SpaceTx: Benchmarking Methods for Spatial Transcriptomic Mapping of Cortical Cell Types

To evaluate and compare the performance of spatially-resolved transcriptomics methods in adult and developing human and mouse neocortex, and to build consensus maps of cortical cell type distributions based on combined analysis of single-cell, single-nucleus and spatially-resolved transcriptomics.

This project is ongoing, but initial work has resulted in a series of openly available protocols. CZI in collaboration with the SpaceTx consortium has produced an open-source computational package of unified pipelines for image-based transcriptomics (starfish). SpaceTx and the starfish team worked together on assessing the analytical challenges of image based transcriptomics during a hackathon hosted at the Allen Institute. Additional results coming soon.