Assistance with Minian final Merge option

[ellahn3]

Hi all,

I’m reaching out for help with using the merge option in Minian. I’ve successfully run Minian and reached the stage where I can manually merge cells. However, I’ve encountered an issue with saving the merged data.

After completing the merge, when I try to save the dataset using minian_ds.to_netcdf("minian_dataset.nc"), the saved data appears as null. Upon inspecting the dataset, it seems that the merge process isn’t fully combining the cells—it retains the original data and only updates the unit labels.

This doesn’t seem to align with how the merge is supposed to function. I’m aiming to save the final, cleaned dataset with the merges fully applied.

Could you please advise on how to resolve this issue?

Best regards,
Ella

[omis-io]

hi，
have you press load data after you merged cells， I think in most occasions load data and refresh are not supposed to press
hope this will fix your problem
best regards
simo

[ellahn3]

hi,
no, I haven’t pressed "Load Data" or "Refresh" after merging the cells. instead, I proceed with running the next few cells and then attempt to save the data using the following lines:
minian_ds = open_minian(dpath)
minian_ds.to_netcdf("minian_dataset.nc")
however, after the merge, the saved data is filled with null.
could you please advise on what might be causing this and how I can ensure the merged data is saved correctly?

[omis-io]

hi,
The final step will not actually merge or remove the data; it will simply label the removed cells using -1. If you really want to remove or merge cells, I think additional code is required for further processing.