CellProfiler 3.0: Next-generation image processing for biology.

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.

journal_name

PLoS Biol

journal_title

PLoS biology

authors

McQuin C,Goodman A,Chernyshev V,Kamentsky L,Cimini BA,Karhohs KW,Doan M,Ding L,Rafelski SM,Thirstrup D,Wiegraebe W,Singh S,Becker T,Caicedo JC,Carpenter AE

doi

10.1371/journal.pbio.2005970

subject

Has Abstract

pub_date

2018-07-03 00:00:00

pages

e2005970

issue

7

eissn

1544-9173

issn

1545-7885

pii

pbio.2005970

journal_volume

16

pub_type

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