Semi-Field Image Processing Pipeline
- Matthew Kutugata
Overview
The Semi-Field Image Processing Pipeline efficiently transforms raw images from our semi-field setups into structured outputs, facilitating plant species identification and morphological analysis. This pipeline automates the data transformation process, enabling high-throughput analysis for plant phenotyping research.
Below is a detailed table that summarizes the Semi-Field Image Processing Pipeline, including the processes, inputs, outputs, and additional columns for tools/software used and key objectives:
Stage | Key Objectives | Processes | Inputs | Outputs | Tools/Software Used |
|---|---|---|---|---|---|
Image Preprocessing | Ensure color consistency and prepare images for analysis | Color calibration, Image conversion | Raw images, Color Calibration Card | Calibrated images (jpg) | RawTherapee |
Potting Area Reconstruction (SfM) | Create a global coordinate reference system for spatial analysis | Orthomosaic creation | Preprocessed images | Metashape project files, camera reference information | Agisoft/Metashape |
Plant Detection | Accurately detect plant locations | individual image detection | Images, YOLOv8 detection model | single class (“plant”) detection results | YOLOv8 |
Remap Plant Detection | Transform bounding box coordinates from pixel representations to real-world global coordinates. | Bounding box coordinate transformation | Images, “plant” detection results | projected bounding box coordinates, external camera parameters | Agisoft/Metashape |
Species Assignment | assign species labels | Species assignment | Shapefiles |
| QGIS and other GIS tools |
Vegetation Segmentation and Cutouts | Extract individual plant regions and classify species | Digital image processing, Semantic & Instance segmentation, Cutout extraction | Annotated images | Semantic masks, Instance masks, Plant cutouts | Image Processing Tools |
Review and Data Compilation | Ensure accuracy and integrity of processed data for analysis | Quality assurance, Error correction, Data aggregation | Processed images, Metadata | Verified image batches, Compiled datasets | Manual Review, Data Management Tools |