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 pretrained 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.

Keywords

• cell counting
• deep learning
• yolov