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Draft examples for BEP032 on animal electrophysiology #430

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Draft examples for BEP032 on animal electrophysiology #430

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ca1d69b
Added BEP032 example dataset
TheChymera Mar 12, 2024
669ff8b
Fixed JSON, better indentation
TheChymera Mar 15, 2024
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3 changes: 3 additions & 0 deletions ephys_BEP032/README.md
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# Dataset Description

Example dataset for BEP032 ( https://gin.g-node.org/NeuralEnsemble/BEP032-examples )
10 changes: 10 additions & 0 deletions ephys_BEP032/dataset_description.json
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{
"LICENCE": "CC-by 4.0",
"Name": "Toy example dataset for patchclamp recordings in BIDS",
"BIDSVersion": "1.0.X",
"License": "CC BY 4.0",
"Authors": [
"Sprenger, Julia",
"Takerkart, Sylvain"
]
}
3 changes: 3 additions & 0 deletions ephys_BEP032/participants.tsv
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subject_id species strain sex age
sub-20220101A rattus norvegicus C57BL/6J male 30
sub-20220101B rattus norvegicus C57BL/6J female 30
8 changes: 8 additions & 0 deletions ephys_BEP032/samples.json
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{
"sample_type": {
"Description": "type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type)",
},
"derived_from": {
"Description": "sample_id from which the sample is derived"
}
}
6 changes: 6 additions & 0 deletions ephys_BEP032/samples.tsv
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sample_id sample_type participant_id derived_from
sample-tissue01 tissue sub-20220101A n/a
sample-cell001 in vitro differentiated cells sub-20220101A sample-tissue01
sample-tissue02 tissue sub-20220101B n/a
sample-cell002 in vitro differentiated cells sub-20220101B sample-tissue02
sample-cell003 in vitro differentiated cells sub-20220101B sample-tissue02
3 changes: 3 additions & 0 deletions ephys_BEP032/sub-20220101A/ephys/sub-20220101A_channels.tsv
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channel_id contact_id gain type unit samping_frequency sampling_frequency_unit channel_name hardware_filters recording_mode
chan-01 con-01 20 CAT mV 30000 Hz attached patch LP_filter_1 current clamp
chan-02 con-02 50 PP mV 50000 Hz perforated patch LP_filter_2 current clamp
3 changes: 3 additions & 0 deletions ephys_BEP032/sub-20220101A/ephys/sub-20220101A_contacts.tsv
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contact_id probe_id x y z physical_unit impedance impedance_unit contact_size contact_shape material location pipette_solution internal_pipette_diameter external_pipette_diameter
con-01 probe-0234 0 0 0 um 5 GOhm 3 circular glass cortical layer 3 5% NaCl 2 4
con-02 probe-0235 0 0 0 um 6.9 GOhm 4 circular glass cortical layer 3 5% NaCl 2 4
18 changes: 18 additions & 0 deletions ephys_BEP032/sub-20220101A/ephys/sub-20220101A_ephys.json
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{
"InstitutionName": "Institute XY",
"Location": "Somewhere on the globe",
"PowerLineFrequency": 50,
"SamplingFrequency": 30000,
"SamplingFrequencyUnit": "Hz",
"Maintainer": "Charly C",
"SoftwareFilters": {
"LP_filter_1":{
"Half amplitude cutoff(Hz)": 0.0159,
"Roll-off":"6dB/Octave"
},
"LP_filter_2":{
"Half amplitude cutoff(Hz)": 0.1159,
"Roll-off":"9 dB/Octave"
}
}
}
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11 changes: 11 additions & 0 deletions ephys_BEP032/sub-20220101A/ephys/sub-20220101A_events.json
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{
"stim_type": {
"Description": "type of the stimulation (square pulse, sinusoid, ...)",
},
"stim_unit": {
"Description": "physical unit of the stimulation"
},
"stim_amplitude": {
"Description": "physical amplitude of the stimulation"
}
}
5 changes: 5 additions & 0 deletions ephys_BEP032/sub-20220101A/ephys/sub-20220101A_events.tsv
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onset duration trial_type data_entity_id channel_id sample_id response_time stim_type stim_unit stim_amplitude
1.23 0.65 start 62342cc5-fe7d-4eca-b702-404f9e7f2ccd chan-01 sample-cell001 1.435 square pulse 1 mV
5.65 0.65 stop 3aca136f-0851-4eb4-bb37-2070b9745537 chan-02 sample-cell001 1.739 square pulse 5 mV
6.21 0.65 start cd16b031-5288-42f5-9a7f-17de24eb1004 chan-01 sample-cell001 2.43 square pulse 10 uA
15.65 0.65 stop b35b9e87-d232-4cb3-9d6a-f8797c859c83 chan-02 sample-cell001 5.68 square pulse 45 uA
3 changes: 3 additions & 0 deletions ephys_BEP032/sub-20220101A/ephys/sub-20220101A_probes.tsv
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probe_id type x y z xyz_position_unit coordinate_space coordinate_reference_point contact_count height dimension_unit
probe-0234 pipette 4 3 2 um sample cortical surface 1 5 cm
probe-0235 pipette 4 3 1 um sample cortical surface 1 5 cm
2 changes: 2 additions & 0 deletions ephys_BEP032/sub-20220101A/sub-20220101A_scans.tsv
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filename acq_time
ephys/sub-20220101A_ephys.nwb 2022-01-01T10:00:00
4 changes: 4 additions & 0 deletions ephys_BEP032/sub-20220101B/ephys/sub-20220101B_channels.tsv
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channel_id contact_id gain type unit samping_frequency sampling_frequency_unit channel_name hardware_filters recording_mode
chan-01 con-01 20 WCP mV 30000 Hz whole cell patch LP_filter_1 current clamp
chan-02 con-02 15 CAT mV 30000 Hz cell attached patch LP_filter_2 current clamp

4 changes: 4 additions & 0 deletions ephys_BEP032/sub-20220101B/ephys/sub-20220101B_contacts.tsv
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contact_id probe_id x y z physical_unit impedance impedance_unit contact_size contact_shape material location pipette_solution internal_pipette_diameter external_pipette_diameter
con-01 probe-0236 0 0 0 um 5 GOhm 3 circular glass cortical layer 3 7% NaCl 2.5 4
con-02 probe-0237 0 0 0 um 4.5 GOhm 2.8 circular glass cortical layer 3 8% NaCl 2.2 3.5

18 changes: 18 additions & 0 deletions ephys_BEP032/sub-20220101B/ephys/sub-20220101B_ephys.json
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{
"InstitutionName": "Institute XY",
"Location": "Somewhere on the globe",
"PowerLineFrequency": 50,
"SamplingFrequency": 30000,
"SamplingFrequencyUnit": "Hz",
"Maintainer": "Charly C",
"SoftwareFilters": {
"LP_filter_1":{
"Half amplitude cutoff(Hz)": 0.0159,
"Roll-off":"6dB/Octave"
},
"LP_filter_2":{
"Half amplitude cutoff(Hz)": 0.1159,
"Roll-off":"9 dB/Octave"
}
}
}
Empty file added ephys_BEP032/sub-20220101B/ephys/sub-20220101B_ephys.nwb
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11 changes: 11 additions & 0 deletions ephys_BEP032/sub-20220101B/ephys/sub-20220101B_events.json
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{
"stim_type": {
"Description": "type of the stimulation (square pulse, sinusoid, ...)",
},
"stim_unit": {
"Description": "physical unit of the stimulation"
},
"stim_amplitude": {
"Description": "physical amplitude of the stimulation"
}
}
5 changes: 5 additions & 0 deletions ephys_BEP032/sub-20220101B/ephys/sub-20220101B_events.tsv
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onset duration trial_id trial_type data_entity_id channel_id sample_id response_time stim_type stim_unit stim_amplitude
5 4 start d7614bcb-8f7d-43e6-879e-877bf227687c chan-01 sample-cell002 2.5 square pulse 3 mV
10 4 stop 0d6df00b-70c9-4785-bf0c-71a7acf39974 chan-01 sample-cell002 2.5 square pulse 3 mV
15 4 start 025c20fc-05e6-401a-9620-95b5e9c9b4bc chan-02 sample-cell003 3 square pulse 3.3 mV
20 4 stop 1fad915b-c2c6-46aa-9755-a7454805f6fc chan-02 sample-cell003 3 square pulse 3.3 mV
3 changes: 3 additions & 0 deletions ephys_BEP032/sub-20220101B/ephys/sub-20220101B_probes.tsv
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probe_id type x y z xyz_position_unit coordinate_space coordinate_reference_point contact_count height dimension_unit
probe-0236 pipette 2 4 1 um sample cortical surface 1 5 cm
probe-0237 pipette 2 4 0 um sample cortical surface 1 5 cm
2 changes: 2 additions & 0 deletions ephys_BEP032/sub-20220101B/sub-20220101B_scans.tsv
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filename acq_time
ephys/sub-20220101B_ephys.nwb 2022-01-01T15:00:00
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