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The-Daphnia-ruler

Automatically collect morphometric traits of Daphnia.

Python build status codecov

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 windows, macOS 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)

The Daphnia ruler can also be used as a python package allowing the user to access more functionality. For more information see tbd.

Installation

The fastest way to get your system setup is to make sure you've installed python 3 and the package installer pip. Then run:

python3 -m pip install -i https://test.pypi.org/simple/ daphruler --extra-index-url https://pypi.org/simple/

Usage

For detailed information on how to use the Daphnia ruler see Manual.md. For quick help on CLI usage run:

python3 -m daphruler -h

usage: python3 -m daphruler [-h] -p PATH [-n] [-e] [-s]

optional arguments:
  -h, --help            show this help message and exit
  -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 README.md

required named arguments:
  -p PATH, --path PATH  Path to your input directory. The program is able to loop through subdirectories of the input.

Contributions

Collaborators are always welcome. Feel free to write pull requests or contact [email protected] for further information.

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