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Updated: May 6, 2026
Application of Membrane and Cell Wall Selective Fluorescent Dyes for Live-Cell Imaging of Filamentous Fungi
Published on: November 28, 2019
Open-source digital tools for filamentous fungi analysis.
Afonso Mota1, Alessa Schiele2, Isabel Santos de Sousa3
1Instituto de Astrofísica e Ciências do Espaço, Universidade do Porto, CAUP, Rua das Estrelas, PT4150-762 Porto, Portugal; Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal; Departamento de Física e Astronomia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, PT4169-007 Porto, Portugal.
Two new open-source tools, SporeQuant and Orbis v2, automate fungal spore counting and colony measurement. These free, accessible image-analysis solutions enhance reproducibility and efficiency in microbiological research.
Area of Science:
- Microbiology
- Mycology
- Bioinformatics
Background:
- Reproducibility and standardization are crucial in microbiological research.
- Fungal biology research faces challenges in accurate spore counting and colony measurement due to subjective techniques.
- Existing methods are vulnerable to operator expertise and equipment variability.
Purpose of the Study:
- To develop standardized, automated image-analysis tools for fungal research.
- To address the need for accurate and consistent spore quantification and colony area measurement.
- To provide accessible solutions for laboratories with varying resources.
Main Methods:
- Development of two free, open-source image-analysis tools: SporeQuant for spore counting and Orbis v2 for colony area measurement.
- SporeQuant utilizes image thresholding and blob detection for spore identification and concentration calculation.
- Orbis v2 employs thresholding and contour detection for colony segmentation and area calculation.
Main Results:
- SporeQuant and Orbis v2 significantly reduce analysis time (63% and 76%, respectively) compared to manual methods.
- SporeQuant demonstrates high reliability with MAE=0, while Orbis v2 achieves R² > 0.975.
- Both tools reduce user-to-user variability and offer comparable or improved accuracy over existing methods.
Conclusions:
- SporeQuant and Orbis v2 provide accessible, scalable, and reliable solutions for fungal research.
- These tools enable consistent analysis of fungal growth and morphology across diverse laboratory settings.
- Web accessibility on various devices requires no specialized hardware or software, benefiting low-budget and high-throughput labs.
