Evaluating virtual staining for high-throughput screening

Samuel Tonks; Chih Hsu; Steve Hood; Ryan Musso; Ceriden Hopely; Minh Doan; Erin Edwards; Alexander Krull; Iain Styles

doi:10.1109/ISBI53787.2023.10230501

Evaluating virtual staining for high-throughput screening

Samuel Tonks, Chih Hsu, Steve Hood, Ryan Musso, Ceriden Hopely, Minh Doan, Erin Edwards, Alexander Krull, Iain Styles

Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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Abstract

Little is known about the feasibility of virtual staining for industry applications such as high-throughput screening (HTS). We provide a thorough analysis of the usability of image-to-image translation for the virtual staining of label-free bright-field microscopy images of live cells, using a pool of more than 1.6 million images across six lung, six ovarian and six breast cell lines consisting of paired bright-field, cytoplasm, nuclei and DNA-damage stains. To our knowledge this is the first time an analysis of virtual staining has been performed on three levels; pixel-based, biological-feature based, and determining if virtual staining can reproduce drug-effect. Our results reveal that while virtually stained nuclei and cytoplasm images often consistently and faithfully reproduce the information found in fluorescence microscopy, virtually stained images of DNA-damage are usually less accurate.

Original language	English
Title of host publication	2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)
Publisher	IEEE
Number of pages	5
ISBN (Electronic)	9781665473583
ISBN (Print)	9781665473590 (PoD)
DOIs	https://doi.org/10.1109/ISBI53787.2023.10230501
Publication status	Published - 1 Sept 2023
Event	20th IEEE International Symposium on Biomedical Imaging - Cartagena , Colombia Duration: 18 Apr 2023 → 21 Apr 2023

Publication series

Name	ISBI
Publisher	IEEE
ISSN (Print)	1945-7928
ISSN (Electronic)	1945-8452

Conference

Conference	20th IEEE International Symposium on Biomedical Imaging
Abbreviated title	ISBI 2023
Country/Territory	Colombia
City	Cartagena
Period	18/04/23 → 21/04/23

Bibliographical note

Acknowledgments:
This work was funded by GSK and a studentship from the Engineering and Physical Sciences Research Council (project reference 2457518).

Keywords

High-temperature superconductors
Microscopy
Industry applications
Lung
Fluorescence
Breast
Biology

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10.1109/ISBI53787.2023.10230501

TonksS2023Evaluating
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Cite this

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title = "Evaluating virtual staining for high-throughput screening",

abstract = "Little is known about the feasibility of virtual staining for industry applications such as high-throughput screening (HTS). We provide a thorough analysis of the usability of image-to-image translation for the virtual staining of label-free bright-field microscopy images of live cells, using a pool of more than 1.6 million images across six lung, six ovarian and six breast cell lines consisting of paired bright-field, cytoplasm, nuclei and DNA-damage stains. To our knowledge this is the first time an analysis of virtual staining has been performed on three levels; pixel-based, biological-feature based, and determining if virtual staining can reproduce drug-effect. Our results reveal that while virtually stained nuclei and cytoplasm images often consistently and faithfully reproduce the information found in fluorescence microscopy, virtually stained images of DNA-damage are usually less accurate.",

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author = "Samuel Tonks and Chih Hsu and Steve Hood and Ryan Musso and Ceriden Hopely and Minh Doan and Erin Edwards and Alexander Krull and Iain Styles",

note = "Acknowledgments: This work was funded by GSK and a studentship from the Engineering and Physical Sciences Research Council (project reference 2457518).; 20th IEEE International Symposium on Biomedical Imaging, ISBI 2023 ; Conference date: 18-04-2023 Through 21-04-2023",

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Tonks, S, Hsu, C, Hood, S, Musso, R, Hopely, C, Doan, M, Edwards, E, Krull, A & Styles, I 2023, Evaluating virtual staining for high-throughput screening. in 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)., 10230501, ISBI, IEEE, 20th IEEE International Symposium on Biomedical Imaging, Cartagena , Colombia, 18/04/23. https://doi.org/10.1109/ISBI53787.2023.10230501

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AU - Tonks, Samuel

AU - Hsu, Chih

AU - Hood, Steve

AU - Musso, Ryan

AU - Hopely, Ceriden

AU - Doan, Minh

AU - Edwards, Erin

AU - Krull, Alexander

AU - Styles, Iain

N1 - Acknowledgments: This work was funded by GSK and a studentship from the Engineering and Physical Sciences Research Council (project reference 2457518).

PY - 2023/9/1

Y1 - 2023/9/1

N2 - Little is known about the feasibility of virtual staining for industry applications such as high-throughput screening (HTS). We provide a thorough analysis of the usability of image-to-image translation for the virtual staining of label-free bright-field microscopy images of live cells, using a pool of more than 1.6 million images across six lung, six ovarian and six breast cell lines consisting of paired bright-field, cytoplasm, nuclei and DNA-damage stains. To our knowledge this is the first time an analysis of virtual staining has been performed on three levels; pixel-based, biological-feature based, and determining if virtual staining can reproduce drug-effect. Our results reveal that while virtually stained nuclei and cytoplasm images often consistently and faithfully reproduce the information found in fluorescence microscopy, virtually stained images of DNA-damage are usually less accurate.

AB - Little is known about the feasibility of virtual staining for industry applications such as high-throughput screening (HTS). We provide a thorough analysis of the usability of image-to-image translation for the virtual staining of label-free bright-field microscopy images of live cells, using a pool of more than 1.6 million images across six lung, six ovarian and six breast cell lines consisting of paired bright-field, cytoplasm, nuclei and DNA-damage stains. To our knowledge this is the first time an analysis of virtual staining has been performed on three levels; pixel-based, biological-feature based, and determining if virtual staining can reproduce drug-effect. Our results reveal that while virtually stained nuclei and cytoplasm images often consistently and faithfully reproduce the information found in fluorescence microscopy, virtually stained images of DNA-damage are usually less accurate.

KW - High-temperature superconductors

KW - Microscopy

KW - Industry applications

KW - Lung

KW - Fluorescence

KW - Breast

KW - Biology

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DO - 10.1109/ISBI53787.2023.10230501

M3 - Conference contribution

SN - 9781665473590 (PoD)

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BT - 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)

PB - IEEE

T2 - 20th IEEE International Symposium on Biomedical Imaging

Y2 - 18 April 2023 through 21 April 2023

ER -

Evaluating virtual staining for high-throughput screening

Abstract

Publication series

Conference

Bibliographical note

Keywords

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