How to use "Mouse Whole Cortex and Hippocampus 10x" to annotate a spatial data set in seuart?

Hi @ivingan01. Sorry for the delay in getting back to you and thank you for your interested in these data. At the moment there is not a separate cortex and hippocampus taxonomy or data set, nor is there a way to only download a subset of the data. However, if you follow the steps listed in this other Community Forum post you can start from the ~5GB hdf5 file instead of the ~68GB csv file and do the subsetting yourself. The analyses we’d suggest would be to:

  1. Download and subset the data as described above
  2. Additionally exclude all cells from cell types largely found outside of hippocampus. You can visualize this generally in the web app and with much more context in the associated publication. To first approximation, all non-neuronal types are in hippocampus, glutamatergic types 318-364 are in hippocampus + subiculum (see Figure 6), and GABAergic cells are more complicated but there are several type enriched in hippocampus (see Figure 2).
  3. Use the resulting data set and associated clusters as your reference (to replace the 2016 data set) and follow the spatial data tutorial mentioned above.

If any of this is not clear, feel free to post.
(If others in the community have other suggestions, please post as well!)