SCOUTing mini-brains

Published in Scientific Reports, the SCOUT pipeline enables rapid staining, imaging, and analysis of 3D cerebral organoids. We applied SCOUT to compare different culture protocols as well as to study how Zika virus inhibits organoid growth.

SCOUT's computational pipeline is a Python package with a pre-built Docker image. The package also includes a pre-trained U-Net model for segmentation of ventricular zones in cerebral organoids based solely on nuclear staining.


MIT News Article
Publication (Open Access)
Github Repo