Layer information in Cell Types database

Technical
, ,
1

Hi,

I’ve been using the Cell Feature Search tool in the Cell Types database to find mouse cortical interneurons. In the search tool, all the neurons found are showcased in this way, with plots showing both their morphological reconstruction (red) and (what I assume is) their layer distribution pattern (yellow). I’m not particularly tech-savvy, but I couldn’t find any attribute in the morphological measurements .xml file that informs of the layer distribution of axons and dendrites.

How can I get that information? Is it accessible through a different resource, or implicit in the coordinates of the reconstruction?

Thanks a lot!

2

Hello @rubtev

The plot is a histogram of the reconstruction with the upper and lower bounds being the pia and white matter. The intermediate tick marks do NOT translate to cortical layer but evenly subdivide the pia to white matter space. Depending on your goals, I might suggest you look at our more recent Patch-seq data set (patch clamp plus transcriptomics) where we have morphology reconstructions plotted in layer aligned space. Dataset linked here Allen Brain Map

-Rachel

3

Thanks a lot @racheld, I’ll take a look