MERlin is an extensible data analysis pipeline for reproducible and scalable analysis of large datasets. Each MERlin workflow consists of a set of analysis tasks, each of which can be run as single task or split among many subtasks that can be executed in parallel. MERlin is able to execute workflows on a single computer, on a high performance cluster, or on the cloud (AWS and Google Cloud).

If MERlin is useful for your research, consider citing: Emanuel, G., Eichhorn, S. W., Zhuang, X. 2020, MERlin - scalable and extensible MERFISH analysis software, v0.1.6, Zenodo, doi:10.5281/zenodo.3758540

Support to python 3.10 has been added! Now version 0.1.7 has released: Release note Please find the most recent version of MERlin here.

MERlin was originally created for decoding MERFISH datasets. MERFISH is a technology for spatially resolved RNA profiling of 10s to 10,000s of RNA species in individual cells with high accuracy and high detection efficiency. The standard MERlin MERFISH analysis workflow decodes and segments MERFISH datasets to determine RNA molecules and the cell boundaries represented in the raw images.

For more information on installation and usage, please see the documentation.

• George Emanuel - Initial work
• Stephen Eichhorn
• Leonardo Sepulveda
• Pu Zheng - v0.1.7

Contributions are welcome! Please see the documentation for contribution guidelines.