gin commit from nit-ope-de04

New files: 26

toy-dataset_patchclamp/dataset_description.json

@@ -0,0 +1,10 @@
+{
+  "LICENCE": "CC-by 4.0",
+  "Name": "Electrophysiology",
+  "BIDSVersion": "1.0.X",
+  "License": "CC BY 4.0",
+  "Authors": [
+    "Alice A",
+    "Bob B"
+  ]
+}

toy-dataset_patchclamp/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

toy-dataset_patchclamp/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"
+    }
+}

toy-dataset_patchclamp/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

toy-dataset_patchclamp/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

toy-dataset_patchclamp/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 wutoff(Hz)": 0.0159,
+        "Roll-off":"6dB/Octave"
+      },
+      "LP_filter_2":{
+        "Half amplitude wutoff(Hz)": 0.1159,
+         "Roll-off":"9 dB/Octave"
+      }
+    }
+  }
+}

toy-dataset_patchclamp/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"
+    }
+}

toy-dataset_patchclamp/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

toy-dataset_patchclamp/sub-20220101A/ephys/sub-20220101A_sample-cell001_run-1_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

toy-dataset_patchclamp/sub-20220101A/ephys/sub-20220101A_sample-cell001_run-1_events.tsv

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+onset	duration	trial_type	response_time	stim_type	stim_unit	stim_amplitude
+1.23	0.65	start	1.435	square pulse	1	mV
+5.65	0.65	stop	1.739	square pulse	5	mV

toy-dataset_patchclamp/sub-20220101A/ephys/sub-20220101A_sample-cell001_run-2_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	100	CAT	uA	30000	Hz	attached patch	LP_filter_1	voltage clamp
+chan-02	con-02	300	PP	uA	50000	Hz	perforated patch	LP_filter_2	voltage clamp

toy-dataset_patchclamp/sub-20220101A/ephys/sub-20220101A_sample-cell001_run-2_events.tsv

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+onset	duration	trial_type	response_time	stim_type	stim_unit	stim_amplitude
+6.21	0.65	start	2.43	square pulse	10	uA
+15.65	0.65	stop	5.68	square pulse	45	uA

toy-dataset_patchclamp/sub-20220101A/sub-20220101A_scans.tsv

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+filename	acq_time
+ephys/sub-2022-01-01-A_run-0_ephys.nix	2022-01-01T10:00:00
+ephys/sub-2022-01-01-A_run-1_ephys.nix	2022-01-01T11:15:00

toy-dataset_patchclamp/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 wutoff(Hz)": 0.0159,
+        "Roll-off":"6dB/Octave"
+      },
+      "LP_filter_2":{
+        "Half amplitude wutoff(Hz)": 0.1159,
+         "Roll-off":"9 dB/Octave"
+      }
+    }
+  }
+}

toy-dataset_patchclamp/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"
+    }
+}

toy-dataset_patchclamp/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

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_sample-cell002_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

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_sample-cell002_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	4

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_sample-cell002_events.tsv

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+onset	duration	trial_type	response_time	stim_type	stim_unit	stim_amplitude
+5	4	start	2.5	square pulse	3	mV
+10	4	stop	2.5	square pulse	3	mV

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_sample-cell003_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-02	con-02	50	WCP	mV	30000	Hz	whole cell patch	LP_filter_2	current clamp

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_sample-cell003_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-02	probe-0237	0	0	0	um	3	GOhm	4	circular	glass	cortical layer 3	3% NaCl	2	4

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_sample-cell003_events.tsv

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+onset	duration	trial_type	response_time	stim_type	stim_unit	stim_amplitude	
+5	4	start	3	square	pulse	3.3	mV
+10	4	stop	3	square	pulse	3.3	mV