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*"]

ephys_nix/participants.json

@@ -1,29 +1,29 @@
 {
-  "SubjectID": {
+  "subject_id": {
     "Description": "Short identifier for monkey (e.g., used in file names)"
   },
-  "Species": {
+  "species": {
     "Description": "binomial species name (genus, species with genus)"
   },
-  "Sex": {
+  "sex": {
     "Description": "Sex of the animal (male/female)"
   },
-  "Birthdate": {
+  "birthdate": {
     "Description": "Date of birth"
   },
-  "Handedness": {
+  "handedness": {
     "Description": "Trained hand (left and/or right)"
   },
-  "SurgeryDate": {
+  "surgerydate": {
     "Description": "Date of the surgery"
   },
-  "Disabilities": {
+  "disabilities": {
     "Description": "Comment on existing disabilities"
   },
-  "Character": {
+  "character": {
     "Description": "Comment on the general character/personality"
   },
-  "GivenName": {
+  "given_name": {
     "Description": "Given Name"
   }
-}
+}

ephys_nix/sub-i/ses-140703/ephys/sub-i_ses-101210_coordsystem.json

@@ -0,0 +1,5 @@
+{
+  "ephysCoordinateSystem": "Pixels”,
+  "ephysCoordinateUnits": "pixels",
+  "ephysCoordinateSystemPhoto": "bids:ephys_nix/sub-l/ses-101210/ephys/sub-l_ses-101210_photo.png",
+}

ephys_nix/sub-i/ses-140703/ephys/sub-i_ses-140703_task-r2g_run-001_probes.tsv

@@ -1,2 +1,2 @@
-probe_id	type	location	placement_picture	hemisphere	manufacturer	device_serial_number	contact_count	depth	width	height	dimension_units	wires_material	wires_diameter	wires_length	wires_units	owner
-Prob-8596-001139	utah array	M1	https://www.nature.com/articles/sdata201855/figures/1	right	Blackrock Microsystems	8596-001139	100	1.5	4	4	mm	Pt/Au	0.000025	0.04	m	RIKEN-BSI, Japan
+probe_id	type	location	x	y	z	alpha_rotation	hemisphere	manufacturer	device_serial_number	contact_count	depth	width	height	dimension_units	wires_material	wires_diameter	wires_length	wires_units	owner
+Prob-8596-001139	utah array	M1	211	345	n/a	239	right	Blackrock Microsystems	8596-001139	100	1.5	4	4	mm	Pt/Au	2.5E-05	0.04	m	RIKEN-BSI, Japan

ephys_nix/sub-i/sub-i_sessions.json

@@ -1,23 +1,32 @@
 {
-  "SessionId": {
+  "session_id": {
     "Description": "Unique identifier of the session"
   },
-  "SessionQuality": {
+  "session_quality": {
     "Description": "General quality of the session (excellent/good/ok/bad)"
   },
-  "DataQuality": {
+  "data_quality": {
     "Description": "Quality of the recorded data (excellent/good/ok/bad)"
   },
-  "#Trials": {
+  "number_of_trials": {
     "Description": "Number of trial within the session"
   },
-  "Comment": {
+  "comment": {
     "Description": "Comment by the experimenter"
   },
-  "Weekday": {
+  "weekday": {
     "Description": "Day of the week the recording was performed (monday,tuesday,...)"
+    "Levels": {
+      "monday" : "The first day of the week",
+      "tuesday": "The second day of the week",
+      "wednesday": "The third day of the week",
+      "thursday" : "The fourth day of the week",
+      "friday": "The fifth day of the week",
+      "saturday": "The sixth day of the week",
+      "sunday": "The seventh day of the week"
+    }
   },
-  "Noisy": {
+  "noisy": {
     "Description": "Was noise observed in the data during the recording (yes/no)"
   }
-}
+}

ephys_nix/sub-l/ses-101210/ephys/sub-l_ses-101210_task-r2g_run-001_coordsystem.json

@@ -0,0 +1,5 @@
+{
+  "ephysCoordinateSystem": "Pixels”,
+  "ephysCoordinateUnits": "pixels",
+  "ephysCoordinateSystemPhoto": "bids:ephys_nix/sub-l/ses-101210/ephys/sub-l_ses-101210_photo.png",
+}

ephys_nix/sub-l/ses-101210/ephys/sub-l_ses-101210_task-r2g_run-001_probes.tsv

@@ -1,2 +1,2 @@
-probe_id	type	location	placement_picture	hemisphere	manufacturer	device_serial_number	contact_count	depth	width	height	dimension_units	wires_material	wires_diameter	wires_length	wires_units	owner
-prob-1025-0503	utah array	M1	https://www.nature.com/articles/sdata201855/figures/1	right	Blackrock Microsystems	1025-0503	100	1.5	4	4	mm	Pt/Au	2.5E-05	0.04	m	RIKEN-BSI, Japan
+probe_id	type	location	hemisphere	x	y	z	alpha_rotation	manufacturer	device_serial_number	contact_count	depth	width	height	dimension_units	wires_material	wires_diameter	wires_length	wires_units	owner
+prob-1025-0503	utah array	M1	right	166	212	n/a	216	Blackrock Microsystems	1025-0503	100	1.5	4	4	mm	Pt/Au	2.5E-05	0.04	m	RIKEN-BSI, Japan

ephys_nix/sub-l/sub-l_sessions.json

@@ -1,23 +1,32 @@
 {
-  "SessionId": {
+  "session_id": {
     "Description": "Unique identifier of the session"
   },
-  "SessionQuality": {
+  "session_quality": {
     "Description": "General quality of the session (excellent/good/ok/bad)"
   },
-  "DataQuality": {
+  "data_quality": {
     "Description": "Quality of the recorded data (excellent/good/ok/bad)"
   },
-  "#Trials": {
+  "number_of_trials": {
     "Description": "Number of trial within the session"
   },
-  "Comment": {
+  "comment": {
     "Description": "Comment by the experimenter"
   },
-  "Weekday": {
+  "weekday": {
     "Description": "Day of the week the recording was performed (monday,tuesday,...)"
+    "Levels": {
+      "monday" : "The first day of the week",
+      "tuesday": "The second day of the week",
+      "wednesday": "The third day of the week",
+      "thursday" : "The fourth day of the week",
+      "friday": "The fifth day of the week",
+      "saturday": "The sixth day of the week",
+      "sunday": "The seventh day of the week"
+    }
   },
-  "Noisy": {
+  "noisy": {
     "Description": "Was noise observed in the data during the recording (yes/no)"
   }
-}
+}

ephys_nix/sub-l/sub-l_sessions.tsv

@@ -1,3 +1,2 @@
-"session_id
-"	session_quality	data_quality	#_trials	comment	weekday	noisy
+session_id	session_quality	data_quality	number_of_trials	comment	weekday	noisy
 101210	excellent	good	204	n/a	friday	yes

ephys_nix/tasks.json

@@ -1,12 +0,0 @@
-{
-  "TaskID": {
-    "Description": "Unique identifier of the task",
-    "Level": {
-      "r2g": {
-        "Description": "A task that involves the reaching of an object and holding it for a specific time",
-        "LongName": "Reach-to-Grasp",
-        "task_type": "two-cue"
-      }
-    }
-  }
-}

ephys_nix/tasks.tsv

@@ -1,2 +0,0 @@
-task_name
-task-r2g

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

@@ -1,10 +1,10 @@
 {
   "LICENCE": "CC-by 4.0",
-  "Name": "Electrophysiology",
+  "Name": "Toy example dataset for patchclamp recordings in BIDS",
   "BIDSVersion": "1.0.X",
   "License": "CC BY 4.0",
   "Authors": [
-    "Alice A",
-    "Bob B"
+    "Sprenger, Julia",
+    "Takerkart, Sylvain"
   ]
 }

toy-dataset_patchclamp_multiple-records-per-file/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

@@ -1,5 +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
+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_multiple-records-per-file/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_multiple-records-per-file/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
-

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/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_single-record-per-file/sub-20220101A/ephys/sub-20220101A_sample-cell001_run-1_events.tsv

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

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

@@ -1,3 +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	2022-01-01T11:15:00
+ephys/sub-20220101A_sample-cell001_run-2_ephys.nwb	2022-01-01T10:06:00

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

@@ -1,4 +0,0 @@
-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_single-record-per-file/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_sample-cell002_contacts.tsv

@@ -1,2 +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	4
+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

@@ -1,3 +1,3 @@
-onset	duration	trial_type	data_identity_id	channel_id	response_time	stim_type	stim_unit	stim_amplitude
-5	4	start	d7614bcb-8f7d-43e6-879e-877bf227687c	chan-01		2.5	square pulse	3	mV
-10	4	stop	0d6df00b-70c9-4785-bf0c-71a7acf39974	chan-01		2.5	square pulse	3	mV
+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

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

@@ -1,2 +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	3	GOhm	4	circular	glass	cortical layer 3	3% NaCl	2	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

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

@@ -1,3 +1,3 @@
-onset	duration	trial_type	data_identity_id	channel_id	response_time	stim_type	stim_unit	stim_amplitude	
-15	4	start	025c20fc-05e6-401a-9620-95b5e9c9b4bc	chan-02		3	square	pulse	3.3	mV
-20	4	stop	1fad915b-c2c6-46aa-9755-a7454805f6fc	chan-02		3	square	pulse	3.3	mV
+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

@@ -1,3 +1,3 @@
 filename	acq_time
 ephys/sub-20220101B_sample-cell002_ephys.nwb	2022-01-01T15:00:00
-ephys/sub-20220101B_sample-cell003_ephys.nwb	2022-01-01T16:30:00
+ephys/sub-20220101B_sample-cell003_ephys.nwb	2022-01-01T15:15:00