[BEP032] Add updated old icephys dataset

microephys_icephys_bep032/.bidsignore

@@ -0,0 +1,5 @@
+# Placeholder empty NWB files and their sidecars - to be replaced with actual data
+sub-20220101B/icephys/sub-20220101B_sample-cell002_icephys.nwb
+sub-20220101B/icephys/sub-20220101B_sample-cell002_icephys.json
+# Conversion notes documentation
+CONVERSION_NOTES.md

microephys_icephys_bep032/channels.json

@@ -0,0 +1,16 @@
+{
+  "contact_id": {
+    "description": "Identifier of the electrode contact associated with this channel. Links to name column in electrodes.tsv."
+  },
+  "patch_type": {
+    "description": "Type of patch clamp recording technique.",
+    "levels": {
+      "CAT": "Cell-attached patch: Pipette attached to cell membrane without breaking through",
+      "PP": "Perforated patch: Membrane perforated using antibiotic to gain electrical access",
+      "WCP": "Whole-cell patch: Membrane ruptured for direct intracellular access"
+    }
+  },
+  "hardware_filters": {
+    "description": "Name/identifier of hardware filter applied to this channel."
+  }
+}

ephys_BEP032/dataset_description.json → microephys_icephys_bep032/dataset_description.json

@@ -1,7 +1,6 @@
 {
-  "LICENCE": "CC-by 4.0",
   "Name": "Toy example dataset for patchclamp recordings in BIDS",
-  "BIDSVersion": "1.0.X",
+  "BIDSVersion": "1.11.0",
   "License": "CC BY 4.0",
   "Authors": [
     "Sprenger, Julia",

microephys_icephys_bep032/participants.tsv

@@ -0,0 +1,3 @@
+participant_id	species	strain	sex	age
+sub-20220101A	rattus norvegicus	Wistar	male	0.08
+sub-20220101B	rattus norvegicus	Wistar	female	0.08

microephys_icephys_bep032/samples.json

@@ -0,0 +1,12 @@
+{
+    "sample_type": {
+        "description": "Type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type).",
+        "levels": {
+            "tissue": "Brain tissue slice from which cells are derived",
+            "in vitro differentiated cells": "Individual cells patched for intracellular recording"
+        }
+    },
+    "derived_from": {
+        "description": "The sample_id from which this sample is derived. For cells, this is the parent tissue sample."
+    }
+}

ephys_BEP032/samples.tsv → microephys_icephys_bep032/samples.tsv

@@ -3,4 +3,3 @@ 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

microephys_icephys_bep032/sub-20220101A/icephys/sub-20220101A_sample-cell001_channels.tsv

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+name	reference	type	units	sampling_frequency	contact_id	gain	patch_type	hardware_filters	recording_mode
+chan-01	n/a	VM	mV	30000	con-01	20	WCP	LP_filter_1	current clamp
+chan-02	n/a	VM	mV	30000	con-02	50	WCP	LP_filter_2	current clamp

microephys_icephys_bep032/sub-20220101A/icephys/sub-20220101A_sample-cell001_electrodes.tsv

@@ -0,0 +1,3 @@
+name	probe_name	x	y	z	impedance	size	electrode_shape	material	location	pipette_solution	internal_pipette_diameter	external_pipette_diameter
+con-01	probe-0234	0	0	0	5	3	circular	glass	cortical layer 3	5% NaCl	2	4
+con-02	probe-0235	0	0	0	6.9	4	circular	glass	cortical layer 3	5% NaCl	2	4

microephys_icephys_bep032/sub-20220101A/icephys/sub-20220101A_sample-cell001_events.json

@@ -0,0 +1,17 @@
+{
+    "channel_id": {
+        "description": "Identifier of the channel on which the event occurred. Links to name column in channels.tsv."
+    },
+    "sample_id": {
+        "description": "Identifier of the sample (cell) associated with this event."
+    },
+    "stim_type": {
+        "description": "Type of the stimulation (square pulse, sinusoid, etc.)."
+    },
+    "stim_unit": {
+        "description": "Physical unit of the stimulation amplitude."
+    },
+    "stim_amplitude": {
+        "description": "Amplitude of the stimulation in the specified unit."
+    }
+}

ephys_BEP032/sub-20220101A/ephys/sub-20220101A_events.tsv → microephys_icephys_bep032/sub-20220101A/icephys/sub-20220101A_sample-cell001_events.tsv

@@ -1,4 +1,4 @@
-onset	duration	trial_type	data_entity_id	channel_id	sample_id	response_time	stim_type	stim_unit	stim_amplitude
+onset	duration	trial_type	data_entity_id	channel_id	sample_id	response_time	stim_type	stim_amplitude	stim_unit
 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

microephys_icephys_bep032/sub-20220101A/icephys/sub-20220101A_sample-cell001_icephys.nwb

@@ -0,0 +1 @@
+placeholder text

microephys_icephys_bep032/sub-20220101A/icephys/sub-20220101A_sample-cell001_probes.tsv

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+probe_name	type	AP	ML	DV	coordinate_reference_point	electrode_count	height
+probe-0234	pipette	4	3	2	cortical surface	1	5
+probe-0235	pipette	4	3	1	cortical surface	1	5

microephys_icephys_bep032/sub-20220101A/sub-20220101A_scans.tsv

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+filename	acq_time
+icephys/sub-20220101A_sample-cell001_icephys.nwb	2022-01-01T10:00:00

microephys_icephys_bep032/sub-20220101B/icephys/sub-20220101B_sample-cell002_channels.tsv

@@ -0,0 +1,3 @@
+name	reference	type	units	sampling_frequency	contact_id	gain	patch_type	hardware_filters	recording_mode
+chan-01	n/a	VM	mV	30000	con-01	20	WCP	LP_filter_1	current clamp
+chan-02	n/a	VM	mV	30000	con-02	15	WCP	LP_filter_2	current clamp

microephys_icephys_bep032/sub-20220101B/icephys/sub-20220101B_sample-cell002_electrodes.tsv

@@ -0,0 +1,3 @@
+name	probe_name	x	y	z	impedance	size	electrode_shape	material	location	pipette_solution	internal_pipette_diameter	external_pipette_diameter
+con-01	probe-0236	0	0	0	5	3	circular	glass	cortical layer 3	7% NaCl	2.5	4
+con-02	probe-0237	0	0	0	4.5	2.8	circular	glass	cortical layer 3	8% NaCl	2.2	3.5

microephys_icephys_bep032/sub-20220101B/icephys/sub-20220101B_sample-cell002_events.json

@@ -0,0 +1,17 @@
+{
+    "channel_id": {
+        "description": "Identifier of the channel on which the event occurred. Links to name column in channels.tsv."
+    },
+    "sample_id": {
+        "description": "Identifier of the sample (cell) associated with this event."
+    },
+    "stim_type": {
+        "description": "Type of the stimulation (square pulse, sinusoid, etc.)."
+    },
+    "stim_unit": {
+        "description": "Physical unit of the stimulation amplitude."
+    },
+    "stim_amplitude": {
+        "description": "Amplitude of the stimulation in the specified unit."
+    }
+}

microephys_icephys_bep032/sub-20220101B/icephys/sub-20220101B_sample-cell002_events.tsv

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+onset	duration	trial_type	data_entity_id	channel_id	sample_id	response_time	stim_type	stim_amplitude	stim_unit
+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-cell002	3	square pulse	3.3	mV
+20	4	stop	1fad915b-c2c6-46aa-9755-a7454805f6fc	chan-02	sample-cell002	3	square pulse	3.3	mV

microephys_icephys_bep032/sub-20220101B/icephys/sub-20220101B_sample-cell002_probes.tsv

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+probe_name	type	AP	ML	DV	coordinate_reference_point	electrode_count	height
+probe-0236	pipette	2	4	1	cortical surface	1	5
+probe-0237	pipette	2	4	0	cortical surface	1	5

microephys_icephys_bep032/sub-20220101B/sub-20220101B_scans.tsv

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+filename	acq_time
+icephys/sub-20220101B_sample-cell002_icephys.nwb	2022-01-01T15:00:00