# Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)

* 1.7 million single cell transcriptomes spanning the whole adult mouse brain
  using 10Xv2 chemistry ([WMB-10Xv2](WMB-10Xv2.md))
* 2.3 million single cell transcriptomes spanning the whole adult mouse brain 
  using 10Xv3 chemistry ([WMB-10Xv3](WMB-10Xv3.md))
* 1687 single cell transcriptomes spanning the whole adult mouse brain using
  the 10X Multiome chemistry ([WMB-10XMulti](WMB-10XMulti.md))
* Clustering analysis of 4.0 million single cell transcriptomes spanning the
  whole adult mouse brain combining the 10Xv2, 10Xv3 and 10XMulti datasets
  ([WMB-10X](WMB-10X.md))
* A four level whole adult mouse brain taxonomy of cell types
  ([WMB-taxonomy](WMB-taxonomy.md))
* 3.9 million cell spatial transcriptomics dataset spanning a single adult
  mouse brain with a 500 gene panel and mapped to the whole mouse brain
  taxonomy ([MERFISH-C57BL6J-638850](MERFISH-C57BL6J-638850.md))
* Definition of 8 cell types neighborhoods and UMAP embeddings for fine grain
  visualization and analysis of neuronal types within and between brain regions
  ([WMB-neighborhoods](WMB-neighborhoods.md))
* An updated Allen CCFv3 with additional annotations for layers of Ammon's
  horns, main olfactory blub and a simplified 5-level anatomical hierarchy
  ([Allen-CCF-2020](Allen-CCF-2020.md))
* CCF mapped coordinates for cells in the whole brain spatial transcriptomics
  dataset ([MERFISH-C57BL6J-638850-CCF](MERFISH-C57BL6J-638850-CCF.md))
*  3.9 million cell spatial transcriptomics dataset with ~8000 genes
   imputed using the 500 genes in the base MERFISH-C57BL6J-638850 dataset
   [MERFISH-C57BL6J-638850-imputed](MERFISH-C57BL6J-638850-imputed.md).