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<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml" xmlns:dc="http://purl.org/dc/terms/" xmlns:doi="http://dx.doi.org/" lang="en" xml:lang="en" itemscope itemtype="http://schema.org/Article" class="no-js"> <head prefix="og: http://ogp.me/ns#"> <link rel="stylesheet" href="/resource/css/desktop/metrics.css?79f248ebefa43b7800a14562e5049ab4"/>   <link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Open+Sans:400,400i,600"> <link media="print" rel="stylesheet" type="text/css" href="/resource/css/print.css"/> <script type="text/javascript"> var siteUrlPrefix = "/plosbiology/"; </script> <script src="/resource/js/vendor/modernizr-v2.7.1.js" type="text/javascript"></script> <script src="/resource/js/vendor/detectizr.min.js" type="text/javascript"></script> <link rel="shortcut icon" href="/resource/img/favicon.ico" type="image/x-icon"/> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <link rel="canonical" href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970" /> <meta name="description" content="Author summary The “big-data revolution” has struck biology: it is now common for robots to prepare cell samples and take thousands of microscopy images. Looking at the resulting images by eye would be extremely tedious, not to mention subjective. Thus, many biologists find they need software to analyze images easily and accurately. The third major release of our free open-source software CellProfiler is designed to help biologists working with images, whether a few or thousands. Researchers can download an online example workflow (that is, a “pipeline”) or create their own from scratch. Pipelines are easy to save, reuse, and share, helping improve scientific reproducibility. In this release, we’ve added the capability to find and measure objects in three-dimensional (3D) images. We’ve also made changes to CellProfiler’s underlying code to make it faster to run and easier to install, and we’ve added the ability to process images in the cloud and using neural networks (deep learning). We’ve also added more explanations to CellProfiler’s settings to help new users get started. We hope these changes will make CellProfiler an even better tool for current users and will provide new users better ways to get started doing quantitative image analysis." /> <meta name="citation_abstract" content="CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler’s infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows."> <meta name="keywords" content="Image processing,Image analysis,Computer software,Deep learning,Open source software,Blastocysts,Biologists,Cell staining" /> <meta name="citation_doi" content="10.1371/journal.pbio.2005970"/> <meta name="citation_author" content="Claire McQuin"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Allen Goodman"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Vasiliy Chernyshev"/> <meta name="citation_author_institution" content="Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia"/> <meta name="citation_author_institution" content="Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia"/> <meta name="citation_author" content="Lee Kamentsky"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Beth A. Cimini"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Kyle W. Karhohs"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Minh Doan"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Liya Ding"/> <meta name="citation_author_institution" content="Allen Institute for Cell Science, Seattle, Washington, United States of America"/> <meta name="citation_author" content="Susanne M. Rafelski"/> <meta name="citation_author_institution" content="Allen Institute for Cell Science, Seattle, Washington, United States of America"/> <meta name="citation_author" content="Derek Thirstrup"/> <meta name="citation_author_institution" content="Allen Institute for Cell Science, Seattle, Washington, United States of America"/> <meta name="citation_author" content="Winfried Wiegraebe"/> <meta name="citation_author_institution" content="Allen Institute for Cell Science, Seattle, Washington, United States of America"/> <meta name="citation_author" content="Shantanu Singh"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Tim Becker"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Juan C. Caicedo"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_author" content="Anne E. Carpenter"/> <meta name="citation_author_institution" content="Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America"/> <meta name="citation_title" content="CellProfiler 3.0: Next-generation image processing for biology"/> <meta itemprop="name" content="CellProfiler 3.0: Next-generation image processing for biology"/> <meta name="citation_journal_title" content="PLOS Biology"/> <meta name="citation_journal_abbrev" content="PLOS Biology"/> <meta name="citation_date" content="Jul 3, 2018"/> <meta name="citation_firstpage" content="e2005970"/> <meta name="citation_issue" content="7"/> <meta name="citation_volume" content="16"/> <meta name="citation_issn" content="1545-7885"/> <meta name="citation_publisher" content="Public Library of Science"/> <meta name="citation_pdf_url" content="https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.2005970&type=printable"> <meta name="citation_article_type" content="Methods and Resources"> <meta name="dc.identifier" content="10.1371/journal.pbio.2005970" /> <meta name="twitter:card" content="summary" /> <meta name="twitter:site" content="plosbiology"/> <meta name="twitter:title" content="CellProfiler 3.0: Next-generation image processing for biology" /> <meta property="twitter:description" content="Author summary The “big-data revolution” has struck biology: it is now common for robots to prepare cell samples and take thousands of microscopy images. Looking at the resulting images by eye would be extremely tedious, not to mention subjective. Thus, many biologists find they need software to analyze images easily and accurately. The third major release of our free open-source software CellProfiler is designed to help biologists working with images, whether a few or thousands. Researchers can download an online example workflow (that is, a “pipeline”) or create their own from scratch. Pipelines are easy to save, reuse, and share, helping improve scientific reproducibility. In this release, we’ve added the capability to find and measure objects in three-dimensional (3D) images. We’ve also made changes to CellProfiler’s underlying code to make it faster to run and easier to install, and we’ve added the ability to process images in the cloud and using neural networks (deep learning). We’ve also added more explanations to CellProfiler’s settings to help new users get started. We hope these changes will make CellProfiler an even better tool for current users and will provide new users better ways to get started doing quantitative image analysis." /> <meta property="twitter:image" content="https://journals.plos.org/plosbiology/article/figure/image?id=10.1371/journal.pbio.2005970.g004&size=inline" /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970"/> <meta property="og:title" content="CellProfiler 3.0: Next-generation image processing for biology"/> <meta property="og:description" content="Author summary The “big-data revolution” has struck biology: it is now common for robots to prepare cell samples and take thousands of microscopy images. Looking at the resulting images by eye would be extremely tedious, not to mention subjective. Thus, many biologists find they need software to analyze images easily and accurately. The third major release of our free open-source software CellProfiler is designed to help biologists working with images, whether a few or thousands. Researchers can download an online example workflow (that is, a “pipeline”) or create their own from scratch. Pipelines are easy to save, reuse, and share, helping improve scientific reproducibility. In this release, we’ve added the capability to find and measure objects in three-dimensional (3D) images. We’ve also made changes to CellProfiler’s underlying code to make it faster to run and easier to install, and we’ve added the ability to process images in the cloud and using neural networks (deep learning). We’ve also added more explanations to CellProfiler’s settings to help new users get started. We hope these changes will make CellProfiler an even better tool for current users and will provide new users better ways to get started doing quantitative image analysis."/> <meta property="og:image" content="https://journals.plos.org/plosbiology/article/figure/image?id=10.1371/journal.pbio.2005970.g004&size=inline"/>  <script type='text/javascript'> var googletag = googletag || {}; googletag.cmd = googletag.cmd || []; (function() { var gads = document.createElement('script'); gads.async = true; gads.type = 'text/javascript'; var useSSL = 'https:' == document.location.protocol; gads.src = (useSSL ? 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Cimini, Kyle W. Karhohs </p> <p class="roles" id="authRoles"> <span class="type">Roles</span> Conceptualization, Formal analysis, Software, Writing – original draft, Writing – review & editing </p> <p id="authAffiliations-0"><span class="type">Affiliation</span> Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose0"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="1" class="author-name" > Allen Goodman <span class="contribute"> </span>,</a> <div id="author-meta-1" class="author-info" data-js-tooltip="tooltip_target"> <p> <span class="contribute"> </span> Contributed equally to this work with: Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs </p> <p class="roles" id="authRoles"> <span class="type">Roles</span> Conceptualization, Investigation, Software </p> <p id="authAffiliations-1"><span class="type">Affiliation</span> Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose1"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="2" class="author-name" > Vasiliy Chernyshev <span class="contribute"> </span>,</a> <div id="author-meta-2" class="author-info" data-js-tooltip="tooltip_target"> <p> <span class="contribute"> </span> Contributed equally to this work with: Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs </p> <p class="roles" id="authRoles"> <span class="type">Roles</span> Data curation, Investigation, Methodology, Software, Validation, Visualization, Writing – review & editing </p> <p id="authAffiliations-2"><span class="type">Affiliations</span> Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose2"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="3" class="author-name" > Lee Kamentsky <span class="contribute"> </span>,</a> <div id="author-meta-3" class="author-info" data-js-tooltip="tooltip_target"> <p> <span class="contribute"> </span> Contributed equally to this work with: Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs </p> <p class="roles" id="authRoles"> <span class="type">Roles</span> Conceptualization, Software </p> <p id="authAffiliations-3"><span class="type">Affiliation</span> Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose3"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="4" class="author-name" > Beth A. Cimini <span class="contribute"> </span>,</a> <div id="author-meta-4" class="author-info" data-js-tooltip="tooltip_target"> <p> <span class="contribute"> </span> Contributed equally to this work with: Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs </p> <p class="roles" id="authRoles"> <span class="type">Roles</span> Conceptualization, Investigation, Methodology, Project administration, Software, Validation, Writing – review & editing </p> <p id="authAffiliations-4"><span class="type">Affiliation</span> Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose4"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="5" class="author-name" > Kyle W. Karhohs <span class="contribute"> </span>,</a> <div id="author-meta-5" class="author-info" data-js-tooltip="tooltip_target"> <p> <span class="contribute"> </span> Contributed equally to this work with: Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs </p> <p class="roles" id="authRoles"> <span class="type">Roles</span> Investigation, Methodology, Software </p> <p id="authAffiliations-5"><span class="type">Affiliation</span> Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose5"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="6" class="author-name" > Minh Doan,</a> <div id="author-meta-6" class="author-info" data-js-tooltip="tooltip_target"> <p class="roles" id="authRoles"> <span class="type">Roles</span> Methodology, Software, Writing – original draft, Writing – review & editing </p> <p id="authAffiliations-6"><span class="type">Affiliation</span> Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose6"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="7" class="author-name" > Liya Ding,</a> <div id="author-meta-7" class="author-info" data-js-tooltip="tooltip_target"> <p class="roles" id="authRoles"> <span class="type">Roles</span> Data curation, Methodology, Software, Validation, Writing – review & editing </p> <p id="authAffiliations-7"><span class="type">Affiliation</span> Allen Institute for Cell Science, Seattle, Washington, United States of America </p> <a data-js-tooltip="tooltip_close" class="close" id="tooltipClose7"> ⨯ </a> </div> </li> <li data-js-tooltip="tooltip_trigger" > <a data-author-id="8" class="author-name" > Susanne M. 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Cimini,  </li> <li data-float-index="6">Kyle W. Karhohs,  </li> <li data-float-index="7">Minh Doan,  </li> <li data-float-index="8">Liya Ding,  </li> <li data-float-index="9">Susanne M. 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