Merge branch 'master' of takerkart/BEP032-examples into master

config.yml

@@ -1,3 +1,3 @@
 annex:
     minsize: 0
-    exclude: ["*README*", "*LICENSE*", "config*", "*.json", "*.tsv", "**/.git*"]
+    exclude: ["*README*", "*LICENSE*", "config*", "*.json", "*.tsv", "*.png", "*.jpg", "*.tif", "**/.git*"]

toy-dataset_patchclamp/dataset_description.json

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

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

@@ -1,3 +0,0 @@
-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

@@ -1,3 +0,0 @@
-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

@@ -1,3 +0,0 @@
-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

@@ -1,3 +0,0 @@
-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_events.tsv

@@ -1,16 +0,0 @@
-onset	duration	trial_id	trial_type	recording_type	data_entity_id	channel_id	onset_index	duration_index	sample_id	response_time	stim_type	stim_unit	stim_amplitude
-5	4	1	stimulation	STIM	025c20fc-05e6-401a-9620-95b5e9c9b4bc	chan-01	150000	120000	sample-cell002	2.5	square pulse	3	mV
-10	4	1	stimulation	INT	3aca136f-0851-4eb4-bb37-2070b9745537	chan-02	300000	120000	sample-cell002	2.5	n/a	n/a	n/a
-15	4	1	stimulation	INT	19d7c9d5-0ea1-43c8-a1f5-4a64b9775656	chan-03	450000	120000	sample-cell003	2.5	n/a	n/a	n/a
-20	4	2	stimulation	INT	62342cc5-fe7d-4eca-b702-404f9e7f2ccd	chan-01	600000	120000	sample-cell002	2.5	n/a	n/a	n/a
-25	4	2	stimulation	STIM	1fad915b-c2c6-46aa-9755-a7454805f6fc	chan-02	750000	120000	sample-cell002	2.5	square pulse	3	mV
-30	4	2	stimulation	INT	1910df49-5ff7-4d83-8737-b74d25fd299f	chan-03	900000	120000	sample-cell003	2.5	n/a	n/a	n/a
-35	4	3	stimulation	INT	19c29e83-be68-4ca4-9ca1-d5abe9594fc7	chan-01	1050000	120000	sample-cell002	2.5	n/a	n/a	n/a
-40	4	3	stimulation	INT	cd16b031-5288-42f5-9a7f-17de24eb1004	chan-02	1200000	120000	sample-cell002	2.5	n/a	n/a	n/a
-45	4	3	stimulation	STIM	fe28827e-d848-4a49-bb20-d77049f75b3a	chan-03	1350000	120000	sample-cell003	2.5	square pulse	3	mV
-50	4	4	rest	INT	d7614bcb-8f7d-43e6-879e-877bf227687c	chan-01	1500000	120000	sample-cell002	2.5	n/a	n/a	n/a
-55	4	4	rest	INT	aaa9fa8b-ad5c-40d4-954f-277af4ad8b56	chan-02	1650000	120000	sample-cell002	2.5	n/a	n/a	n/a
-60	4	4	rest	INT	0b254394-9e40-4b00-9c3b-d793b835611e	chan-03	1800000	120000	sample-cell003	2.5	n/a	n/a	n/a
-65	4	5	stimulation	STIM	0d6df00b-70c9-4785-bf0c-71a7acf39974	chan-01	1950000	120000	sample-cell002	2.5	square pulse	3	mV
-70	4	5	stimulation	INT	b35b9e87-d232-4cb3-9d6a-f8797c859c83	chan-02	2100000	120000	sample-cell002	2.5	n/a	n/a	n/a
-75	4	5	stimulation	INT	981fbce9-3d00-444b-8f82-8295e5ceb173	chan-03	2250000	120000	sample-cell003	2.5	n/a	n/a	n/a

toy-dataset_patchclamp_multiple-records-per-file/dataset_description.json

@@ -0,0 +1,10 @@
+{
+  "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"
+  ]
+}

toy-dataset_patchclamp/sub-20220101A/ephys/sub-20220101A_ephys.json

@@ -7,11 +7,11 @@
     "Maintainer": "Charly C",
     "SoftwareFilters": {
       "LP_filter_1":{
-        "Half amplitude wutoff(Hz)": 0.0159,
+        "Half amplitude cutoff(Hz)": 0.0159,
         "Roll-off":"6dB/Octave"
       },
       "LP_filter_2":{
-        "Half amplitude wutoff(Hz)": 0.1159,
+        "Half amplitude cutoff(Hz)": 0.1159,
          "Roll-off":"9 dB/Octave"
       }
     }

toy-dataset_patchclamp_multiple-records-per-file/sub-20220101A/ephys/sub-20220101A_events.tsv

@@ -0,0 +1,5 @@
+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

toy-dataset_patchclamp_multiple-records-per-file/sub-20220101A/sub-20220101A_scans.tsv

@@ -0,0 +1,2 @@
+filename	acq_time
+ephys/sub-20220101A_ephys.nwb	2022-01-01T10:00:00

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_channels.tsv

@@ -1,4 +1,4 @@
 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
-chan-03	con-03	22	CAT	mV	30000	Hz	cell attached patch	LP_filter_2	current clamp
+

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_contacts.tsv

@@ -1,4 +1,4 @@
 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
-con-03	probe-0238	0	0	0	um	5.5	GOhm	3.1	circular	glass	cortical layer 3	9% NaCl	2.8	4.4
+

toy-dataset_patchclamp_multiple-records-per-file/sub-20220101B/ephys/sub-20220101B_ephys.json

@@ -0,0 +1,19 @@
+{
+    "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"
+      }
+    }
+  }
+}

toy-dataset_patchclamp_multiple-records-per-file/sub-20220101B/ephys/sub-20220101B_events.tsv

@@ -0,0 +1,5 @@
+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

toy-dataset_patchclamp_multiple-records-per-file/sub-20220101B/ephys/sub-20220101B_probes.tsv

@@ -0,0 +1,3 @@
+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_multiple-records-per-file/sub-20220101B/sub-20220101B_scans.tsv

@@ -0,0 +1,2 @@
+filename	acq_time
+ephys/sub-20220101B_ephys.nwb	2022-01-01T15:00:00

toy-dataset_patchclamp_single-record-per-file/dataset_description.json

@@ -0,0 +1,10 @@
+{
+  "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"
+  ]
+}

toy-dataset_patchclamp_single-record-per-file/participants.tsv

@@ -0,0 +1,3 @@
+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_single-record-per-file/samples.json

@@ -0,0 +1,8 @@
+{
+    "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_single-record-per-file/samples.tsv

@@ -0,0 +1,6 @@
+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_single-record-per-file/sub-20220101A/ephys/sub-20220101A_channels.tsv

@@ -0,0 +1,3 @@
+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_single-record-per-file/sub-20220101A/ephys/sub-20220101A_contacts.tsv

@@ -0,0 +1,3 @@
+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_single-record-per-file/sub-20220101A/ephys/sub-20220101A_ephys.json

@@ -0,0 +1,19 @@
+{
+    "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"
+      }
+    }
+  }
+}

toy-dataset_patchclamp_single-record-per-file/sub-20220101A/ephys/sub-20220101A_events.json

@@ -0,0 +1,11 @@
+{
+    "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_single-record-per-file/sub-20220101A/ephys/sub-20220101A_probes.tsv

@@ -0,0 +1,3 @@
+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_single-record-per-file/sub-20220101A/ephys/sub-20220101A_sample-cell001_run-1_events.tsv

@@ -0,0 +1,3 @@
+onset	duration	trial_type	channel_id	response_time	stim_type	stim_unit	stim_amplitude
+1.23	0.65	start	chan-01	1.435	square pulse	1	mV
+5.65	0.65	stop	chan-02	1.739	square pulse	5	mV

toy-dataset_patchclamp_single-record-per-file/sub-20220101A/ephys/sub-20220101A_sample-cell001_run-2_events.tsv

@@ -0,0 +1,3 @@
+onset	duration	trial_type	channel_id	response_time	stim_type	stim_unit	stim_amplitude
+0.21	0.65	start	chan-01	2.43	square pulse	10	uA
+9.65	0.65	stop	chan-02	5.68	square pulse	45	uA

toy-dataset_patchclamp_single-record-per-file/sub-20220101A/sub-20220101A_scans.tsv

@@ -0,0 +1,3 @@
+filename	acq_time
+ephys/sub-20220101A_sample-cell001_run-1_ephys.nwb	2022-01-01T10:00:00
+ephys/sub-20220101A_sample-cell001_run-2_ephys.nwb	2022-01-01T10:06:00

toy-dataset_patchclamp/sub-20220101B/ephys/sub-20220101B_ephys.json

@@ -7,11 +7,11 @@
     "Maintainer": "Charly C",
     "SoftwareFilters": {
       "LP_filter_1":{
-        "Half amplitude wutoff(Hz)": 0.0159,
+        "Half amplitude cutoff(Hz)": 0.0159,
         "Roll-off":"6dB/Octave"
       },
       "LP_filter_2":{
-        "Half amplitude wutoff(Hz)": 0.1159,
+        "Half amplitude cutoff(Hz)": 0.1159,
          "Roll-off":"9 dB/Octave"
       }
     }

toy-dataset_patchclamp_single-record-per-file/sub-20220101B/ephys/sub-20220101B_events.json

@@ -0,0 +1,11 @@
+{
+    "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

@@ -1,4 +1,3 @@
 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
-probe-0238	pipette	2	4	2	um	sample	cortical surface	1	5	cm

toy-dataset_patchclamp_single-record-per-file/sub-20220101B/ephys/sub-20220101B_sample-cell002_channels.tsv

@@ -0,0 +1,2 @@
+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_single-record-per-file/sub-20220101B/ephys/sub-20220101B_sample-cell002_contacts.tsv

@@ -0,0 +1,2 @@
+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

toy-dataset_patchclamp_single-record-per-file/sub-20220101B/ephys/sub-20220101B_sample-cell002_events.tsv

@@ -0,0 +1,3 @@
+onset	duration	trial_type	channel_id	response_time	stim_type	stim_unit	stim_amplitude
+5	4	start	chan-01	2.5	square pulse	3	mV
+10	4	stop	chan-01	2.5	square pulse	3	mV

toy-dataset_patchclamp_single-record-per-file/sub-20220101B/ephys/sub-20220101B_sample-cell003_channels.tsv

@@ -0,0 +1,2 @@
+channel_id	contact_id	gain	type	unit	samping_frequency	sampling_frequency_unit	channel_name	hardware_filters	recording_mode
+chan-02	con-02	15	CAT	mV	30000	Hz	cell attached patch	LP_filter_2	current clamp

toy-dataset_patchclamp_single-record-per-file/sub-20220101B/ephys/sub-20220101B_sample-cell003_contacts.tsv

@@ -0,0 +1,2 @@
+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	4.5	GOhm	2.8	circular	glass	cortical layer 3	8% NaCl	2.2	3.5

toy-dataset_patchclamp_single-record-per-file/sub-20220101B/ephys/sub-20220101B_sample-cell003_events.tsv

@@ -0,0 +1,3 @@
+onset	duration	trial_type	channel_id	response_time	stim_type	stim_unit	stim_amplitude	
+0	4	start	chan-02	3	square	pulse	3.3	mV
+5	4	stop	chan-02	3	square	pulse	3.3	mV

toy-dataset_patchclamp_single-record-per-file/sub-20220101B/sub-20220101B_scans.tsv

@@ -0,0 +1,3 @@
+filename	acq_time
+ephys/sub-20220101B_sample-cell002_ephys.nwb	2022-01-01T15:00:00
+ephys/sub-20220101B_sample-cell003_ephys.nwb	2022-01-01T15:15:00