Purpose / General Information
This SOP walks through the NLX-Event-Viewer apps to process raw microwire and macrowire ephys data from the NLX system.
Last update: Sept 14 2021
Requirements
- The matnwb interface library needs to be downloaded to read and write Neurodata Without Borders (NWB) files that are created with the Stage 3 app (see below).
- The interface library can be found in the
NLX-Event-Viewer
repository - Instructions and further information about the interface library can be found on the NWB website
- The Stage 3 app will download the matnwb interface library if it is not already on your machine
- The interface library can be found in the
- Download the patient's
macroChanInfo.csv
andmicroChanInfo.csv
files. These contain information about the patient's electrodes such channel numbers of the macro/microwires, and where each electrode was implanted. - Download the patient's
CSC.ncs
andEvents.nev
files- Only download the
CSC.ncs
files up to the number of macrowire channels that the patient had. CheckmacroChanInfo.csv
to determine the number of macro channels.
- Only download the
- Create subfolder within Patient's folder called
Processing
, and a subfolder withinProcessing
calledEvents
- Copy
.csv
files intoProcessing
subfolder - Copy
CSC.ncs
andEvents.nev
files intoEvents
subfolder
- Copy
Apps
-
NLX_Stage_Select: Meta-app to select app (listed below) you would like to use for stage 1, 2 or 3 of processing
-
STAGE1_NLX_EventFinder: Sort through event files (.nev) to find useable data; creates folder/file structure setup
-
STAGE2_NLX_SessionInspect: View event file contents and split files into different experiments or epochs
Note: This app is optional and only used if splitting an event file
-
STAGE3_NLX_Session2NWB: Convert data file into NWB format
Stage 1
- Click on gear icon button and select the patient's
Events
folder.- Will create
NWB
andSessionSave
folders as well asNWB_Process_Folder_Check.m
to be used in later steps.
- Will create
- Click through the available
Events.nev
files and choosing which ones you want to analyze- The event list will populate as you choose to keep certain files
- Create an event log
- Fill in 'Start' and 'Stop' index
- 'Start' index = found in 'Start Index' column of table
- 'Stop' index = Number in 'Start Index' column + Number in 'Num events' column
- Decide whether the event file is 'Resting' or 'Behavior' by looking at the number of TTLs and the length of time of the recording
- Switch the 'Accept' button to 'On' to add the event log for that file
- Fill in 'Start' and 'Stop' index
- Click the 'Session' button to select the next event
- When there is no more events, click 'Export' to save
- Use patient ID when saving
- Close program
Stage 2
- Click on gear icon button and select the patient's
NWB_Process_Folder_Check.m
file to load in ID'ed sessions from the Stage 1 app - Select the session you would like to split
- Click the 'Process Session' button
- Enter session information into 'Session Split' box
- Number Sessions = The number of sessions you would like to split the file into
- If splitting into 2 sessions:
- Click 'SET" button
- Check the file details in the 'New Session' box. If it looks good, click the 'SPLIT' button. If not, click the 'RESET' button to restart the process
- Continue with the rest of the sessions that need to be split
- Click 'DONE' when complete
- You are able to unclick 'DONE' to make any changes
- Click the 'EXPORT SESSIONS' button
- Close program
Stage 3
- Click on gear icon button and select the patient's
NWB_Process_Folder_Check.m
file to load in ID'ed sessions from the Stage 1 app - Click on 'CONFIRM Directories' button if information in the 'Directory Locations' spaces are correct
- Click on 'START Process' button
- The 'Session Processing' table will populate with information such as which
CSC.ncs
files correspond to theEvents.nev
files
- The 'Session Processing' table will populate with information such as which
- Click on the Step 1 button: 'Import Neuro Labels'
- Navigate to the patient's
microChanInfo.csv
file - Navigate to the patient's
macroChanInfo.csv
file - Click on the Step 2 button: 'Check for NWB'
- This step will check to see if you have the matnwb inferface library on your path and will add it if not
- Click on the Step 3 button: 'Export to NWB' to create the NWB file
- Close program when all sessions have been exported