Publication

Imputing single-cell protein abundance in multiplex tissue imaging

Authors: Kirchgaessner R, Watson C, Creason A, Keutler K, Goecks J
Journal: Nature Communications  Pubmed: 40404617   DOI: 10.1038/s41467-025-59788-x
Atlas: Oregon Health & Science University (OHSU)

Abstract

Multiplex tissue imaging enables single-cell spatial proteomics and transcriptomics but remains limited by incomplete molecular profiling, tissue loss, and probe failure. Here, we apply machine learning to impute single-cell protein abundance using multiplex tissue imaging data from a breast cancer cohort. We evaluate regularized linear regression, gradient-boosted trees, and deep learning autoencoders, incorporating spatial context to enhance imputation accuracy. Our models achieve mean absolute errors between 0.05-0.3 on a [0,1] scale, closely approximating ground truth values. Using imputed data, we classify single cells as pre- or post-treatment, demonstrating their biological relevance. These findings establish the feasibility of imputing missing protein abundance, highlight the advantages of spatial information, and support machine learning as a powerful tool for improving single-cell tissue imaging.


Data Availability
FilesCDS/SB-CGC (Open Access )Synapse (Open Access )
CyCIF Level 260
CyCIF Level 3018
CyCIF Level 4018
Level
Columns (11/25)
Filename
Atlas Name
Publications
Biospecimen
Assay
Level
Organ
Diagnosis
Data Access
Metadata
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HTAN OHSU
HTA9_3_21
CyCIF
Level 4
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
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HTAN OHSU
HTA9_3_21
CyCIF
Level 4
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
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HTAN OHSU
HTA9_3_21
CyCIF
Level 4
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
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HTAN OHSU
HTA9_3_11
CyCIF
Level 4
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_11
CyCIF
Level 4
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_11
CyCIF
Level 4
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_21
CyCIF
Level 3
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_21
CyCIF
Level 3
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_21
CyCIF
Level 3
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_11
CyCIF
Level 3
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_11
CyCIF
Level 3
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_3_11
CyCIF
Level 3
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
Synapse
BEMS342281.ome.tif
HTAN OHSU
HTA9_3_21
CyCIF
Level 2
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
CDS/SB-CGC (open access)

BEMS342289.ome.tif
HTAN OHSU
HTA9_3_11
CyCIF
Level 2
Lower-outer quadrant of breast
Infiltrating duct carcinoma NOS
CDS/SB-CGC (open access)

HTAN OHSU
HTA9_15_15
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_15
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_15
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_7
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_7
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_7
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_14_14
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_14_14
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_14_14
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
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HTAN OHSU
HTA9_14_6
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_14_6
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_14_6
CyCIF
Level 4
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_15
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_15
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_15
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_7
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_7
CyCIF
Level 3
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Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_15_7
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
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HTAN OHSU
HTA9_14_6
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Level 3
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Infiltrating duct carcinoma NOS
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HTA9_14_6
CyCIF
Level 3
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Infiltrating duct carcinoma NOS
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HTAN OHSU
HTA9_14_6
CyCIF
Level 3
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Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_14_14
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
Synapse
HTAN OHSU
HTA9_14_14
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
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HTAN OHSU
HTA9_14_14
CyCIF
Level 3
Breast NOS
Infiltrating duct carcinoma NOS
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LSP11996.ome.tif
HTAN OHSU
HTA9_15_7
CyCIF
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CDS/SB-CGC (open access)

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CyCIF
Level 2
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Infiltrating duct carcinoma NOS
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HTAN OHSU
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CyCIF
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