CellProfiler 3.0: Next-generation Image Processing for Biology

Overview

Journal PLoS Biol

Specialty Biology

Date 2018 Jul 4

PMID 29969450

Citations 909

Authors

Claire McQuin

Allen Goodman

Vasiliy Chernyshev

Lee Kamentsky

Beth A Cimini

Kyle W Karhohs

Minh Doan

Liya Ding

Susanne M Rafelski

Derek Thirstrup

Winfried Wiegraebe

Shantanu Singh

Tim Becker

Juan C Caicedo

Anne E Carpenter

Affiliations

Soon will be listed here.

Abstract

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.

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References

Bray M, Singh S, Han H, Davis C, Borgeson B, Hartland C . Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat Protoc. 2016; 11(9):1757-74. PMC: 5223290. DOI: 10.1038/nprot.2016.105. View

Rueden C, Schindelin J, Hiner M, DeZonia B, Walter A, Arena E . ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics. 2017; 18(1):529. PMC: 5708080. DOI: 10.1186/s12859-017-1934-z. View

Fillbrunn A, Dietz C, Pfeuffer J, Rahn R, Landrum G, Berthold M . KNIME for reproducible cross-domain analysis of life science data. J Biotechnol. 2017; 261:149-156. DOI: 10.1016/j.jbiotec.2017.07.028. View

LeCun Y, Bengio Y, Hinton G . Deep learning. Nature. 2015; 521(7553):436-44. DOI: 10.1038/nature14539. View

Eliceiri K, Berthold M, Goldberg I, Ibanez L, Manjunath B, Martone M . Biological imaging software tools. Nat Methods. 2012; 9(7):697-710. PMC: 3659807. DOI: 10.1038/nmeth.2084. View

Wiesmann V, Franz D, Held C, Munzenmayer C, Palmisano R, Wittenberg T . Review of free software tools for image analysis of fluorescence cell micrographs. J Microsc. 2014; 257(1):39-53. DOI: 10.1111/jmi.12184. View

Caicedo J, Singh S, Carpenter A . Applications in image-based profiling of perturbations. Curr Opin Biotechnol. 2016; 39:134-142. DOI: 10.1016/j.copbio.2016.04.003. View

Sadanandan S, Ranefall P, Le Guyader S, Wahlby C . Automated Training of Deep Convolutional Neural Networks for Cell Segmentation. Sci Rep. 2017; 7(1):7860. PMC: 5552800. DOI: 10.1038/s41598-017-07599-6. View

Caicedo J, Cooper S, Heigwer F, Warchal S, Qiu P, Molnar C . Data-analysis strategies for image-based cell profiling. Nat Methods. 2017; 14(9):849-863. PMC: 6871000. DOI: 10.1038/nmeth.4397. View

10.

Svoboda D, Ulman V . MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. IEEE Trans Med Imaging. 2016; 36(1):310-321. DOI: 10.1109/TMI.2016.2606545. View

11.

Snijder B, Vladimer G, Krall N, Miura K, Schmolke A, Kornauth C . Image-based ex-vivo drug screening for patients with aggressive haematological malignancies: interim results from a single-arm, open-label, pilot study. Lancet Haematol. 2017; 4(12):e595-e606. PMC: 5719985. DOI: 10.1016/S2352-3026(17)30208-9. View

12.

Long F, Zhou J, Peng H . Visualization and analysis of 3D microscopic images. PLoS Comput Biol. 2012; 8(6):e1002519. PMC: 3375219. DOI: 10.1371/journal.pcbi.1002519. View

13.

Hartwell K, Miller P, Mukherjee S, Kahn A, Stewart A, Logan D . Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat Chem Biol. 2013; 9(12):840-848. PMC: 4009363. DOI: 10.1038/nchembio.1367. View

14.

Carpenter A, Jones T, Lamprecht M, Clarke C, Kang I, Friman O . CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006; 7(10):R100. PMC: 1794559. DOI: 10.1186/gb-2006-7-10-r100. View

15.

Ching T, Himmelstein D, Beaulieu-Jones B, Kalinin A, Do B, Way G . Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 2018; 15(141). PMC: 5938574. DOI: 10.1098/rsif.2017.0387. View

16.

Stanley S, Barczak A, Silvis M, Luo S, Sogi K, Vokes M . Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 2014; 10(2):e1003946. PMC: 3930586. DOI: 10.1371/journal.ppat.1003946. View

17.

Wen Q, Goldenson B, Silver S, Schenone M, Dancik V, Huang Z . Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL. Cell. 2012; 150(3):575-89. PMC: 3613864. DOI: 10.1016/j.cell.2012.06.032. View

18.

Rivron N, Frias-Aldeguer J, Vrij E, Boisset J, Korving J, Vivie J . Blastocyst-like structures generated solely from stem cells. Nature. 2018; 557(7703):106-111. DOI: 10.1038/s41586-018-0051-0. View

19.

Rohban M, Singh S, Wu X, Berthet J, Bray M, Shrestha Y . Systematic morphological profiling of human gene and allele function via Cell Painting. Elife. 2017; 6. PMC: 5386591. DOI: 10.7554/eLife.24060. View

20.

Pennisi E . IMAGING. 'Cell painting' highlights responses to drugs and toxins. Science. 2016; 352(6288):877-8. DOI: 10.1126/science.352.6288.877. View