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general_elegant_setup.md

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Installing Elegant: tools and pipelines for C. elegans data

Author: Nicolette Laird

Date: 2019-07-16

http://zplab.wustl.edu

1. Install Miniconda

  • Download Miniconda for Python 3. Make sure you download the Python 3.7 installer that best fits your machine.

  • Install miniconda: In your terminal window, run:

    bash Miniconda3-latest-*-x86_64.sh -b -p $HOME/miniconda
rehash
rm Miniconda3-latest-*-x86_64.sh

  • Follow the prompts on the installer screens

  • Close and re-open your terminal window to enable changes

If you need help, look through the Miniconda Documentation

Here is a quick guide to Anaconda, although for basic use you don't need to know any of this.

2. Setup Python Environment

  • Create a new environment with specific packages:

    Install the basic suite of zplab tools into the root miniconda environment.

    In a terminal window, run:

    -NOTE: replace myenv to the environment name you want

    cat > user_env.yml << EOF
dependencies:
    - ipython
    - numpy
    - scipy
    - pip:
        - git+https://github.com/zplab/freeimage-py
        - git+https://github.com/zplab/zplib
        - git+https://github.com/zplab/RisWidget
        - git+https://github.com/zplab/elegant
EOF
pip install --upgrade pip
conda update conda

conda env update -n myenv -f user_env.yml
pip install celiagg --global-option=--no-text-rendering

rm user_env.yml

  • Activate your new environment!

    conda activate myenv

NOTE: if you ever need to update to the latest version of zplab-specific libraries, run lines like the following:

pip install --upgrade git+https://github.com/zplab/freeimage-py

3. Start annotating!

  • Use Elegant to annotate centerlines and straighten images of worms!

    To begin the general pose annotator, open a terminal and run

    general_pose_annotator

    A RisWidget window should appear. You can drag and drop images into the window to begin annotating. If you need a specific pixels per micron or load up specific images via command line use:

      general_pose_annotator `bc -l <<< 'pixels_per_micron'` 'path to image 1' 'path to image 2'

    NOTE: you can add as many images as you want.

You can also access the annotator via ipython. See Elegant Documentation for more help.