an image-based transcriptomics workshop and jamboree

Image-based transcriptomics is an emerging technology that measure gene expression of cells in-situ. The SpaceTx consortium formed among the developers of these assays in an effort to systematically compare how these assays differentiate cell types in the human brain. A team of computational biologists and software engineers from CZI are working with SpaceTx to develop starfish, an open-source software library that solves many of the computational challenges these assays share in processing these data. Through open science and open source software, SpaceTx and starfish aim to enable and accelerate the adoption and utility of multiplexed image-based transcriptomics.


The goals of this jamboree are to support the completion of the SpaceTx benchmarking effort, which will result in a publication that rigorously compares and contrasts various image-based transcriptomic assays and create pilot spatial data for the Human Cell Atlas.


Spacejam will be held on February 4th - 7th, 2020.


Spacejam is hosted by the Chan Zuckerberg Initiative and organized in partnership with the Allen Institute.

Cover image provided by Codeluppi et al., 2018.