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The Duckbot: A system for automated imaging and manipulation of duckweed

This repository hosts files to build and operate a Duckbot, aka a Jubilee outfitted for use by plant biologists.

For more details on buidling a Jubilee for lab automation, check out our science_jubilee repository and its documentation!

Quickstart Info

Installation

  • Clone this repositository recursively: git clone --recursive https://github.com/machineagency/duckbot.git
    • Note that the --recursive flag is necessary as this repository relies on science_jubilee
  • We recommend using python virtual environments to handle dependencies. To do this:
    • Move into the new directory: cd duckbot
    • Create a virtual environment named .venv: python3 -m venv .venv
    • Activate the virtual environment: source .venv/bin/activate
    • You should now see (.venv) to the left of your command line prompt! (If you wish to leave the virtual environment, type deactivate from any directory)
  • Make sure you're using the latest version of pip: python3 -m pip install --upgrade pip
  • Install the science_jubilee package: python3 -m pip install -e ./science_jubilee
  • Additional requirements have been separated out into two files to avoid installation issues:
    • First install required packages with python3 -m pip install -r requirements.txt
    • Then install additional packages without their dependencies: python3 -m pip install --no-deps -r requirements-no-dep.txt
  • Installation complete! You can launch your Jupyter environment as usual, e.g. jupyter lab

Software

The core of the software is a python interface for the Jubilee, intended to be used in Jupyter notebooks to design and run experiments. As a case study, we contribute 4 Jupyter notebooks designed to walk you through setting up and running a duckweed growth assay. The folders are organized as follows:

  • experiments: This is where experimental definitions and image data are saved. Take a look at experiments/GrowthAssayCaseStudy to see the raw setup file and all collected images.
  • notebooks: Automated duckweed growth assays are scaffolded across the 4 Jupyter notebooks in this folder. Note that this code is intended to run locally on Jubilee's Raspberry Pi; steps 0 (experimental setup) and 3 (data analysis) can be run without a machine. Auxiliary code (for e.g. calibration and other examples) can be found in the subdirectories.
  • science_jubilee: Our core implementation for operating the machine is found in the science_jubilee repository.

Hardware

This repository is designed to be used with a Jubilee platform set up with tools and bedplate for laboratory automation. You can read about Jubilee generally at the project page. Information about specific tools used on the Duckbot can be found on the Wiki.

Wetware and labware

The basic functionality supported by this software is for liquid handling and imaging using up to 6 standard size microplates.

Troubleshooting

  • If you have issues using the installed packaged in your notebook environment, try adding the python kernel explicitly: python3 -m ipykernel install --user --name=<insert_name_here>, where you should replace <insert_name_here> with any name you'd like. You can then select this kernel in the top-right of you Jupyter notebook.