The-Daphnia-ruler

Automatically collect morphometric traits of Daphnia.

Overview

The Daphnia ruler is a command line program that can measure morphometric traits of Daphnia from images taken under a microscope. The Daphnia ruler works in both windows and linux and can measure the following traits:

• body size: measured from the center of the eye to the base of the tail (red line in image)
• body size: approximated by fitting an ellipse around the Daphnia body (green line in image)
• tail length (blue line in image)
• tail angle
• body area (area within red outline in image)
• body perimeter (length of red outline in image)
• body width (purple line in image)

Installation

The fastest way to get your system setup is to make sure you've installed python 3 (https://www.python.org/) and clone this repository to your local drive. Once complete use the package manager pip to install the necessary dependencies:

1. Open your command prompt and navigate to the cloned directory
2. Run this command:

pip install -r requirements.txt

Users who wish to install dependencies manually run:

pip install opencv-python
pip install scikit-image
pip install pandas
pip install tqdm

Usage

For detailed information on how to use the Daphnia ruler see Manual.md.

usage: python daphnia_ruler.py [-h] [-p PATH] [-n] [-e] [-s]

optional arguments:
  -h, --help            show this help message and exit
  -p PATH, --path PATH  Path to your input directory. The program is able to
                        loop through subdirectories of the input.
  -n, --noImages        Don't write images with results overplotted.
  -e, --eyeMethod       Implement eye method on top of ellipse method.
  -s, --scaleMM         Scale measurement to mm. For more information see
                        Manual.md.

Author

• Nelson Stevens
• Contact: nelson.stevens92@gmail.com