Sparta-Lab-CRF-Ephys-Paper-Scripts-and-Data

The collection of Matlab and NeuroExplorer scripts and templates used for our analysis, plus figure files.

Updated Original Email Re: Contents

See below for important file locations and my contributions for the rebuttal that are complete as of today 02/06/19.

1. LOCATION FOR REBUTTAL / RESUBMISSION FILES: I've been saving my files in a folder called [REBUTTAL][This RepoCRF NPP EPHYS PAPER]

2. MY CONTRIBUTIONS FOR THE REBUTTAL READY TO BE USED: (as of 02/06/19)

   • I have a doc "Answers for Reviewer 1.docx" which discusses the questions from reviewer 1 about figure 2B.

   • I have a .AI with new version of figure 2A with ethanol intake (g/kg) instead of licks.

   • I have a References to Add.docx that has 3 references asked for by the reviewers (for phototagging and DID)

   • I have a .docx called CRF Manuscript Submitted _to update_JMI_02-06-19.docx which contains updated text, highlighted in blue.

   • Additional phototagging details, plus reference.

   • Location for DID references to be added to.

3. LOCATION OF RAW PLEXON & NEUROEXPLORER DATA FILES FROM THE ORIGINAL EPHYS RECORDINGS:

   • In Dropbox (Sparta Lab) Electrophysiology Data BackupCRF FINAL DATA SETS

   • Note: I no long have access to these files on Dropbox so I cannot update them or maintain them or re-create any links to the foder.

4. LOCATION OF ARCHIVE OF MY MATLAB & NEUROEXPLORER SCRIPTS

   • [This Repo\ Matlab & Neuroexplorer Scripts]

   • Documentation:

     • Original Workflow Docs are in the Documentation Folder

     • Excel Spreadsheet containing the original and new simplified script names;

5. INSTALLATION - To Use the Matlab Workflow You Must:

   1. In Matlab, click Set Path from Menu Bar > Add With Subfolders:
      • Select: [This Repo\Matlab & Neuroexplorer Scripts\ Matlab Scripts]
        
   
   2. In NeuroExplorer, click VIew \> Options -\> Scripts Tab and Template Tab: - On Scripts Tab: select folder - [This Repo& Neuroexplorer ScriptsNex Files] - On Templates Tab: select fodler - [This Repo& Neuroexplorer ScriptsNex Files]

6. PRE-MATLAB WORKFLOW INSTRUCTIONS.

   1. Make sure all nex files have a DIDSessionInts interval.
      • Pick an interval without phototagging.
      • Generally if PT done post-session and no problems:
        • DIDSessionInts=0 14400
   2. Edit the filenames so they include 'ethanol','sucrose', or 'water'.
      • If ethanol, add day## as well.
   3. Put all nex files in the same folder and launch Matlab.

7. MATLAB WORKFLOW:

Run By User	Order	Simplified Script Name	Description	Changed
Y	1	import_nex_files_spikes_and_bursts.m	Saves all units, neurons, intervals into DATA, calculates BURSTunits. Runs Nex templates.	x
Y	2	calculate_light_lick_responses	Process each unit's timestamps to calssify its lick and light-responsiveness	x
Y	3	calc_spike_binned_data_remove_outliers.m	Uses rolling window to calculate outlier-removed binned data. Runs counts_unit_responses_for_table	x
Y	4	print_results_table_to_excel.m	prints out a table of all unit's results	x
Y	5	prep_data_for_norm_firing_fig	Calculates normalized firing data and creates structures for color plot	x
Y	6	plot_normalized_firing_CRF_by_lick_types	Generates normalized firing rate figure	x
Y	7	copyPasteSORTdata	Prints out grouped data for Prism/Excel
Y	8	copyPasteSORTdata_EarlyVsLate	Prints out grouped data for Prism/Excel
Y	9	copyPasteSORTdata_EarlyVsLateSPLITS	Prints out grouped data for Prism/Excel