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CellProfiler 3.0: Next-generation image processing for biology

by Ding, Liya , McQuin, Claire , Doan, Minh , Singh, Shantanu , Thirstrup, Derek , Kamentsky, Lee , Goodman, Allen , Karhohs, Kyle W. , Becker, Tim , Rafelski, Susanne M. , Cimini, Beth A. , Caicedo, Juan C. , Carpenter, Anne E. , Chernyshev, Vasiliy , Wiegraebe, Winfried

in Algorithms / Animals / Automation / Bioinformatics / Biologists / Biology and Life Sciences / Cell Nucleus - metabolism / Cells / Computer and Information Sciences / Computer applications / Computer programs / Deep Learning / DNA - metabolism / Ebola virus / Ecosystem biology / Engineering and Technology / Forecasts and trends / Humans / Image analysis / Image processing / Image Processing, Computer-Assisted / Imaging, Three-Dimensional / Induced Pluripotent Stem Cells - cytology / Induced Pluripotent Stem Cells - metabolism / Machine learning / Methods / Methods and Resources / Mice / Microscopy / Neural networks / Observations / People and Places / Physical Sciences / Research and Analysis Methods / RNA, Messenger - genetics / RNA, Messenger - metabolism / Science / Science Policy / Software / Stem cells / Supervision / Three dimensional analysis / Usability

2018

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2018

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2018

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Journal Article

CellProfiler 3.0: Next-generation image processing for biology

Ding, Liya,

McQuin, Claire,

Doan, Minh,

Singh, Shantanu,

Thirstrup, Derek,

Kamentsky, Lee,

Goodman, Allen,

Karhohs, Kyle W.,

Becker, Tim,

Rafelski, Susanne M.,

Cimini, Beth A.,

Caicedo, Juan C.,

Carpenter, Anne E.,

Chernyshev, Vasiliy,

Wiegraebe, Winfried

2018

Overview

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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Publisher

Public Library of Science,Public Library of Science (PLoS)

Subject

/ Animals

/ Biology and Life Sciences

/ Cell Nucleus - metabolism