lemna 0.1.0

Toolset for analysis of plant growth in wells.

Lemna

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

Getting Started

Dependencies

• Python 3
• Click
• numpy
• openCV

Following the install process below will add all dependecies (except for Python since it is required for installation and use).

Installing

Clone or download a zip of the repository.

git clone https://github.com/jonathanmsnow/frond-area-cv.git

Navigate to the root directory of the cloned repository. You should see a file called setup.py.

Now you should create and activate a virtual environment for Python.

Once you are in your virtualenv, install the app using pip.

pip install --editable .

Commands

You can use the app by typing analyzer in the terminal. Typing analyzer --help will show available commands.

threshold

This allows you to open an image to determine the HSV upper and lower bound needed to isolate your points of interest in the image (e.g. fronds in wells).

• Usage analyzer threshold -i <path_to_image> -w <width_to_display_image>

process

This allows you to open an image or directory of images to be processed by identifying wells and measuring area in each of those wells.

• Usage analyzer process -i <path_to_image>