Fig. 1

Schematic representation of the image analysis workflow. Users initially (i) define the µm/pixel ratio; (ii) specify the required file suffix (e.g., JPEG); (iii) define the input directory containing all required raw images; (iv) specify a desired output directory, and (v) select whether to analyse pellets, dispersed mycelium, or both morphologies. In all instances, definitions of fungal structures into either dispersed/pellet morphologies are based on area (µm²), with a minimal cut-off to remove artefacts that fall below user-specified definitions. If required, default parameters can be used (see main text). All files with the required suffix are analysed in the input directory. Note that the pipeline is compatible with sub-directories, and will calculate raw data files (.csv) for every such folder contained in the input directory. Raw data files contain all pellet/dispersed measurement data (e.g., diameter and aspect ratio) for images contained in the respective sub-directory. Once all images/sub-directories have been analysed, results are generated at the level of input directory (i.e., for every image contained in this folder, irrespective of whether it is divided into a sub-directory). This result file has all parameters for pellet and/or dispersed morphologies extracted into respective .csv files (e.g., diameter, aspect ratio, etc.). Note that, for simplicity, quality control images consisting of the indexed outline of the fungal structure (Fig. 2) are saved in the respective sub-folder of the input directory. Finally, if both pelleted and dispersed morphologies are analysed, the percentage of pelleted morphologies (µm²) is calculated as a function of total fungal area (µm²), thus, giving a measurement of pelleted and dispersed growth in each image. This latter measurement is recorded for all sub-folders in the input directory, and is saved as a single .csv file