CellProfiler 3.0: Next-generation image processing for biology

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, in...

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Detalles Bibliográficos
Autores principales: McQuin, Claire, Goodman, Allen, Chernyshev, Vasiliy, Kamentsky, Lee, Cimini, Beth A., Karhohs, Kyle W., Doan, Minh, Ding, Liya, Rafelski, Susanne M., Thirstrup, Derek, Wiegraebe, Winfried, Singh, Shantanu, Becker, Tim, Caicedo, Juan C., Carpenter, Anne E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Methods and Resources
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6029841/
https://www.ncbi.nlm.nih.gov/pubmed/29969450
http://dx.doi.org/10.1371/journal.pbio.2005970
Descripción
Sumario: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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