HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi

Researchers from the Department of Biotechnology and Biophysics, Julius-Maximilian University Würzburg, Biocenter (Germany) described an implementation for the open source ImageJ for the analysis of Fusarium fujikuroi conidial germination.

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  • HyphaTracker: an implementation for the open source software ImageJ for computer-assisted, time-resolved analysis of fungal area extension
  • Designed for the analysis of germinating fungal spores
  • Semi-automatic image processing of multiple germlimgs per field of view



Conidial or sexual spores are the essential elements of fungal life cycle and their germination is the starting point of fungal development. Fungal spore germination is highly regulated by environmental conditions and a deeper knowledge of this process represents an import tool to develop strategies to reduce fungal contaminations and/or to optimize fungal growth in bioprocessing. Microscopic analysis is actually the most convenient method for a qualitative analysis of germination dynamics but manual evaluation is time-consuming. The availability of an automated or semi-automated image analysis of the early hyphal development of multiple germlings in parallel is of great utility to acquire information in the dynamics of the spore germination.

In the present work Researchers from the Department of Biotechnology and Biophysics, Julius-Maximilian University Würzburg (Germany) analysed the germination profile of the conidia of rhodopsin-deficient Fusarium fujikuroi strains in comparison to their reference strains by using HyphaTracker, an implementation of the open source ImageJ, here designed for the analysis of germinating fungal spores. This toolbox allows for semi-automatic image processing of multiple germlings per field of view - 20–100 conidia at the same time - while using a low magnification. It is designed to adapt the raw images for data analysis and to report the area of every germling at each time point, while omitting crossing hyphae and other objects from the data analysis. HyphaTracker toolbox can be applied to the analysis of mutant strains where physiologically relevant proteins are knocked down. This dynamic analysis of early germination under varying treatments and conditions might provide novel information on the physiological response of fungi, potentially of help for the development of new antifungal agents.


The dynamics of early fungal development and its interference with physiological signals and environmental factors is yet poorly understood. Especially computational analysis tools for the evaluation of the process of early spore germination and germ tube formation are still lacking. For the time-resolved analysis of conidia germination of the filamentous ascomycete Fusarium fujikuroi we developed a straightforward toolbox implemented in ImageJ. It allows for processing of microscopic acquisitions (movies) of conidial germination starting with drift correction and data reduction prior to germling analysis. From the image time series germling related region of interests (ROIs) are extracted, which are analysed for their area, circularity, and timing. ROIs originating from germlings crossing other hyphae or the image boundaries are omitted during analysis. Each conidium/hypha is identified and related to its origin, thus allowing subsequent categorization. The efficiency of HyphaTracker was proofed and the accuracy was tested on simulated germlings at different signal-to-noise ratios. Bright-field microscopic images of conidial germination of rhodopsin-deficient F. fujikuroi mutants and their respective control strains were analysed with HyphaTracker. Consistent with our observation in earlier studies the CarO deficient mutant germinated earlier and grew faster than other, CarO expressing strains.



SCIENTIFIC REPORTS 8: 605 (2018) doi:10.1038/s41598-017-19103-1HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi. Michael Brunk, Sebastian Sputh, Sören Doose, Sebastian van de Linde, Ulrich Terpitz

Sabrina Sarrocco

PhD in Plant Pathology, University of Pisa

Plant pathologist, mycologist. Biocontrol of plant diseases by beneficial fungi. Fungal genome editing. Under the spell of fungi! @SarroccoSabrina