|Publication Type||Journal Article|
|Year of Publication||2018|
|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|
|Date Published||2018 Jul|
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.
|Alternate Journal||PLoS Biol.|
|PubMed Central ID||PMC6029841|