ClearDepth-WRT (ClearDepth Wall Root Tracker)

Purpose and background

Purpose: Segment images and extract traits from segmentation masks for clearpot images with different species (canola and soybean).

Background: To be updated with manuscript

Installation

1. Clone the repository:

   git clone https://github.com/Salk-Harnessing-Plants-Initiative/ClearDepth-WRT.git
   

2. Navigate to the cloned directory:

   cd ClearDepth-WRT
   

Organize the pipeline and your images

Models can be downloaded from Box.

Please make sure to organize the downloaded pipeline, model, and your own images in the following architecture:

ClearDepth-WRT/
├── images/
│   ├── experimental design (e.g., day7, or batchA)/
│   │   ├── image (e.g., E-102_1.PNG)/
├── model/
│   ├── label_class_dict_lr.csv (class color)
│   ├── model name
├── env.yaml (environment file)