Change in Electrode Table of NWB File does not change Table in Database

[leond32]

Hi,
I already created a database and inserted an NWB File of a session with an electrode table. I then found out, that I entered a wrong reference electrode, so I changed this in my NWB File.
The problem is, that even if I delete the NWB File from the database and insert the new one, it is still using the old reference electrode. This deletion of the NWB File should also delete all entries in electrodes, which it does but then, when I insert the new file, it is as if I never deleted anything.
Do you know why this error occurs or how to solve it?
Thank you very much in advance!

[edeno]

Hi @leond32,

Thanks for trying out spyglass. When deleting the NWB file, what code are you using? For example, the following is the recommended way of deleting an NWB file from the database. Notice the second line is needed to delete the actual underlying NWB file.

import spyglass.common as sgc

(sgc.Nwbfile & {"nwb_file_name": nwb_copy_file_name}).delete()
sgc.Nwbfile().cleanup(delete_files=True)

@CBroz1 do you have any other thoughts on what could be causing this issue?

[CBroz1]

Not sure.

@leond32 Which table is it that still has entries after a deletion? spyglass.common.common_ephys.Electrode?

If you can tell me more about your setup to help me replicate, that would be great

[leond32]

Hey,

Thank you for your help already! I created an example nwb file for you. The table with the wrong value is the spyglass.common.common_ephys.Electrode table. The wrong value is the "original_reference_electrode" column. As you see from my screenshots, the value in my nwb file is -2, but in the table created from the nwb file, it is always -1. Might not be a stored value, but already predefined in the spyglass library. If that is the case, how can I insert my value for this column?

Thanks in advance for further help!

Google Drive link for sample nwb file

[CBroz1]

Hi @leond32 - We took a closer look at our Electrode make function. I think you're getting the default reference -1 because your data isn't our assumed ndx_franklab_novela.Probe type checked here. We're still figuring out how to address this internally, but safe to say Spyglass should warn you if your data isn't being ingested as expected. In order for us to ingest your data, we would need a mapping of these variables

As a direct solve for your case, you can fetch the data that did get inserted, update the values, and then re-insert with the allow_direct_insert flag (datajoint insert doc).

[leond32]

Thanks for your help, that explains what causes this problem, with your help it works now :)