csmolnar/invasivegrowth

Relative invasiveness value

This repository contains code for imaging based analysis and calculation of relative invasiveness value of invasive growth phenotype in manuscript Compensatory evolution promotes the emergence of morphological novelties by Farkas et al. 2022.

Setting environment

The path to images can be set in setOptions.m.

The code is working with the following folder structure (NOTE: results folder is automatically created by the code):

/<project directory>/ # options.projectDir
    ├── data
    |       ├── <experiment 1> # options.plateName
    |       |       └── <imaging type> # options.imagingType, default is bottom
    |       |              ├── <pre-wash image 1> # options.beforeRegexp
    |       |              ├── <post-wash image 1> # options.afterRegexp
    |       |              ├── <pre-wash image 2>
    |       |              ├── <post-wash image 2>
    |       |              └── ...
    |       ├── <experiment 2> 
    |       |        └── ...
    |       └── ...
    └── results
            ├── <experiment 1> # options.plateName
            |       ├── results_<experiment 1>_<imaging type>.csv
            |       ├── <segmentation result 1>
            |       ├── <segmentation result 2>
            |       └── ...
            |       
            ├── <plate 2> 
            └── ...

Running image analysis

The analysis can be performed for a single plate by running script processPlateMainScript.m. The measured values will be saved under results directory.