Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations

View ORCID ProfileSrinivas Niranj Chandrasekaran, View ORCID ProfileBeth A. Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, View ORCID ProfileNasim Jamali, View ORCID ProfileJohn Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, View ORCID ProfileJohn Arevalo, View ORCID ProfileJuan C. Caicedo, View ORCID ProfileDaniel Kuhn, Desiree Hernandez, Jim Berstler, View ORCID ProfileHamdah Shafqat-Abbasi, David Root, Sussane Swalley, View ORCID ProfileShantanu Singh, View ORCID ProfileAnne E. Carpenter
doi: https://doi.org/10.1101/2022.01.05.475090
Srinivas Niranj Chandrasekaran
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Srinivas Niranj Chandrasekaran
Beth A. Cimini
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Beth A. Cimini
Amy Goodale
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lisa Miller
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Maria Kost-Alimova
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nasim Jamali
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nasim Jamali
John Doench
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for John Doench
Briana Fritchman
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adam Skepner
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michelle Melanson
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John Arevalo
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for John Arevalo
Juan C. Caicedo
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Juan C. Caicedo
Daniel Kuhn
2Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Daniel Kuhn
Desiree Hernandez
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jim Berstler
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hamdah Shafqat-Abbasi
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Hamdah Shafqat-Abbasi
David Root
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sussane Swalley
3Biogen, Inc., 125 Broadway Street, Cambridge, MA 02139
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shantanu Singh
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Shantanu Singh
  • For correspondence: anne@broadinstitute.org
Anne E. Carpenter
1Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Anne E. Carpenter
  • For correspondence: anne@broadinstitute.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

We present a new, carefully designed and well-annotated dataset of images and image-based profiles of cells that have been treated with chemical compounds and genetic perturbations. Each gene that is perturbed is a known target of at least two compounds in the dataset. The dataset can thus serve as a benchmark to evaluate methods for predicting similarities between compounds and between genes and compounds, measuring the effect size of a perturbation, and more generally, learning effective representations for measuring cellular state from microscopy images. Advancements in these applications can accelerate the development of new medicines.

Competing Interest Statement

AEC has optional ownership interest in Recursion, a public biotechnology company using image-based profiling for drug discovery. SES is an employee of Dewpoint Therapeutics. Daniel Kuhn is an employee of Merck Healthcare KGaA, Darmstadt, Germany.

Footnotes

  • ↵^ co-senior author

  • https://github.com/jump-cellpainting/2021_Chandrasekaran_submitted

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted January 05, 2022.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
Srinivas Niranj Chandrasekaran, Beth A. Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, John Arevalo, Juan C. Caicedo, Daniel Kuhn, Desiree Hernandez, Jim Berstler, Hamdah Shafqat-Abbasi, David Root, Sussane Swalley, Shantanu Singh, Anne E. Carpenter
bioRxiv 2022.01.05.475090; doi: https://doi.org/10.1101/2022.01.05.475090
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
Srinivas Niranj Chandrasekaran, Beth A. Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, John Arevalo, Juan C. Caicedo, Daniel Kuhn, Desiree Hernandez, Jim Berstler, Hamdah Shafqat-Abbasi, David Root, Sussane Swalley, Shantanu Singh, Anne E. Carpenter
bioRxiv 2022.01.05.475090; doi: https://doi.org/10.1101/2022.01.05.475090

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4384)
  • Biochemistry (9610)
  • Bioengineering (7104)
  • Bioinformatics (24897)
  • Biophysics (12632)
  • Cancer Biology (9974)
  • Cell Biology (14373)
  • Clinical Trials (138)
  • Developmental Biology (7966)
  • Ecology (12126)
  • Epidemiology (2067)
  • Evolutionary Biology (16002)
  • Genetics (10936)
  • Genomics (14756)
  • Immunology (9880)
  • Microbiology (23698)
  • Molecular Biology (9490)
  • Neuroscience (50924)
  • Paleontology (370)
  • Pathology (1541)
  • Pharmacology and Toxicology (2687)
  • Physiology (4023)
  • Plant Biology (8674)
  • Scientific Communication and Education (1511)
  • Synthetic Biology (2402)
  • Systems Biology (6444)
  • Zoology (1346)