | |
| detection models, testing instance-tracking methods, evaluating image-stitching algorithms, | |
| extracting plant morphology and canopy traits, computing vegetation indices, studying spectral and | |
| texture features, developing self-supervised learning methods, and longitudinal analysis of plant | |
| growth and stress. | |
| The manuscript reports that the full processing framework generated 863 quantitative features per | |
| plant and imaging date, spanning vegetation indices, spectral statistics, texture descriptors, and | |
| morphological traits. These derived features are products of the companion analysis pipeline | |
| rather than a definition of every file included in the release package. | |
| ## Hosting plan | |
| - **Hugging Face Hub** (`fahimehorvatinia/PGP_v2`) — primary host, for the citable DOI and for | |
| practical browsing / `load_dataset(...)` access; handles the full file/byte counts comfortably. | |
| - Link the permanent host from the existing project site: | |
| https://advanced-vision-and-learning-lab.github.io/PGP_Website/ | |
| ## Related resources | |
| - Project website: https://advanced-vision-and-learning-lab.github.io/PGP_Website/ | |
| - Analysis pipeline: https://github.com/Advanced-Vision-and-Learning-Lab/Plant_Analysis_Tool_Pipeline | |
| ## Citation | |
| Please cite the companion article when using this dataset: | |
| Orvati Nia, F., Peeples, J., et al. *A Data-Driven Image Extraction and Analysis Pipeline for | |
| Plant Phenotyping in Controlled Environments.* The Plant Phenome Journal. | |
| Pipeline code: https://github.com/Advanced-Vision-and-Learning-Lab/Plant_Analysis_Tool_Pipeline | |