What's the difference between x_reconstructed and x_ccf

Technical
1

In the merfish mouse brain dataset, what’s the difference between x(y)_reconstructed and x(y)_ccf? I can’t tell any difference in this tutorial by eye.

I am asking this question because I want to look at the cells in my own region of interest (e.g. a subset of LHA neurons within a specific anatomical region)

Kind Regards
Xinyu

2

Hi Xinyu,

The difference is that the reconstructed coordinates are in the space of the section, and the CCF coordinates are in the space of the CCF. The reconstructed coordinates are modified to have a pseudo 3D version of all sections. If you want to select all LHA neurons you can select them by assignment to the CCF (that’s a seperate column). Which coordinates you use to plot them is up to you.

Best,

Michael