ariadne-roots 0.0.1a3

Ariadne root tracing GUI and trait calculator.

Ariadne

🌱 is a small software package for analyzing images of Arabidopsis thaliana roots.

📷 It features a GUI for semi-automated image segmentation

⏰ with support for time-series GIFs

☠️ that creates dynamic 2D skeleton graphs of the root system architecture (RSA).

🔍 It's designed specifically to handle complex, messy, and highly-branched root systems well — the same situations in which current methods fail.

📊 It also includes some (very cool) algorithms for analyzing those skeletons, which were mostly developed by other (very cool) people^1,2. The focus is on measuring cost-performance trade-offs and Pareto optimality in RSA networks.

⚠️ This is very much a work-in-progress! These are custom scripts written for a small, ongoing research project — so all code is provided as-is.

🔨 That said, if you're interested in tinkering with the code, enjoy! PRs are always welcome. And please reach out with any comments, ideas, suggestions, or feedback.

Installation

Ariadne is installed as a Python package called ariadne-roots. We recommend using a package manager and creating an isolated environment for ariadne-roots and its dependencies. Our recommended package manager is Mamba. Follow the instructions to install Miniforge3.

You can find the latest version of ariadne-roots on the Releases page.

Step-by-Step Installation

1. Create an isolated environment:

   mamba create --name ariadne python=3.11
   

2. Activate your environment:

   mamba activate ariadne
   

3. Install ariadne-roots using pip:

   pip install ariadne-roots
   

Usage

1. Activate your environment:

   mamba activate ariadne
   

2. Open the GUI:

   ariadne-trace
   

Trace with Ariadne

1. Click on “Trace” to trace roots.

2. The following window should open:

   

3. Click on “Import image file” and select the image to trace the roots.

4. Trace the first root:

   • Start tracing the entire primary root first (it should appear green).
   • To save time, place a dot on each region where a lateral root is emitted.

5. Save the traced root:

   • When the first root is fully traced, click on the “Save” button on the left-hand menu of Ariadne or press “g” on your keyboard.
   • A new window will pop up asking for the plant ID. For the first plant, enter “A”.
     • Each time you click on “Save”, a .json file will be saved in the folder at the location of Location_1 (see above).

6. Trace additional roots:

   • When you are done tracing the first root, click on the “Change root” button on the left-hand menu of Ariadne.
   • Select a new plant ID, like “B”, to trace the second root.
   • Continue tracing each root on your image following these steps.

7. Finish tracing:

   • When you have traced all roots on your image, click on “Change root” and repeat from “Step 3” above for any new images.

Analyze with Ariadne

1. Organize your files:

   • Gather all the .json files stored in “location_1” into a new folder named “OUTPUT_JSON” (referred to as “location_2” later on).
   • Create a folder named “RESULTS” (referred to as “location_3”).
   • Create a new folder named “Output”.

2. Prepare for analysis:

   • Close Ariadne but keep the terminal open.
   • Follow the instructions in step 2 above to set up the terminal.

3. Run the analysis:

   • Click on “Analyze” in Ariadne.
   
   • Select the .json files to analyze from “location_2”.
   • Then select “location_3” for the output.
   • The software will analyze all the selected .json files.

Results

• In the “location_3” folder, you will find:
  • A graph for each root showing the Pareto optimality.
  • A .csv file storing all the RSA traits for each root.

The RSA traits included in the CSV are

• Material cost: Total root length
• Wiring cost: Sum of the length from the hypocotyl to each root tip (Pareto related trait)
• Alpha: Trade-off value between growth and transport efficiency (Pareto related trait)
• Scaling distance from the front: Pareto optimality value (Pareto related trait)
• Material cost (random): Random total root length
• Wiring cost (random): Random sum of the length from the hypocotyl to each root tip (Pareto related trait)
• Alpha (random): Random trade-off value between growth and transport efficiency (Pareto related trait)
• Scaling distance from the front (random): Random Pareto optimality value (Pareto related trait)
• Mean LR lengths: Average length of all lateral roots
• Median LR lengths: Median length of all lateral roots
• Mean LR angles: Average lateral root set point angles
• Median LR angles: Median lateral root set point angles
• Mean LR minimal distances: Average Euclidean distance between each lateral root tip and its insertion on the primary root for all lateral roots
• Median LR minimal distances: Median Euclidean distance between each lateral root tip and its insertion on the primary root for all lateral roots
• Sum LR minimal distances: Sum of the Euclidean distances between each lateral root tip and its insertion on the primary root for all lateral roots
• PR minimal length: Euclidean distance from the hypocotyl to the primary root tip
• PR length: Length of the primary root
• LR count: Number of lateral roots
• LR lengths: Length of each individual lateral root
• LR angles: Lateral root set point angle of each individual lateral root
• LR minimal distance: Euclidean distance between each lateral root tip and its insertion on the primary root for each lateral root
• LR density: Number of lateral roots divided by primary root length, multiplied by 100
• Total minimal distance: Sum of LR minimal distances plus PR minimal length
• Material/Total Distance Ratio: Total root length divided by total minimal distance

Keybinds

• Left-click: place/select node. To pan, hold Alt or Ctrl and drag
• t: toggle skeleton visibility (default: on)
• e: next frame (GIFs only)
• q: previous frame (GIFs only)
• r: toggle proximity override. By default, clicking on or near an existing node will select it. When this override is on, a new node will be placed instead. Useful for finer control in crowded areas (default: off)
• i: toggle insertion mode. By default, new nodes extend a branch (i.e., have a degree of 1). Alternatively, use insertion mode to intercalate a new node between 2 existing ones. Useful for handling emering lateral roots in regions you have already segmented (default: off)
• g: Save output file
• d: Delete currently selected node(s)
• c: Erase the current tree and ask for a new plant ID
• Ctrl-Z: Undo last action

Contributing

Follow these steps to set up your development environment and start making contributions to the project.

1. Navigate to the desired directory: Change directories to where you would like the repository to be downloaded:

   cd /path/on/computer/for/repos
   

2. Clone the repository:

   git clone https://github.com/Salk-Harnessing-Plants-Initiative/Ariadne.git
   

3. Navigate to the root of the cloned repository:

   cd Ariadne
   

4. Create a development environment: This will install the necessary dependencies and the ariadne-roots package in editable mode:

   mamba env create -f environment.yaml
   

5. Activate the development environment:

   mamba activate ariadne_dev
   

6. Create a branch for your changes: Before making any changes, create a new branch:

   git checkout -b your-branch-name
   

Contributors

• Kian Faizi
• Matt Platre
• Elizabeth Berrigan

Contact

For any questions or further information, please contact:

• Matt Platre: [e-mail]

References

1. Chandrasekhar, Arjun, and Navlakha, Saket. "Neural arbors are Pareto optimal." Proceedings of the Royal Society B 286.1902 (2019): 20182727. https://doi.org/10.1098/rspb.2018.2727 ↩

2. Conn, Adam, et al. "High-resolution laser scanning reveals plant architectures that reflect universal network design principles." Cell Systems 5.1 (2017): 53-62. https://doi.org/10.1016/j.cels.2017.06.017 ↩