CellProfiler 3.0: Next-generation image processing for biology

Publishing date: 2018-07-03

Published on: PLOS Biology

summary: CellProfiler is a free software that has enabled researchers, without training in computer vision or programming community to create flexible, modular image analysis pipelines since its release in 2005. In this article the authors introduce CellProfiler 3.0 which now enables analysis of three-dimensional (3D) image stacks, provides a protocol for cloud-based, large-scale image processing and enables running pre trained deep learning models on images.

CellProfiler is an exceptional open source package which follows best practices and has created a large active community. Their GitHub repository has currently more than 2,000 closed issues, 1,045 closed pull requests and 41 contributors.

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

link to paper: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005970

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