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GENERAL INFORMATION 
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This readme file was generated on 2024-08-14 by Daisuke Kase in Turner lab at the University of Pittsburgh

Title of Dataset: Source Data for Analyzing Reach-related Single Unit Activity in the Internal Segment of the Globus Pallidus in Parkinsonian Macaque
Description of Dataset: This dataset includes source data summarizing the results of analyses on the electrophysiological data. 
Principal Investigator: Robert S. Turner, rturner@pitt.edu, https://orcid.org/0000-0002-6074-4365 
Date of Data Collection: 2015-03-03 through 2019-01-31
Software Dependencies: All source data are stored in a non-proprietary CSV format. Additionally, one MatLab format file that contains all source data is stored in this dataset.
Update History: 25-04-25 Daisuke Kase (DK) added metrics of the activity at rest into "SourceData_dur_Movement.csv" and "SourceData.mat" to plot the figures in the revised manuscript. DK also added a new souce data "SourceData_TH_cell_count.csv"

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FILE OVERVIEW 
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Directory of Files: 
	_README_general.txt
	Code/
	SourceData/
		_README_source_data.txt
		SourceData_at_Rest.csv
		SourceData_Behavior.csv
		SourceData_dur_Movement.csv
		SourceData_periMovement_SDF.csv
		SourceData_examplar_spike.csv
		SourceData_TH_cell_count.csv
		SourceData.mat

Relationship Between Files: The "SourceData" directory contains the source data in the non-proprietary CSV format. These source data contain all the information we obtained and used to prepare our research article.
File Formats: CSV and TXT
File Naming Convention: <define your file naming convention>

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DATA SPECIFIC INFORMATION FOR SourceData_at_Rest.csv
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Date of Creation: 2024/08/23
Description of Data: This file contains general information of the neuronal data sampled in the internal segment of Globus Pallidus of two macaques both pre- and post-MPTP treatment. In addition, this file includes summary of neural activity at rest (intervals of unpredictable duration during which an animal held its left hand stationary at the start position while awaiting onset of the go-cue).
Number of Rows: 371
Number of Columns: 35
Column Names: 
1. CellID: Identifier number of the recorded GPi neuron
2. Animal: Name of the subject (either Gaia or Isis)
3. MPTP: Condition of MPTP treatment (0: no treatment, 1: after treatment)
4. Date: Date of the recording
5-10. Session1-Session6: Session numbers in which the GPi neuron was collected. Note that we collected some data from same coordinates in multiple consecutive sessions. Such set of data were concatenated into one continuous data before running the analysis code. The session numbers in Session2-6 indicate such concatenated session number. For example, when we collected cell #120 (CellID = 120), we recorded at ML: -6.58, AP: -5.62, DV: -1.90 in session 2 and 3. The number of the first session (2 in this example) was put in Session1 column, the number of the second session (3 in this example) was put in Session2 column, and the rest of Session columns (Session3 through Session6) are left as NaN.
11. ML: Medio-lateral coordinate of the recorded GPi neuron relative to the crossing of anterior commissure (ACX). Unit: mm
12. AP: Antero-posterior coordinate relative to the ACX (unit: mm)
13. DV: Dorso-ventral coordinate relative to the ACX (unit: mm)
14. BrainArea: Name of the brain area where the neural activity was recorded
15. Electrode: Type of electrode used for the data collection (either Glass-insulated Tungsten electrode or 16-channel V-Probe)
16. DataChannel: Channel number on the recording system
17. ElectChannel: Recording site number on the electrode
18. SortQuality: Quality of signal isolation in the spike-sorting (A=Excellent, B=Good)
19. SortID: Identifier number of the sorted unit. SortID is used to identify each unit if multiple units are sorted from single-channel data. For example, if we sorted two units from one channel, the first and the second unit will have identifier number 1 and 2.
20. GoodPeriod_start: The beginning of good signal isolation in the spike-sorting (unit: second)
21. GoodPeriod_end: The end of good signal isolation in the spike-sorting (either end or actual past time in the recording session, unit: second)
22. NumSuccessTrial: Total number of successful trials in the recording session
23. FR_rest: Firing rate at rest (unit: Hz)
24. CV_ISI: Coefficient of Variation of inter-spike-interval
25. ProportionSpikeBurst: Fraction of spikes in the burst activity. For example, if a GPi unit fired 4000 times in the burst and 36000 times in the inter-burst-interval, the proportion of spike in the burst is 4000/ (4000+36000) = 0.1
26. IntraBurstFR: Mean firing rate in the burst activity (unit: Hz)
27. NormalizedIntraBurstFR: Firing rate in the burst activity normalized by the firing rate at rest
28. ThetaOscil: Observation of theta-band (4-7.9 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
29. AlphaOscil: Observation of alpha-band (8-12 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
30. BetaOscil: Observation of beta-band (12.5-30 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
31. LowBetaOscil: Observation of low beta-band (12.5-20 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
32. HighBetaOscil: Observation of high beta-band (20.5-30 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
33. GammaOscil: Observation of gamma-band (30.5-100 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
34. SignificantRamp_rest: Observation of significant ramping activity at rest (0: no ramping, 1: significant ramping)
35. RampingSlope: Slope of the ramping activity at rest (Hz/second)


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DATA SPECIFIC INFORMATION FOR SourceData_Behavior.csv
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Date of Creation: 2024/08/27
Description of Data: This file contains time stamps of the behavioral event in our behavioral task. Each row represents data from a single trial. 
Number of Rows: 371
Number of Columns: 35
Column Names: 
1. Animal: Name of the subject (either Gaia or Isis)
2. Date: Date of the recording 
3. Session: Session number
4. MPTP: Condition of MPTP treatment (0: no treatment, 1: after treatment)
5. Trial: Trial number in the recording session
6. Target: Target number (1: left, 2: right)
7. cue_onset: Time stamp for the go-cue presentation (unit: sec)
8. mvt_onset: Time stamp for the initiation of movement (unit: sec)
9. mvt_end: Time stamp for the end of movement (unit: sec)
10. reward_onset: Time stamp for the initiation of reward delivery (unit: sec)
11. reward_end: Time stamp for the end of reward delivery (unit: sec)
12. return_onset: Time stamp for the initiation of return movement (unit: sec)
13. return_end: Time stamp for the end of return movement (unit: sec)
14. end_of_trial: Time stamp for the end of trial (unit: sec)
Missing data codes: 
   There is no missing data. NaN values are assigned to the timestamps of behavioral events that did not occur during the trial. For instance, in a trial recorded in the 611th row, the animal started reaching 5.52 seconds after the trial began. This movement onset occurred before the go-cue instruction, causing the trial to be classified as a failure. Consequently, behavioral events that did not occur in this trial (such as cue onset, movement end, reward onset, reward end, and return onset) are assigned NaN values.


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DATA SPECIFIC INFORMATION FOR SourceData_dur_Movement.csv
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Date of Creation: 2024/08/25
Description of Data: This file contains metrics of peri-movement activity obtained by running our analysis codes. 
Number of Rows: 371
Number of Columns: 88
Column Names: 
1. UnitID: Identifier number of the GPi unit
	2-21. The assignment of columns 2-21 are same as the assignment of columns 2-21 in the SourceData_at_rest.csv
	22. Target: Target direction (1: left target, 2: right target)
	23. NumSuccessTrial: Total number of successful trials in the recording session
	24. Directionality
	25. periMvt_Resp_Type: This column indicates one of five response types. 0: no significant change in SDF, 1: Increase in SDF, 2: Decrease in SDF, 3: Poly-phasic change in SDF (Increase first, then decrease), 4: Poly-phasic change in SDF (Decrease first, then increase)
	26. periMvt_Cntl_const: Constant of linear regression model fit to the baseline ramping activity (unit: Hz)
	27. periMvt_Cntl_slope: Slope of linear regression model fit to the baseline ramping activity (unit: Hz/sec)
	28. periMvt_Cntl_thre: 95% Confidence interval of the baseline firing rate (unit: Hz). The actual thresholds are mean baseline firing rate +/- confidence interval.
	29. periMvt_Cntl_mean: Mean firing rate during the baseline ramping activity (unit: Hz)
	30. periMvt_Cntl_std: Standard deviation during the baseline ramping activity (unit: Hz)
	31. periMvt_Cntl_std_adj: Standard deviation of the residual baseline activity after subtracting the linear trend (unit: Hz)
	32. meanRT: Mean reaction time (unit: sec)
	33. meanMD: Mean movement duration (unit: sec)
	34. periMvt_Incr_sgn: Observation of significant increase in peri-movement SDF (0: no increase, 1: significant increase)
	35. periMvt_Incr_onset: Onset of the significant increase in peri-movement SDF relative to the movement onset (unit: msec)
	36. periMvt_Incr_magnitude: Magnitude of the significant increase in peri-movement SDF (unit: Hz)
	37. periMvt_Incr_duration: Duration of the significant increase in peri-movement SDF measured (full width at half max, unit: msec)
	38. periMvt_Decr_sgn: Observation of significant decrease in peri-movement SDF (0: no decrease, 1: significant decrease)
	39. periMvt_Decr_onset: Onset of the significant decrease in peri-movement SDF relative to the movement onset (unit: msec)
	40. periMvt_Decr_magnitude: Magnitude of the significant decrease in peri-movement SDF (unit: Hz)
	41. periMvt_Decr_duration: Duration of the significant decrease in peri-movement SDF measured (full width at half max, unit: msec)
	42. periCue_Resp_Type: Response type of peri-go-cue SDF. 0: no significant change in SDF, 1: Increase in SDF, 2: Decrease in SDF, 3: Poly-phasic change in SDF (Increase first, then decrease), 4: Poly-phasic change in SDF (Decrease first, then increase)
	43. periCue_Cntl_const: Constant of linear regression model fit to the baseline ramping activity (unit: Hz)
	44. periCue_Cntl_slope: Slope of linear regression model fit to the baseline ramping activity (unit: Hz/sec)
	45. periCue_Cntl_thre: 95% Confidence interval of the baseline firing rate (unit: Hz). The actual thresholds are mean baseline firing rate +/- confidence interval.
	46. periCue_Cntl_mean: Mean firing rate during the baseline ramping activity (unit: Hz)
	47. periCue_Cntl_std: Standard deviation during the baseline ramping activity (unit: Hz)
	48. periCue_Cntl_std_adj: Standard deviation of the residual baseline activity after subtracting the linear trend (unit: Hz)
	49. periCue_Incr_sgn: Observation of significant increase in peri-go-cue SDF (0: no increase, 1: significant increase)
	50. periCue_Incr_onset: Onset of the significant increase in peri- go-cue SDF relative to the movement onset (unit: msec)
	51. periCue_Incr_magnitude: Magnitude of the significant increase in peri- go-cue SDF (unit: Hz)
	52. periCue_Incr_duration: Duration of the significant increase in peri- go-cue SDF measured (full width at half max, unit: msec)
	53. periCue_Decr_sgn: Observation of significant decrease in peri- go-cue SDF (0: no decrease, 1: significant decrease)
	54. periCue_Decr_onset: Onset of the significant decrease in peri- go-cue SDF relative to the movement onset (unit: msec)
	55. periCue_Decr_magnitude: Magnitude of the significant decrease in peri- go-cue SDF (unit: Hz)
	56. periCue_Decr_duration: Duration of the significant decrease in peri- go-cue SDF measured (full width at half max, unit: msec)
	57. periResp_Resp_Type: Response type of response-aligned SDF. 0: no significant change in SDF, 1: Increase in SDF, 2: Decrease in SDF, 3: Poly-phasic change in SDF (Increase first, then decrease), 4: Poly-phasic change in SDF (Decrease first, then increase)
	58. periResp_Incr_sgn: Observation of significant increase in peak-aligned SDF (0: no increase, 1: significant increase)
	59. periResp_Incr_onset: Onset of the significant increase in peak-aligned SDF relative to the movement onset (unit: msec)
	60. periResp_Incr_magnitude: Magnitude of the significant increase in peak-aligned SDF (unit: Hz)
	61. periResp_Incr_duration: Duration of the significant increase in peak-aligned SDF measured (full width at half max, unit: msec)
	62. periResp_Decr_sgn: Observation of significant decrease in peak-aligned SDF (0: no decrease, 1: significant decrease)
	63. periResp_Decr_onset: Onset of the significant decrease in peak-aligned SDF relative to the movement onset (unit: msec)
	64. periResp_Decr_magnitude: Magnitude of the significant decrease in peak-aligned SDF (unit: Hz)
	65. periResp_Decr_duration: Duration of the significant decrease in peak-aligned SDF measured (full width at half max, unit: msec)
	66. TimeLock_Incr_LockType: Type of event-locked increase in firing rate (1: Cue-locked, 2: Intermediate, 3: Move-locked, 4: Indeterminate)
	67. TimeLock_Incr_ELI: Event-lock-index of the increase in firing rate
	68. TimeLock_Incr_OnsetDispersion: Residual temporal dispersion of increase-type response onset (unit: msec)
	69. TimeLock_Incr_meanCue2RespInterval: Mean interval from go-cue to increase-type response onsets (unit: msec)
	70. TimeLock_Incr_meanResp2MvtInterval: Mean interval from increase-type response onsets to movement onsets (unit: msec)
	71. TimeLock_Decr_LockType: Type of event-locked decrease in firing rate (1: Cue-locked, 2: Intermediate, 3: Move-locked, 4: Indeterminate)
	72. TimeLock_Decr_ELI: Event-lock-index of the decrease in firing rate
	73. TimeLock_Decr_OnsetDispersion: Residual temporal dispersion of decrease-type response onset (unit: msec)
	74. TimeLock_Decr_meanCue2RespInterval: Mean interval from go-cue to decrease-type response onsets
	75. TimeLock_Decr_meanResp2MvtInterval: Mean interval from decrease-type response onsets to movement onsets
	76. FR_rest: Mean firing rate during the whole delay period (Hz)
	77. ThetaOscil_sgn: Observation of theta-band (4-7.9 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
	78. ThetaOscil_pow: Peak power spectrum density in the theta-band (4-7.9 Hz) range at rest
	79. AlphaOscil_sgn: Observation of alpha-band (8-12 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
	80. AlphaOscil_pow: Peak power spectrum density in the alpha-band (8-12 Hz) range at rest
	81. BetaOscil_sgn: Observation of beta-band (12.5-30 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
	82. BetaOscil_pow: Peak power spectrum density in the beta-band (12.5-30 Hz) range at rest
	83. LowBetaOscil_sgn: Observation of low beta-band (12.5-20 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
	84. LowBetaOscil_pow: Peak power spectrum density in the low beta-band (12.5-20 Hz) range at rest
	85. HighBetaOscil_sgn: Observation of high beta-band (20.5-30 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
	86. HighBetaOscil_pow: Peak power spectrum density in the high beta-band (20.5-30 Hz) range at rest
	87. GammaOscil_sgn: Observation of gamma-band (30.5-100 Hz) oscillation at rest (0: no oscillation, 1: significant oscillation)
	88. GammaOscil_pow: Peak power spectrum density in the gamma-band (30.5-100 Hz) range at rest
	

Missing data codes: 
	There is no missing data. NaN values are assigned for the results that we did (could) not analyze (for example, a magnitude of response could not be measured if a GPi unit did not show a significant change in firing rate).


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DATA SPECIFIC INFORMATION FOR SourceData_periMovement_SDF.csv
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Date of Creation: 2024/08/25
Description of Data: This source data contains SDF around the movement (2500 msec prior to the movement onset to 2500 msec after the movement onset) with 1 msec of resolution (5001 data points in total).
Number of Rows: 371
Number of Columns: 5002
Column Names: 
1. UnitID: Identifier number of the GPi unit
2-5002. periMvt_SDF_[index]: SDF at [index] msec in the peri-movement SDF (unit: Hz). Our peri-movement SDF covers -2500 msec to +2500 msec relative to the movement onset with 1 msec of resolution. Therefore, for example, the numbers in periMvt_SDF_2501 column indicate the SDFs at the movement onset.

Missing data codes: 
	There is no missing data.


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DATA SPECIFIC INFORMATION FOR SourceData_examplar_spike.csv
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Date of Creation: 2024/08/25
Description of Data: This data contains the time stamps of spike that occurred around the movement onset (from -2500 msec to +2500 msec relative to the movement onset). This data was used to plot exemplar SDFs and spike rasters.
Number of Rows: 107
	Each row contains the time stamps of the spike activity around the movement onset in one trial.
Number of Columns: 505
Column Names: 
1. UnitID: Identifier of the GPi unit
2. Trial: Trial number
3. Target: Reach target (1: left, 2: right)
4. ReactionTime: Reaction time (time from the presentation of go-cue to the initiation of movement, unit: sec)
5. MovementDur: Movement duration (time from movement onset to movement end, unit: sec)
6-505. Spike_1 through Spike_500: Time stamps of the spike relative to the movement onset (msec). The time stamp of nth spike in the trial is stored in a column Spike_n. If there are m spikes in a trial, Spike_m+1 through Spike_500 will be Nan.


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DATA SPECIFIC INFORMATION FOR SourceData_TH_cell_count.csv
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Date of Creation: 2025/05/28
Description of Data: This file contains the numbers of tyrosine hydroxylase (TH) positive soma in the substantia nigra and ventral tegmental area. This data was used to describe the degree of dopaminergic neuron depletion.
Number of Rows: 13
Number of Columns: 7
Column Names: 
1. Animal: Name of the animal
2. MPTP_Treatment: Condition of MPTP treatment 
    0: No MPTP treatment
    1: Partial MPTP treatment (e.g., minor leakage from internal carotid artery injection to the contralateral side and/or low-dose intramuscular injection)
    2: Full MPTP treatment
3. SectionID: Identifier number of the brain section
4. BrainSide: Side of the brain
5. BrainAreaName: Name of the brain area
    SN: Substantia Nigra
    VTA: Ventral Tegmental Area
6. BrainAreaSurface: Surface size of the brain area (scale: square mm)
7. NumSoma: Number of TH-positive soma in the target brain area

Missing data codes: 
	There is no missing data.


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DATA SPECIFIC INFORMATION FOR SourceData.mat
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Date of Creation: 2024/08/28
Description of Data: This file contains all source data described above. There is no discrepancy in data/structure/column names between CSV format data and MatLab format data.






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DATA ACCESS AND SHARING
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Publications based on this dataset: To be updated
Recommended citation for this dataset: To be updated
License information: To be updated

