lamm-mit/rhizomorphic-networks-data

Rhizomorphic Networks — Data and Analysis Outputs

This dataset contains the experimental image data, segmentation outputs, and downstream analysis results used for the quantitative analysis of Armillaria gallica rhizomorphic networks.

The directory structure is organised according to the main stages of the analysis pipeline:

Rhizomorphic Networks/
│
├── 01_raw inputs/
│   ├── control/
│   ├── furnace/
│   └── nutrient density/
│
├── 02_segmentation outputs/
│   ├── raw segmentation output/
│   └── corrected segmentation output/
│
└── 03_data analysis outputs/
    ├── figures/
    └── statistical analyses/

01_raw inputs

This folder contains the original experimental image data before segmentation and quantitative image analysis.

The data are separated into the three experimental datasets:

• control/ — images from the control condition of the light-exposure experiment.
• furnace/ — images from the furnace condition of the light-exposure experiment.
• nutrient density/ — images from the nutrient-density experiment.

These files represent the original experimental inputs and should remain unmodified.

02_segmentation outputs

This folder contains the outputs of the image-segmentation pipeline used to identify rhizomorphic growth in the raw images.

raw segmentation output

Contains the initial automatically generated segmentation outputs before manual inspection and correction.

These files are retained to document the direct output of the automated segmentation procedure.

corrected segmentation output

Contains the segmentation outputs after manual inspection and, where necessary, correction of segmentation errors.

The corrected segmentations represent the final segmentation dataset used for downstream quantification and analysis. Where both a raw and corrected segmentation are available for the same image, the corrected version should therefore be used for the final analysis.

03_data analysis outputs

This folder contains the final outputs produced from the processed image data.

figures

Contains figures generated during the quantitative analysis, including visualisations of growth, brightness, network morphology, Gompertz growth models, comparisons between experimental conditions, and image-processing outputs.

statistical analyses

Contains the numerical outputs of the statistical analyses. These include, where applicable, fitted growth-model parameters, statistical tests, multiple-comparison corrections, effect-size estimates, and other summary statistics used in the analysis.

Analysis workflow

The overall workflow represented by this directory is:

Raw experimental images
        ↓
Automatic segmentation
        ↓
Manual inspection and correction
        ↓
Final corrected segmentations
        ↓
Quantification and network analysis
        ↓
Statistical analysis and figure generation

The 01_raw inputs folder therefore contains the original experimental data, the 02_segmentation outputs folder documents the image-processing stage, and the 03_data analysis outputs folder contains the final analytical results.

Associated code

The code used for image processing, segmentation, quantification, and statistical analysis is maintained separately in the Rhizomorphic Networks GitHub repository:

https://github.com/lamm-mit/rhizomorphic-networks

Citation

Please cite this work as:

@article{NaeherBuehler2026Rhizomorph,
  author  = {Naeher, Sarah C. and Buehler, Markus J.},
  title   = {Nutrient Availability Regulates an Exploration-Elaboration Trade-off in Fungal Rhizomorph Networks},
  journal = {bioRxiv},
  year    = {2026},
  note    = {Preprint}
}