Classification of fungal genera from microscopic images using artificial intelligence

Md Arafatur Rahman, Madelyn Clinch, Jordan Reynolds, Bryan Dangott, Diana M. Meza Villegas, Aziza Nassar, D. Jane Hata, Zeynettin Akkus

Research output: Contribution to journalArticlepeer-review


Microscopic image examination is fundamental to clinical microbiology and often used as the first step to diagnose fungal infections. In this study, we present classification of pathogenic fungi from microscopic images using deep convolutional neural networks (CNN). We trained well-known CNN architectures such as DenseNet, Inception ResNet, InceptionV3, Xception, ResNet50, VGG16, and VGG19 to identify fungal species, and compared their performances. We collected 1079 images of 89 fungi genera and split our data into training, validation, and test datasets by 7:1:2 ratio. The DenseNet CNN model provided the best performance among other CNN architectures with overall accuracy of 65.35% for top 1 prediction and 75.19% accuracy for top 3 predictions for classification of 89 genera. The performance is further improved (>80%) after excluding rare genera with low sample occurrence and applying data augmentation techniques. For some particular fungal genera, we obtained 100% prediction accuracy. In summary, we present a deep learning approach that shows promising results in prediction of filamentous fungi identification from culture, which could be used to enhance diagnostic accuracy and decrease turnaround time to identification.

Original languageEnglish (US)
Article number100314
JournalJournal of Pathology Informatics
StatePublished - Jan 2023


  • Artificial intelligence
  • Convolutional neural network
  • Fungal genera classification
  • Mycology

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Health Informatics
  • Computer Science Applications


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