Deep Learning for Microfluidic-Assisted Caenorhabditis elegans Multi-Parameter Identification Using YOLOv7

Abstract

The Caenorhabditis elegans (C. elegans) is an ideal model organism for studying human diseases and genetics due to its transparency and suitability for optical imaging. However, manually sorting a large population of C. elegans for experiments is tedious and inefficient. The microfluidic-assisted C. elegans sorting chip is considered a promising platform to address this issue due to its automation and ease of operation. Nevertheless, automated C. elegans sorting with multiple parameters requires efficient identification technology due to the different research demands for worm phenotypes. To improve the efficiency and accuracy of multi-parameter sorting, we developed a deep learning model using You Only Look Once (YOLO)v7 to detect and recognize C. elegans automatically. We used a dataset of 3931 annotated worms in microfluidic chips from various studies. Our model showed higher precision in automated C. elegans identification than YOLOv5 and Faster R-CNN, achieving a mean average precision (mAP) at a 0.5 intersection over a union (mAP@0.5) threshold of 99.56%. Additionally, our model demonstrated good generalization ability, achieving an mAP@0.5 of 94.21% on an external validation set. Our model can efficiently and accurately identify and calculate multiple phenotypes of worms, including size, movement speed, and fluorescence. The multi-parameter identification model can improve sorting efficiency and potentially promote the development of automated and integrated microfluidic platforms.

A PDMS–Agar Hybrid Microfluidic Device for the Investigation of Chemical–Mechanical Associative Learning Behavior of C. elegans

“…Recently, microfluidic chips [ 21 , 22 , 23 ], a powerful technology, have been used to conduct scientific research on nematodes [ 24 , 25 , 26 ]. The main advantages of microfluidic chips for C. elegans research include their size compatibility, gas-permeable and transparent materials, high-throughput manipulation with a single-nematode resolution, and convenient, real-time observation under a microscope.…”