Rapid and stain-free quantification of viral plaque via lens-free holography and deep learning

Tairan Liu; Yuzhu Li; Hatice Ceylan Koydemir; Yijie Zhang; Ethan Yang; Merve Eryilmaz; Hongda Wang; Jingxi Li; Bijie Bai; Guangdong Ma; Aydogan Ozcan

doi:10.1038/s41551-023-01057-7

Rapid and stain-free quantification of viral plaque via lens-free holography and deep learning

Nat Biomed Eng. 2023 Aug;7(8):1040-1052. doi: 10.1038/s41551-023-01057-7. Epub 2023 Jun 22.

Authors

Tairan Liu^#^{1

2

3}, Yuzhu Li^#^{1

2

3}, Hatice Ceylan Koydemir^{1

4

5}, Yijie Zhang^{1

2

3}, Ethan Yang^{1

6}, Merve Eryilmaz^{1

2}, Hongda Wang^{1

2

3}, Jingxi Li^{1

2

3}, Bijie Bai^{1

2

3}, Guangdong Ma^{1

7}, Aydogan Ozcan^{8

9

10

11}

Affiliations

¹ Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA.
² Bioengineering Department, University of California, Los Angeles, USA.
³ California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA.
⁴ Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.
⁵ Center for Remote Health Technologies and Systems, Texas A&M University, College Station, TX, USA.
⁶ Department of Mathematics, University of California, Los Angeles, CA, USA.
⁷ School of Physics, Xi'an Jiaotong University, Xi'an, China.
⁸ Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA. ozcan@ucla.edu.
⁹ Bioengineering Department, University of California, Los Angeles, USA. ozcan@ucla.edu.
¹⁰ California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA. ozcan@ucla.edu.
¹¹ Department of Surgery, University of California, Los Angeles, CA, USA. ozcan@ucla.edu.

^# Contributed equally.

Abstract

A plaque assay-the gold-standard method for measuring the concentration of replication-competent lytic virions-requires staining and usually more than 48 h of runtime. Here we show that lens-free holographic imaging and deep learning can be combined to expedite and automate the assay. The compact imaging device captures phase information label-free at a rate of approximately 0.32 gigapixels per hour per well, covers an area of about 30 × 30 mm² and a 10-fold larger dynamic range of virus concentration than standard assays, and quantifies the infected area and the number of plaque-forming units. For the vesicular stomatitis virus, the automated plaque assay detected the first cell-lysing events caused by viral replication as early as 5 h after incubation, and in less than 20 h it detected plaque-forming units at rates higher than 90% at 100% specificity. Furthermore, it reduced the incubation time of the herpes simplex virus type 1 by about 48 h and that of the encephalomyocarditis virus by about 20 h. The stain-free assay should be amenable for use in virology research, vaccine development and clinical diagnosis.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Coloring Agents
Deep Learning*
Holography*
Viral Plaque Assay
Virus Replication

Substances

Coloring Agents