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ephys_pipeline:phys_gui

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Phys gui

Initiate phys_gui by using the command phys_gui_working
A figure will pop up which looks something like this: Select your monkey from the dropdown menu
Select the session folders you want to process afer hitting the “Add date from list” button
If you hit “Run”, phys_gui will do all the preprocessing that you checked (see below) on the selected folders

Rename folders

In later TDT software versions (synapse - setup 3), the folder naming is different. For converting folders recorded with synapse to the old (our standard) folder naming, check the box “RenameSynapseTankNameToOldTankFormat”.

Automatic waveclus clustering

If you want to use the waveclus pipeline, you first need to create waveclus sortcodes. You can do so by checking “WCFromBB”

Create Plexon files from snippets

If you want (or have) to use the online detected snippets, check “PLXFromSnippets”. If you first want to Realign your snippets to the minima, check “PLXFromRealignedSnippets” instead.

Create Plexon files from waveclus sortcodes

After you sorted with waveclus, you can create a plexon file from your saved sortcodes. Check “PLXFromWCFromBB”

Create TDT sortcode from PLX

In case you used the online snippets to create your plexon files, you can simply add another sortcode attached to the original TDT blocks.
Something missing here

Combine ephys and behavioral data

After you are done with sorting, you can synchronize your recorded data with behavioral data, adding LFP and spike information in the trial structure format that monkeypsych uses.
In order to indicate which type of sorting you want to use, select one option in the “Choose spikes” section
“Snippets” uses the sortcodes based on the original snippets
“Realigned” uses the sortcodes based on realigned snippets
“FromBB” uses the sortcodes based on WC clustered PLX files
Chose “none” in case you are only interested in LFP. No spikes will be added to your combined data.

ephys_pipeline/phys_gui.1508858981.txt.gz · Last modified: 2022/12/29 07:15 (external edit)