data_STARmap_plus

[naveedishaque]

Update metadata: https://docs.google.com/spreadsheets/d/1QCeAF4yQG4bhZSGPQwwVBj_XF7ADY_2mK5xivAIfHsc/edit#gid=1453488771

Details of data(publication, GitHub): https://www.spatial-atlas.net/Brain/ Code: https://github.com/wanglab-broad/mCNS-atlas https://www.nature.com/articles/s41586-023-06569-5#data-availability Ground truth: CCF registration

[heylf]

Not sure about the ground truth here @naveedishaque. The paper states:

"It is worth mentioning that the cell-typing results in this study were based on the consensus between the STARmap PLUS dataset and published scRNA-seq datasets, followed by manual annotation. The STARmap PLUS dataset mapped more cells than the previous scRNA-seq dataset1, potentiating more detailed cell typing and annotations in the future."

Reading the paper it ssems that they integrated the data with a reference to get an overview and then refined the cell type clusters "manually" by marker genes and spatial cell distribution.

I can integrate the data but I just want to point this out.

[naveedishaque]

Not sure why the cell typing is relevant here. The ground truth is based on the CCF registration:

To compare and annotate the molecularly defined tissue regions with anatomically defined tissue regions, we registered sample slices into the established Allen Mouse Brain Common Coordinate Framework20,21,22 (CCFv3) (Fig. 2b,c) and labelled individual cells in our datasets with CCF anatomical definitions (Extended Data Fig. 5a and Methods).

[heylf]

Tackled with this PR https://github.com/SpatialHackathon/SpaceHack2023/pull/204