ABC MERFISH cell coordinates magnitude is different from template image section resolution?

I am exploring the ABC atlas MERFISH data. I found that the cell x, y coordinates (specifically, “x_reconstructed” and “y_reconstrcted”) are in ~10^-9 mm, whereas the template image “resampled_average_template” have image resolution of 10 micron. If I am going to overlay the cell maps to the template image, these two are in different magnitude so cannot be overlaid. Any suggestions on how to solve this issue? Thank you!

Hi @selinahxy,

The notebook below has some example code to overlay cells on the resampled_average_template that might be helpful to you.

MERFISH CCF mapped coordinates — Allen Brain Cell Atlas - Data Access (

The “x_reconstructed” and “y_reconstructed” values are in mm

The plot cells on a particular section, you first need to work out the z-index, get the slice from the volume and then give the image an extent.

The extent information anchors in the image in mm coordinates