Cytomining Ecosystem
Year: 2025
Type: article
Abstract: In this session, you’ll see how a modular ecosystem of open-source tools from the Cytomining organization such as DeepProfiler, Pycytominer, CytoTable, coSMicQC, and CytoDataFrame can be composed into reproducible, scalable workflows for image-based profiling. Together, these tools link every stage of the data lifecycle, from feature extraction and harmonization to quality control, visualization, and analysis. Built on shared open standards and transparent design, this ecosystem exemplifies the practice of opensource science where software, data, and methods are openly developed, tested, and improved by the community. By promoting interoperability and reproducibility, these tools allow researchers to build upon one another’s work, adapt workflows to new biological questions, and scale from small experiments to large imaging screens. The Cytomining organization tools demonstrate how collaborative, open infrastructure can accelerate discovery and make image-based profiling more accessible, transparent, and sustainable.
Authors: Caicedo, Juan C., Chandrasekaran, Srinivas Niranj, Bunten, David
Language: English
Subfield: Biophysics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7104031484