Add ASt ecephys (OpenEphys) experiment pipeline

[weiglszonja]

ASt: Amygdalostriatal transition zone experiment notes

• [x] Add openephys data (16 channel, 30kHz)
• [x] Add electrodes location metadata (ASt)
• [x] Add plexon spike sorting data (using the file that ends with "sort.plx")
• [x] Add events data (similar to Neurotensin experiment)
• [x] Add SLEAP pose estimation output
• [x] Add source video for SLEAP
• [x] Add processed spikes ("Group" data)
• [ ]

[CodyCBakerPhD]

Notes for OpenEphys part

• only 15 channels, you mentioned it should be 16?
• How does the NeuroPixels data fit into this experiment?

[weiglszonja]

@CodyCBakerPhD There should be 16 channels indeed, the reason that file had less was because I didn't download one of the .continuous files. The new file at catalystneuro-processing/tye_lab_to_nwb/3014_illidanDiscD4_filtered_sorting_ecephys_behavior.nwb should contain 16 channels, with the 'filtered' units described in their document.

How does the NeuroPixels data fit into this experiment?

I asked Laurel, I'll update this comment once I know more.

According to the recent reply on this thread @CodyCBakerPhD

Regarding how NPX and Ephys fit in, the data in this experiment was collected over a 5-6 year period and spanned the lab's move from MIT to Salk. As such, there were a lot of different cohorts collected, some of which made it into this paper. NPX and Ephys were NOT simultaneously recorded. It was just different hardware associated with separate cohorts.

So we'll add NPX in a separate conversion folder, right?

The stubbed session for this PR is updated at catalystneuro-processing/tye_lab_to_nwb

[CodyCBakerPhD]

So we'll add NPX in a separate conversion folder, right?

Sounds like it

[CodyCBakerPhD]

Let me know when there's an updated prototype file to check out and then this should be good to go

Did you test that you can run everything in a fresh clean environment?

[weiglszonja]

Let me know when there's an updated prototype file to check out and then this should be good to go

The updated prototype is up

Did you test that you can run everything in a fresh clean environment?

Yes, this should be good to go.

[CodyCBakerPhD]

Looks great, thanks for all of the work on this!