Quick start: A user guide

1. Introduction

  • “Tree Ring Analyzer” is a Python module allowing to segment tree rings from 2D stained microscopic cross-sectional tree images.

  • “Napari Tree Rings” is a Napari plugin in case you would need a graphical interface.

  • The segmentation allows user to segment bark, pith, and annual rings of xylem cells.

  • The measures (exported in CSV files by running batch) include:

    • bbox

    • perimeter

    • area

    • area_convex

    • axis_major_length

    • axis_minor_length

    • eccentricity

    • orientation

    • area_growth

  • From the GUI (Napari), a batch mode is available allowing you to run the whole workflow on an entire folder.

_images/overview_noted.png

2. Install the plugin

  • We strongly recommend to use conda or any other virtual environment manager instead of installing Napari and tree-ring-analyzer in your system’s Python.

  • Napari is only required if you want to use tree-ring-analyzer with a graphical interface.

  • Napari is not part of tree-ring-analyzer’s dependencies, so you will have to install it separately.

  • Each of the commands below is supposed to be run after you activated your virtual environment.

  • If the installation is successful, you will see the plugin in Napari in the top bar menu: Plugins > Segment Trunk (Napari Tree Rings).

A. Development versions

Method

Instructions

pip

pip install git+https://github.com/MontpellierRessourcesImagerie/tree-ring-analyzer.git

GitHub

pip install git+https://github.com/MontpellierRessourcesImagerie/tree-ring-analyzer.git.

From an archive

  • Download the archive pyproject.toml.

  • From the terminal containing your virtual env, move to the folder containing the file pyproject.toml.

  • Run the command pip install -e .

B. Stable versions

Method

Instructions

pip

Activate your conda environment, and type pip install tree-ring-analyzer.

NapariHub

Go in the plugins menu of Napari and search for “Napari Tree Rings”

3. Notes

  • The plugin provides detailed output, so it’s recommended to monitor the terminal if you want detailed information about its actions.

  • If a crash occurs, please create an issue and include the relevant image(s) and a copy of your terminal for further investigation.

  • Napari currently supports only open file formats, so make sure to convert your images to TIF format before using them with Napari.

4. Quick start

Features