DIRT/mu 1.1

A software to automatically extract root hairs from microscopy images, developed by Peter Pietrzyk.

This software is written and tested in:

• Python 3.9.10 (https://www.python.org)

Updates in version 1.1

• Upgraded to Python 3.9.10
• Calculates Root Mean Square for distance and curvature metrics
• Adds min, mean and std for rolling sum density
• Adjust curvature when merging candidates
• Improves normalization of metrics
• Accepts images without root

Installation

1. Clone the repository into your local machine

git clone https://github.com/Computational-Plant-Science/DIRTmu.git

2. Use conda to create the environment from the provided .yml file

conda env create -f dirtmu_environment_python3.yml

Running the sample file

To process the sample image from the command line type (example):

python3 hairyroots.py -i sample/TAKFA3-n3-1_Classes.tiff -o sample/ --id_root 3 --id_roothair 1 --id_background 2 --pixel_size 1.72 -p 

Help

To show a help messeage type:

python hairyroots.py -h

or

python hairyroots.py --help