Gating mass cytometry data by deep learning

Bioinformatics
Huamin LiYuval Kluger

Abstract

Mass cytometry or CyTOF is an emerging technology for high-dimensional multiparameter single cell analysis that overcomes many limitations of fluorescence-based flow cytometry. New methods for analyzing CyTOF data attempt to improve automation, scalability, performance and interpretation of data generated in large studies. Assigning individual cells into discrete groups of cell types (gating) involves time-consuming sequential manual steps, untenable for larger studies. We introduce DeepCyTOF, a standardization approach for gating, based on deep learning techniques. DeepCyTOF requires labeled cells from only a single sample. It is based on domain adaptation principles and is a generalization of previous work that allows us to calibrate between a target distribution and a source distribution in an unsupervised manner. We show that DeepCyTOF is highly concordant (98%) with cell classification obtained by individual manual gating of each sample when applied to a collection of 16 biological replicates of primary immune blood cells, even when measured across several instruments. Further, DeepCyTOF achieves very high accuracy on the semi-automated gating challenge of the FlowCAP-I competition as well as two CyTOF datasets generated f...Continue Reading

References

Jul 29, 2006·Bioinformatics·Karsten M BorgwardtAlex J Smola
May 10, 2011·Science·Christophe Benoist, Nir Hacohen
Feb 22, 2012·Nature Reviews. Immunology·Holden T MaeckerRobert Nussenblatt
Feb 12, 2013·Nature Methods·Nima AghaeepourRichard H Scheuermann
Mar 21, 2013·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Rachel FinckSean C Bendall
Jun 22, 2013·IEEE Transactions on Pattern Analysis and Machine Intelligence·Yoshua BengioPascal Vincent
Jul 24, 2013·Expert Opinion on Investigational Drugs·Gentian Denas, Vittorio Pengo
Jul 24, 2013·Proceedings of the National Academy of Sciences of the United States of America·Arnold HanMark M Davis
Oct 25, 2013·Science Translational Medicine·Amir HorowitzCatherine A Blish
Mar 1, 2014·Medical Image Computing and Computer-assisted Intervention : MICCAI·Dan C CireşanJürgen Schmidhuber
Mar 4, 2014·Nature Medicine·Michael AngeloGarry P Nolan
Mar 4, 2014·Nature Methods·Charlotte GiesenBernd Bodenmiller
Jun 17, 2014·Bioinformatics·Michael K K LeungBrendan J Frey
Jun 22, 2014·Homo : internationale Zeitschrift für die vergleichende Forschung am Menschen·S SchraderJ Irish
Oct 12, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Sangwook KimMinho Lee
Oct 29, 2014·Drug Metabolism and Disposition : the Biological Fate of Chemicals·Kondala R AtkuriHendrik Neubert
Dec 3, 2014·Journal of Immunological Methods·Yi YaoRuth R Montgomery
Dec 3, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Jürgen Schmidhuber
Jan 15, 2015·Vision Research·Wei Ji MaRonald van den Berg
Jul 19, 2015·The Journal of Immunology : Official Journal of the American Association of Immunologists·Cariad Chester, Holden T Maecker
Jul 24, 2015·Science Translational Medicine·Dara M Strauss-AlbeeCatherine A Blish
Aug 19, 2015·Frontiers in Immunology·Chris P VerschoorDawn M E Bowdish
Jun 18, 2016·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Yavin Shaham, Harriet de Wit

Citations

Oct 3, 2018·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Daniel CommengesRodolphe Thiébaut
Mar 13, 2019·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Tamim AbdelaalAhmed Mahfouz
Sep 14, 2019·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Ryan R Brinkman
Nov 7, 2019·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Disi JiPadhraic Smyth
Dec 8, 2019·Nature Communications·Loukia G KaracostaSylvia K Plevritis
Apr 7, 2020·Current Protocols in Cytometry·Caroline E RoeJonathan M Irish
Jun 22, 2019·Scientific Reports·Benjamin SzubertIgnat Drozdov
Jul 1, 2020·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Timothy J KeyesKara L Davis
Jul 29, 2020·Nature Communications·Natalie StanleyNima Aghaeepour
Apr 7, 2019·BMC Systems Biology·Xiaoxin Ye, Joshua W K Ho
May 10, 2019·International Journal of Laboratory Hematology·Sebastiano Montante, Ryan R Brinkman
Oct 22, 2019·European Journal of Immunology·Andrea CossarizzaArturo Zychlinsky
May 16, 2020·Frontiers in Cell and Developmental Biology·Peng LiuLiza Konnikova
Dec 15, 2018·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Florian Mair

Related Concepts

Machine Learning
Blood Cells
Calibration
Cell Separation
Flow Cytometry
Standardization
Reproducibility of Results
Computational Molecular Biology
Single-Cell Analysis
Blood Cells

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Computational Methods for Protein Structures

Computational methods employing machine learning algorithms are powerful tools that can be used to predict the effect of mutations on protein structure. This is important in neurodegenerative disorders, where some mutations can cause the formation of toxic protein aggregations. This feed follows the latests insights into the relationships between mutation and protein structure leading to better understanding of disease.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.

© 2021 Meta ULC. All rights reserved