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20.11.2019

Scanpy on the rise: Helmholtz Zentrum München expands single-cell platform with new Chan Zuckerberg Initiative funding

The Institute of Computational Biology at Helmholtz Zentrum München will grow its open source software Scanpy for single-cell analysis and visualization with the support of a new grant awarded by the Chan Zuckerberg Initiative (CZI). Within the next two years, Scanpy 2.0 aims to substantially increase its community and accessibility at a large scale.

Image 1: Visualization of gene expression in 1.3M neurons, dataset from 10x Genomics. ©Helmholtz Zentrum München / Alex Wolf

Image 2: PAGA visualization of 50k cells of the regenerating flatworm Planaria. ©Helmholtz Zentrum München / Alex Wolf

Image 3: PAGA visualization of 50k cells of the regenerating flatworm Planaria – tissue level vs. cell level. ©Helmholtz Zentrum München / Alex Wolf

In late 2016, Alex Wolf and Philipp Angerer at Helmholtz Zentrum München started to develop Scanpy to help analyze gene-expression data of large numbers of individual cells using machine learning methods. As a powerful and popular Python framework for scalable processing, analyzing, and visualizing single cell data, Scanpy is now used in big data projects such as the Human Cell Atlas – the global effort to map the molecular states of all cells in the human body.

“To grow the Scanpy community, we need to focus on making participation more accessible”, states Prof. Dr. Dr. Fabian Theis, Director at the Institute of Computational Biology at Helmholtz Zentrum München. “To this end, we will improve tutorials and documentation and build a cohesive community platform welcoming all scientists and enthusiasts. To foster contributions, Scanpy 2.0 will become more easily maintainable and extensible. We will also make sure Scanpy stays relevant in the future by extending it to spatial transcriptomics and laying the base for further multi-omics data analysis”.

While Philipp Angerer wrote the bulk of the CZI grant application for Scanpy 2.0, meanwhile, many contributions come from an international developer community with 47 contributors around the project founders. Most noteworthy are Isaac Virshup from the University of Melbourne, Gökcen Eraslan from Broad Institute, and Fidel Ramirez from Boehringer-Ingelheim.

Leading excellence in Munich for international scientific progress

The new funding is proof for the continued success of the researchers at Helmholtz Zentrum München. The group was awarded two further CZI grants in 2019, e.g. in collaboration with the University of Harvard and the Human Lung Cell Atlas project. In the past two years, Helmholtz Zentrum München received CZI funding worth more than 1 million US dollars.

In the current funding round, the Chan Zuckerberg Initiative awarded 5 million US dollars to support more than 40 open source software projects that are essential to biomedical research. The full list of CZI grantees can be seen here.

Related publication:
Wolf, Angerer, Theis (2018): Scanpy: large-scale single-cell gene expression data analysis. Genome Biology, DOI: 10.1186/s13059-017-1382-0