How to upsample the data&atlas?

so does the downsample factor set on the --affine-n-steps? and how to upsample the brain data&registered atlas together?

The downsampling is set by the --atlas flag, your data is resampled to match the atlas you choose. E.g. for mice, the default atlas is allen_mouse_25um which is at 25um resolution, or you could choose allen_mouse_10um which is at 10um. There’s no other way of choosing the resolution of the registration.

If you want to upsample the registered data, it depends on what software you’re using, and what you want to achieve, it’s relatively simple to do in FIJI, Python etc. This forum would be a great place to ask.

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