SpaceTx: Benchmarking Methods for Spatial Transcriptomic Mapping of Cortical Cell Types
Project Goal
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.
Results & Resources
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.
Investigators
Lead Investigator
![Ed Lein](https://chanzuckerberg.com/wp-content/uploads/2020/03/Lein_Ed.jpg)
Co-Principal Investigators
![Paula Arlotta](https://chanzuckerberg.com/wp-content/uploads/2020/03/Arlotta_Paola.jpg)
![Ed Boyden](https://chanzuckerberg.com/wp-content/uploads/2020/03/Boyden_Ed.jpg)
![Long Cai](https://chanzuckerberg.com/wp-content/uploads/2020/03/Cai_Long.jpg)
![Fei Chen](https://chanzuckerberg.com/wp-content/uploads/2020/03/Chen_Fei.jpg)
![George Church](https://chanzuckerberg.com/wp-content/uploads/2020/03/Church_George.jpg)
![Samuel Inverso](https://chanzuckerberg.com/wp-content/uploads/2020/03/Inverso_Sam.jpg)
![Sten Linnarsson](https://chanzuckerberg.com/wp-content/uploads/2020/03/Linnarsson_Sten-1.jpg)
![Joakim Lundeberg](https://chanzuckerberg.com/wp-content/uploads/2020/03/Lundeberg_Joakim-1.jpeg)
![Evan Macosko](https://chanzuckerberg.com/wp-content/uploads/2020/03/Macosko_Evan-1.jpg)
![Mats Nilsson](https://chanzuckerberg.com/wp-content/uploads/2020/03/Nilsson_Mats-1.jpg)
![Aviv Regev](https://chanzuckerberg.com/wp-content/uploads/2020/03/Regev_Aviv.jpg)
![Anthony Zador](https://chanzuckerberg.com/wp-content/uploads/2020/03/Zador_Anthony.jpg)
![Hongkui Zeng](https://chanzuckerberg.com/wp-content/uploads/2020/03/Zeng_Hongkui.jpg)
![Kun Zhang](https://chanzuckerberg.com/wp-content/uploads/2020/03/Zhang_Kun.jpg)
![Xiaowei Zhuang](https://chanzuckerberg.com/wp-content/uploads/2020/03/Zhuang_Xiaowei.jpg)