I have been exploring the fantastic MERFISH atlas of the mouse brain. Once I have identified the cell cluster which interests us the most, how can we download the related transcriptomic information?
Of those cell clusters I can only see their brain location at the moment, and their main identity and neurotransmitter class. But I would love to download some transcriptomic information as well. Is it possible??
Absolutely! See the data access documentation at Allen Brain Cell Atlas - Data Access — Allen Brain Cell Atlas - Data Access (or GitHub - AllenInstitute/abc_atlas_access: Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas if you want to download the tutorial .ipynb notebooks directly).
The data isn’t organized by cluster, but you can download a single section or the full dataset and then subset to a given cluster.
Many thanks for your reply! We will definitely give it a try.
Glad to hear you’re enjoying the atlas tool! We have planed for expanded download capabilities for a future version of the application, but thank you for the early feedback so we can get it prioritized appropriately.