Automatic Cell Counting With YOLOv5: A Fluorescence Microscopy Approach

Abstract

Counting cells in a Neubauer chamber on microbiological culture plates is a laborious task that depends on technical experience. As a result, efforts have been made to advance computer vision-based approaches, increasing efficiency and reliability through quantitative analysis of microorganisms and calculation of their characteristics, biomass concentration, and biological activity. However, variability that still persists in these processes poses a challenge that is yet to be overcome. In this work, we propose a solution adopting a YOLOv5 network model for automatic cell recognition and counting in a case study for laboratory cell detection using images from a CytoSMART Exact FL microscope. In this context, a dataset of 21 expert-labeled cell images was created, along with an extra Sperm DetectionV dataset of 1024 images for transfer learning. The dataset was trained using the pre-trained YOLOv5 algorithm with the Sperm DetectionV database. A laboratory test was also performed to confirm result’s viability. Compared to YOLOv4, the current YOLOv5 model had accuracy, precision, recall, and F1 scores of 92%, 84%, 91%, and 87%, respectively. The YOLOv5 algorithm was also used for cell counting and compared to the current segmentation-based U-Net and OpenCV model that has been implemented. In conclusion, the proposed model successfully recognizes and counts the different types of cells present in the laboratory.