Quantitative Analyses Using Video Bioinformatics and Image Analysis Tools During Growth and Development in the Multicellular Fungus Neurospora crassa

  • Ilva E. Cabrera
  • Asongu L. Tambo
  • Alberto C. Cruz
  • Benjamin X. Guan
  • Bir Bhanu
  • Katherine A. BorkovichEmail author
Part of the Computational Biology book series (COBO, volume 22)


Neurospora crassa (Neurospora) is a nonpathogenic multicellular fungus. Neurospora has many attributes that make it an ideal model organism for cell biology and genetic studies, including a sequenced genome, a predominantly haploid life cycle and the availability of knock-out mutants for the ~10,000 genes. Neurospora grows by polar extension of tube-like structures called hyphae. Neurospora has a complex life cycle, with two asexual sporulation pathways and a sexual cycle that produces meiotic progeny. This study analyzes stages during the formation of a colony, from asexual spore to mature hyphae with the use of video bioinformatics and image analysis tools. We are the first to analyze the asexual spore size, hyphal compartment size and hyphal growth rate in an automated manner, using video and image analysis algorithms. Quantitative results were obtained for all three phenotypic assays. This novel approach employs phenotypic parameters that can be utilized for streamlined analysis of thousands of mutants. This software, to be made publicly available in the future, eliminates subjectivity, and allows high-throughput analysis in a time saving manner.


Filamentous Fungus Human Visual System Neurospora Crassa Phase Objective Pavement Cell 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank Jhon Gonzalez for his insightful conversations and comments on this work. We also thank Alexander Carrillo and Caleb Hubbard for assistance in determining the optimal conditions for capture of microscopic images. I.E.C., A.L.T, A.C.C., and B.X.G. were supported by NSF IGERT Video Bioinformatics Grant DGE 0903667.

Supplementary material

Supplementary material 1 (AVI 44120 kb)


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Ilva E. Cabrera
    • 1
  • Asongu L. Tambo
    • 2
  • Alberto C. Cruz
    • 2
  • Benjamin X. Guan
    • 2
  • Bir Bhanu
    • 2
  • Katherine A. Borkovich
    • 1
    Email author
  1. 1.Department of Plant Pathology and MicrobiologyUniversity of CaliforniaRiversideUSA
  2. 2.Center for Research in Intelligent SystemsUniversity of CaliforniaRiversideUSA

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