HyphaTracker: 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

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13 Citations (Scopus)
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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. Brightfield 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.
Original languageEnglish
Article number605
Pages (from-to)1-13
Number of pages13
JournalScientific Reports
Publication statusPublished - 12 Jan 2018


  • bioinformatics
  • cell growth
  • fungal biology
  • microscopy
  • fungal development

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