lemna 0.1.1

Toolset for analysis of plant growth in wells.

Lemna

A simple app utilizing computer vision which identifies wells and calculates the area for any region that matches the given mask (HSV lower-upper).

Getting Started

Installing

Install via pip (recommended to use a virtual environment):

pip install lemna

Usage

This tool provides several commands via the CLI. You can use the app by typing lemna in the terminal. Typing lemna --help will show available commands.

threshold — Tune HSV Thresholds

Determine optimal HSV thresholds for identifying areas of interest in wells.

lemna threshold -i path/to/image.jpg -w 640 -c config.toml

Options:

• -i, --image: Path to the image file
• -w, --width: Optional display width for thresholding UI
• -c, --config: Path to the config file to update HSV values

process — Analyze Images

Detect wells, analyze plant area, and output CSV + annotated images.

lemna process -i path/to/image_or_folder -o ./output -c config.toml

Options:

• -i, --image: Path to image or folder of images
• -o, --output: Output directory
• -c, --config: Path to config file
• --dp: Inverse accumulator resolution ratio (default: 1)
• --min_dist: Minimum distance between circle centers (default: 270)
• --param1: First Canny param (default: 45)
• --param2: Accumulator threshold (default: 20)
• --min_radius: Minimum circle radius (default: 120)
• --max_radius: Maximum circle radius (default: 145)

If a config file is provided, values are defaulted as list above.

config — Generate Config File

Create a new default configuration TOML file which can be used while processing images.

lemna config -f config.toml