title: Automated image-based analysis of spatio-temporal fungal dynamics.
abstract: Due to their ability to grow in complex environments, fungi play an important role in most ecosystems and have for that reason been the subject of numerous studies. Some of the main obstacles to the study of fungal growth are the heterogeneity of growth environments and the limited scope of laboratory experiments. Given the increasing availability of image capturing techniques, a new approach lies in image analysis. Most previous image analysis studies involve manual labelling of the fungal network, tracking of individual hyphae, or invasive techniques that do not allow for tracking the evolution of the entire fungal network. In response, this work presents a highly versatile tool combining image analysis and graph theory to monitor fungal growth through time and space for different fungal species and image resolutions. In addition, a new experimental set-up is presented that allows for a functional description of fungal growth dynamics and a quantitative mutual comparison of different growth behaviors. The presented method is completely automated and facilitates the extraction of the most studied fungal growth features such as the total length of the mycelium, the area of the mycelium and the fractal dimension. The compactness of the fungal network can also be monitored over time by computing measures such as the number of tips, the node degree and the number of nodes. Finally, the average growth angle and the internodal length can be extracted to study the morphology of the fungi. In summary, the introduced method offers an updated and broader alternative to classical and narrowly focused approaches, thus opening new avenues of investigation in the field of mycology.
authors.affiliation: KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium. Electronic address: guillermo.vidal@ugent.be.
authors.forename: G
authors.initials: G
authors.lastname: Vidal-Diez de Ulzurrun
authors.affiliation: KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium. Electronic address: jan.baetens@ugent.be.
authors.forename: J M
authors.initials: JM
authors.lastname: Baetens
authors.affiliation: Laboratory of Wood Technology, Department of Forest and Water Management, Ghent University, Coupure links 653, 9000 Gent, Belgium. Electronic address: jan.vandenbulcke@ugent.be.
authors.forename: J
authors.initials: J
authors.lastname: Van den Bulcke
authors.affiliation: Dpto. Automática y Computación, Universidad Publica de Navarra, 31006 Pamplona, Spain; KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium. Electronic address: carlos.lopez@unavarra.es.
authors.forename: C
authors.initials: C
authors.lastname: Lopez-Molina
authors.affiliation: Laboratory of Wood Technology, Department of Forest and Water Management, Ghent University, Coupure links 653, 9000 Gent, Belgium. Electronic address: imke.dewindt@ugent.be.
authors.forename: I
authors.initials: I
authors.lastname: De Windt
authors.affiliation: KERMIT, Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Gent, Belgium. Electronic address: bernard.debaets@ugent.be.
authors.forename: B
authors.initials: B
authors.lastname: De Baets
mesh_terms: D003196:Computer Graphics; D005658:Fungi / Q000166:cytology* / Q000254:growth & development*; D025301:Hyphae / Q000166:cytology / Q000254:growth & development; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008962:Models, Theoretical; D025282:Mycelium / Q000166:cytology; D009172:Mycology / Q000295:instrumentation / Q000379:methods; D010363:Pattern Recognition, Automated / Q000379:methods*
keywords: Automated image analysis; Fungal growth measures; Fungal imagery; Fungal networks; Graph theory; Spatio-temporal fungal dynamics