Please use this identifier to cite or link to this item: http://hdl.handle.net/20.500.11861/10457
Title: Deep learning approach for large-scale, real-time quantification of green fluorescent protein-labeled biological samples in microreactors
Authors: Wei, Yuanyuan 
Abaxi, Sai Mu Dalike 
Dr. NAWAZ Mehmood 
Li, Luoquan 
Qu, Fuyang 
Cheng, Guangyao 
Hu, Dehua 
Ho, Yi-Ping 
Yuan, Scott Wu 
Ho, Ho-Pui 
Issue Date: 2023
Source: Quantitative Biology, 2023, article no. arXiv:2309.01384.
Journal: Quantitative Biology 
Abstract: Absolute quantification of biological samples entails determining expression levels in precise numerical copies, offering enhanced accuracy and superior performance for rare templates. However, existing methodologies suffer from significant limitations: flow cytometers are both costly and intricate, while fluorescence imaging relying on software tools or manual counting is time-consuming and prone to inaccuracies. In this study, we have devised a comprehensive deep-learning-enabled pipeline that enables the automated segmentation and classification of GFP (green fluorescent protein)-labeled microreactors, facilitating real-time absolute quantification. Our findings demonstrate the efficacy of this technique in accurately predicting the sizes and occupancy status of microreactors using standard laboratory fluorescence microscopes, thereby providing precise measurements of template concentrations. Notably, our approach exhibits an analysis speed of quantifying over 2,000 microreactors (across 10 images) within remarkably 2.5 seconds, and a dynamic range spanning from 56.52 to 1569.43 copies per micron-liter. Furthermore, our Deep-dGFP algorithm showcases remarkable generalization capabilities, as it can be directly applied to various GFP-labeling scenarios, including droplet-based, microwell-based, and agarose-based biological applications. To the best of our knowledge, this represents the first successful implementation of an all-in-one image analysis algorithm in droplet digital PCR (polymerase chain reaction), microwell digital PCR, droplet single-cell sequencing, agarose digital PCR, and bacterial quantification, without necessitating any transfer learning steps, modifications, or retraining procedures. We firmly believe that our Deep-dGFP technique will be readily embraced by biomedical laboratories and holds potential for further development in related clinical applications.
Type: Peer Reviewed Journal Article
URI: http://hdl.handle.net/20.500.11861/10457
DOI: https://doi.org/10.48550/arXiv.2309.01384
Appears in Collections:Applied Data Science - Publication

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