Ephys_analysis_code

The description below details the contents of the ‘mEPSC_analysis’ folder you have downloaded. To ensure that the code, as presently constructed, works smoothly with your data, you MUST:

1. Name and filter your raw traces in the same format as they exist in the sample_data. See details below for naming structure/filtering of data
2. Your folder structure must also be identical to what is provided here in the sample data: a. ____________/cell_type/Condition_x/cell_x i. _____whatever your pathing is to get to this point does not matter ii. cell_type: PV cell, pyramidal cell, etc. iii. Condition_x: KO, KI, KD, control, etc iv. cell_x: number cell, this folder contains all the recordings from your cell

Two folders:

1. ‘MATLAB’ contains: a. mPSC_detection.m: primary ‘master’ code you will need to open and execute i. line 73-77: change function depending on if you are running the code for pyramidal cells or PV cells ii. line 119: you must change if your recordings are anything other than 1 minute, gap-free recordings. If you take 30s recordings, for example, change 60 to 30 b. mPSC_detection_functions: folder containing all necessary functions i. abfload_fcollman.m: reads in .abf files (raw traces from clampex)
2. documentation available online, I did not write this ii. detrend_y_convert.m
3. helps correct for drift in baseline, if there is any
4. detrends your trace and removes any signal ~6pA above baseline (potential oscillation/noise in your rig) iii. find_EPSCs_PVIN.m
5. primary function that you will run if you are analyzing mEPSCS from parvalbumin interneurons (PV-INs) (fast kinetics, larger amplitudes) iv. find_EPSCs_PYR.m
6. primary function that you will run if you are analyzing mEPSCs from pyramidal neurons (PYR) (slower kinetics, smaller amplitudes)
7. ‘sample_data’ contains: a. PV-IN: data from PV-INs b. PYR: data from PYR c. Note: the folder structure of both PV-IN and PYR are identical, so I will describe the contents of both in general: i. Condition_X: folder containing data (multiple 1 minute gap-free raw .abf traces) from two cells each per ‘condition’
8. cell_x: folder containing: a. raw_trace (.abf) i. all raw traces must be listed in the following format
9. YYYY_MM_DD_xxxx_filtered.abf a. YYYY_MM_DD date of recording b. xxxx = number of recording that day (e.g. 0001 or 0019 for the first and nineteenth recording that day, respectively) c. filtered: all of my raw traces are filtered in clampfit. Analyze->Filter->Lowpass (boxcar, 7 smoothing points, filter the whole trace) d. .abf: the natural clampex file extension ii. AFTER YOU RUN THE CODE, EACH cell_x FOLDER WILL ALSO CONTAIN:
10. YYYY_MM_DD_xxxx_filtered.abf_Cell_output.xlsx: excel that has all the data for that one recording to which the name corresponds
11. YYYY_MM_DD_xxxx_filtered.abf_Figure: figure that can be opened in matlab that has the raw trace and all the events that were identified by the code
12. cell_x_Final_Results.xlsx: excel that combines the average amplitude, frequency, rise, and decay from each of the recordings of a given cell. Also gives the overall average (and standard deviation) of the amplitude, frequency, rise, and decay of the cell overall by averaging (or taking the standard deviation) of the 4 metrics from each of that cell’s recordings
13. cell_x_Final_Results_w_IEI.xlsx: gives the IEIs, amplitudes, rise, and decay of each individual event from all recordings from that given cell ii. Condition_X_all_IEIs.xlsx: excel that contains every inter-event interval and amplitude for each event from all recordings of given cell in a given condition_x folder, organized on a cell-by-cell basis (i.e. concatenates all the data from all the recordings of a given cell)
14. This is used for cumulative frequency distributions iii. Condition_X_all_Kinetics.xlsx: excel that contains the Decay and Rise for each event from all recordings of given cell in a given condition_x folder, organized on a cell-by-cell basis (i.e. concatenates all the data from all the recordings of a given cell)
15. This is used for cumulative frequency distributions iv. Condition_X_Final_Results.xlsx: excel that contains the average amplitude, frequency, rise, and decay for all cells within a condition_x folder
16. This is the main data you would plot