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Realtime morphological characterization and sorting of unlabeled viable cells using deep learning

Mahyar Salek, Nianzhen Li, Hou-Pu Chou, Kiran Saini, Andreja Jovic, Kevin B. Jacobs, Chassidy Johnson, Esther J. Lee, Christina Chang, Phuc Nguyen, Jeanette Mei, Krishna P. Pant, Amy Y. Wong-Thai, Quillan F. Smith, Stephanie Huang, Ryan Chow, Janifer Cruz, Jeff Walker, Bryan Chan, Thomas J. Musci, Euan A. Ashley, Maddison (Mahdokht) Masaeli
doi: https://doi.org/10.1101/2022.02.28.482368
Mahyar Salek
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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  • For correspondence: yar@deepcellbio.com
Nianzhen Li
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Hou-Pu Chou
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Kiran Saini
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Andreja Jovic
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Kevin B. Jacobs
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Chassidy Johnson
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Esther J. Lee
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Christina Chang
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Phuc Nguyen
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Jeanette Mei
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Krishna P. Pant
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Amy Y. Wong-Thai
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Quillan F. Smith
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Stephanie Huang
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Ryan Chow
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Janifer Cruz
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Jeff Walker
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Bryan Chan
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Thomas J. Musci
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Euan A. Ashley
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
2Department of Medicine, Genetics, & Biomedical Data Science, Stanford University, Stanford, CA USA
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Maddison (Mahdokht) Masaeli
1Deepcell Inc; 4025 Bohannon Dr., Menlo Park, CA 94025, USA
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Abstract

Although cell morphology is often the gold standard for diagnosis and prognosis of many diseases, and conditions, it has seen limited application in combination with comprehensive molecular and functional characterization. This is largely due to the manual and subjective process of collecting cell morphology information and limited methods for sorting that do not perturb the cells. Here, we introduce the COSMOS platform, which is capable of high-throughput cell imaging and sorting, based on deep learning interpretation of high-content morphology information in realtime, yielding populations of cells that are label-free, viable, and minimally perturbed. We demonstrate the utility of the platform by enriching tumor cells and performing gene expression analysis on sorted cells showing concordance between morphological and molecular assessments.

One sentence summary A novel platform capable of high-throughput imaging and gently sorting cells using deep morphological assessment.

Competing Interest Statement

All authors are current or former employees at or are affiliated with Deepcell Inc.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 01, 2022.
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Realtime morphological characterization and sorting of unlabeled viable cells using deep learning
Mahyar Salek, Nianzhen Li, Hou-Pu Chou, Kiran Saini, Andreja Jovic, Kevin B. Jacobs, Chassidy Johnson, Esther J. Lee, Christina Chang, Phuc Nguyen, Jeanette Mei, Krishna P. Pant, Amy Y. Wong-Thai, Quillan F. Smith, Stephanie Huang, Ryan Chow, Janifer Cruz, Jeff Walker, Bryan Chan, Thomas J. Musci, Euan A. Ashley, Maddison (Mahdokht) Masaeli
bioRxiv 2022.02.28.482368; doi: https://doi.org/10.1101/2022.02.28.482368
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Realtime morphological characterization and sorting of unlabeled viable cells using deep learning
Mahyar Salek, Nianzhen Li, Hou-Pu Chou, Kiran Saini, Andreja Jovic, Kevin B. Jacobs, Chassidy Johnson, Esther J. Lee, Christina Chang, Phuc Nguyen, Jeanette Mei, Krishna P. Pant, Amy Y. Wong-Thai, Quillan F. Smith, Stephanie Huang, Ryan Chow, Janifer Cruz, Jeff Walker, Bryan Chan, Thomas J. Musci, Euan A. Ashley, Maddison (Mahdokht) Masaeli
bioRxiv 2022.02.28.482368; doi: https://doi.org/10.1101/2022.02.28.482368

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