Atlas smooth parameters

[Whiteglad]

Hi, I used this tool to smooth our atlas, which caused excessive smoothing, so we want to modify the parameters of smoothing. I found a paragraph in your paper. Is ‘atlas_profile’ the parameter to control the smoothing？How can I modify it to set refinement in my own atlas？

[yoda-vid]

Thanks for asking, @Whiteglad! Yes, you can use the atlas_profile argument to load a profile that adjusts the smoothing.

For example, if you save this in a new profile file named atlas_lowsmoothing.yaml:

smooth: 1

you can load the profile by adding it to the above command:

python run.py --img ADMBA-E18pt5 --register import_atlas --plane xz --atlas_profile abae18pt5,atlas_lowsmoothing.yaml

I replaced the nosmooth profile here since the new one replaces its smoothing value. The atlas import should then run with the lower smoothing value of 1 from the profile you created.

Alternatively, you could edit the smooth parameter in the aba18pt5 profile (or the one that you are using):

https://github.com/sanderslab/magellanmapper/blob/fac5e9d5f2b76611b95b21fd022f55a306e18ee7/magmap/settings/atlas_prof.py#L471

to reduce the smoothing value to a smaller filter size such as 1 (also exclude the nosmooth profile so it doesn't turn off smoothing).

Hope that helps, let me know if you have any questions!