SpaceTx: experimental and computational methods
comparison for spatially resolved transcriptomics

SpaceTx Consortium

The SpaceTx Consortium was created as part of the Chan Zuckerberg Initiative's support for the Human Cell Atlas with the goal of benchmarking spatial transcriptomics methods by comparing standardized outputs in the mouse visual cortex and human middle temporal gyrus. Generating this data was challenging, as the experimental methods were in early days of development in academic labs. Data from multiple modalities was finally aggregated for a hackathon in February of 2020, just as the SARS-COv-2 virus was beginning to circulate across the globe.

SpaceJam Hackathon

There have been two SpaceJam Hackathons, one in 2019 and one in 2020. The 2019 SpaceJam Hackathon was held at the Allen Insitute in Seattle, Washington. The 2020 SpaceJam Hackathon was held at the Chan Zuckerberg Initiative in Redwood City, California.

Results and Code

Our results include a direct comparison of six different matched experiments performed in mouse primary visual cortex, and our efforts to address critical issues such as the standardization of computational analysis and file formats, cell segmentation, cell type assignment, and big data visualization.