[BEP032]: add microelectrode electrophysiology example dataset

dataset_listing.tsv

@@ -94,3 +94,4 @@ emg_MultiBodyParts	EMG recording from multiple body parts with different electro
 emg_TwoHDsEMG	High-density EMG grid recordings from two body parts demonstrating grid placement documentation	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg
 emg_TwoWristbands	EMG recordings using two wristbands with dry electrodes to capture forearm muscle activity	n/a	[@neuromechanist](https://github.com/neuromechanist)	emg	channels, electrodes, coordsystem, emg
 mri_chunk	Example MRI dataset to illustrate BIDS chunk entity. A single subject, two chunks.		[@valosekj](https://github.com/valosekj)	anat	T1w
+microephys	Example microelectrode electrophysiology dataset demonstrating extracellular (ecephys) and intracellular (icephys) recordings in NWB format			ecephys, icephys	channels, ecephys, electrodes, events, icephys, probes, scans

microephys_toy/README

@@ -0,0 +1,65 @@
+Example Microelectrode Electrophysiology Dataset
+=================================================
+
+This example dataset demonstrates the BIDS microelectrode electrophysiology 
+(microephys) specification for both extracellular (ecephys) and intracellular 
+(icephys) recordings.
+
+Features Demonstrated
+---------------------
+
+This dataset demonstrates the following key features:
+
+* **Registration to Allen CCF v3 space**: Electrode positions are provided in 
+  Allen Common Coordinate Framework v3 (see space-AllenCCFv3 files)
+
+* **Multiple probes in a single subject**: sub-mouse01 uses two probes 
+  simultaneously (probe01 and probe02) targeting different brain regions
+
+* **Probe defined in ProbeInterface Library**: probe01 uses the 
+  A1x32-Poly3-10mm-50-177 model from the ProbeInterface library, referenced 
+  via TermURL in the probes.json sidecar
+
+* **Probe defined using a custom ProbeInterface definition**: probe02 uses a 
+  custom probe definition stored in the probes/ directory, referenced via 
+  BIDS URI (bids::probes/customprobe1.json)
+
+Dataset Structure
+-----------------
+
+The dataset contains two subjects:
+
+- sub-mouse01: Extracellular electrophysiology (ecephys) recordings
+  - Session 1: Two recording sessions with different tasks
+  - Uses two silicon probes:
+    - probe01: NeuroNexus A1x32 (32 electrodes) in left motor cortex
+    - probe02: Custom 16-channel probe in right hippocampus CA1
+
+- sub-mouse02: Intracellular electrophysiology (icephys) recordings
+  - Patch-clamp recordings from identified neurons
+  - Current-clamp and voltage-clamp recordings
+
+Data Format
+-----------
+
+All electrophysiology data is stored in NWB format (.nwb files). 
+Note: In this example, placeholder .nwb files are used to demonstrate 
+the file structure. In a real dataset, these would contain actual 
+neural recording data.
+
+Metadata Files
+--------------
+
+Each recording includes:
+- *_probes.tsv: Information about recording probes/pipettes
+- *_probes.json: Probe model definitions with ProbeInterface references
+- *_electrodes.tsv: Electrode positions and properties
+- *_channels.tsv: Recording channel configurations
+- *_ecephys.json or *_icephys.json: Recording parameters and metadata
+- *_events.tsv: Event timing for task-related recordings
+- *_coordsystem.json: Coordinate system information (Allen CCF v3)
+
+
+For more information about the BIDS microelectrode electrophysiology 
+specification, see:
+https://bids-specification.readthedocs.io/en/latest/modality-specific-files/microelectrode-electrophysiology.html

microephys_toy/dataset_description.json

@@ -0,0 +1,27 @@
+{
+    "Name": "Example Microelectrode Electrophysiology Dataset",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "raw",
+    "License": "CC0",
+    "Authors": [
+        "Jane Doe",
+        "John Smith"
+    ],
+    "Acknowledgements": "This example dataset demonstrates the BIDS microelectrode electrophysiology specification.",
+    "HowToAcknowledge": "Please cite the BIDS specification and this example dataset.",
+    "Funding": [
+        "NIH Grant R01-12345",
+        "NSF Grant BCS-67890"
+    ],
+    "ReferencesAndLinks": [
+        "https://bids-specification.readthedocs.io"
+    ],
+    "DatasetDOI": "doi:10.0000/example",
+    "GeneratedBy": [
+        {
+            "Name": "Manual",
+            "Description": "Example dataset created manually for demonstration purposes"
+        }
+    ],
+    "SourceDatasets": []
+}

microephys_toy/participants.json

@@ -0,0 +1,24 @@
+{
+    "participant_id": {
+        "Description": "Unique participant identifier"
+    },
+    "species": {
+        "Description": "Species of the subject"
+    },
+    "strain": {
+        "Description": "Strain of the subject"
+    },
+    "sex": {
+        "Description": "Sex of the subject",
+        "Levels": {
+            "M": "male",
+            "F": "female"
+        }
+    },
+    "age": {
+        "Description": "Age of the subject in postnatal days (P)"
+    },
+    "weight": {
+        "Description": "Weight of the subject"
+    }
+}

microephys_toy/participants.tsv

@@ -0,0 +1,3 @@
+participant_id	species	strain	sex	age	weight
+sub-mouse01	Mus musculus	C57BL/6J	M	P90	25g
+sub-mouse02	Mus musculus	C57BL/6J	F	P85	22g

microephys_toy/probes/customprobe1.json

@@ -0,0 +1,61 @@
+{
+  "specification": "probeinterface",
+  "version": "0.2.21",
+  "probes": [
+    {
+      "ndim": 2,
+      "si_units": "um",
+      "annotations": {
+        "name": "customprobe1",
+        "manufacturer": "Custom Lab"
+      },
+      "contact_positions": [
+        [0, 0],
+        [0, 25],
+        [0, 50],
+        [0, 75],
+        [0, 100],
+        [0, 125],
+        [0, 150],
+        [0, 175],
+        [0, 200],
+        [0, 225],
+        [0, 250],
+        [0, 275],
+        [0, 300],
+        [0, 325],
+        [0, 350],
+        [0, 375]
+      ],
+      "contact_plane_axes": [
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]],
+        [[1, 0], [0, 1]]
+      ],
+      "contact_shapes": "circle",
+      "contact_shape_params": {"radius": 6},
+      "contact_ids": ["e033", "e034", "e035", "e036", "e037", "e038", "e039", "e040", "e041", "e042", "e043", "e044", "e045", "e046", "e047", "e048"],
+      "shank_ids": ["0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0"],
+      "probe_planar_contour": [
+        [-25, -25],
+        [25, -25],
+        [25, 400],
+        [0, 425],
+        [-25, 400]
+      ]
+    }
+  ]
+}

microephys_toy/sub-mouse01/ecephys/sub-mouse01_channels.tsv

@@ -0,0 +1,50 @@
+name	reference	type	units	sampling_frequency	gain	low_cutoff	high_cutoff	status	status_description
+ch001	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch002	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch003	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch004	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch005	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch006	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch007	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch008	e032	LFP	uV	1000	500	0.1	300	bad	high_noise
+ch009	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch010	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch011	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch012	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch013	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch014	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch015	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch016	e032	LFP	uV	1000	500	0.1	300	good	n/a
+ch017	e032	HP	uV	30000	500	300	10000	good	n/a
+ch018	e032	HP	uV	30000	500	300	10000	good	n/a
+ch019	e032	HP	uV	30000	500	300	10000	good	n/a
+ch020	e032	HP	uV	30000	500	300	10000	good	n/a
+ch021	e032	HP	uV	30000	500	300	10000	good	n/a
+ch022	e032	HP	uV	30000	500	300	10000	good	n/a
+ch023	e032	HP	uV	30000	500	300	10000	good	n/a
+ch024	e032	HP	uV	30000	500	300	10000	good	n/a
+ch025	e032	HP	uV	30000	500	300	10000	good	n/a
+ch026	e032	HP	uV	30000	500	300	10000	good	n/a
+ch027	e032	HP	uV	30000	500	300	10000	good	n/a
+ch028	e032	HP	uV	30000	500	300	10000	good	n/a
+ch029	e032	HP	uV	30000	500	300	10000	good	n/a
+ch030	e032	HP	uV	30000	500	300	10000	good	n/a
+ch031	e032	HP	uV	30000	500	300	10000	good	n/a
+ch032	e032	HP	uV	30000	500	300	10000	good	n/a
+ch033	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch034	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch035	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch036	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch037	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch038	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch039	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch040	e048	LFP	uV	1000	500	0.1	300	good	n/a
+ch041	e048	HP	uV	30000	500	300	10000	good	n/a
+ch042	e048	HP	uV	30000	500	300	10000	good	n/a
+ch043	e048	HP	uV	30000	500	300	10000	good	n/a
+ch044	e048	HP	uV	30000	500	300	10000	good	n/a
+ch045	e048	HP	uV	30000	500	300	10000	good	n/a
+ch046	e048	HP	uV	30000	500	300	10000	good	n/a
+ch047	e048	HP	uV	30000	500	300	10000	good	n/a
+ch048	e048	HP	uV	30000	500	300	10000	good	n/a
+sync01	n/a	SYNC	V	30000	1	n/a	n/a	good	n/a

microephys_toy/sub-mouse01/ecephys/sub-mouse01_electrodes.tsv

@@ -0,0 +1,49 @@
+name	probe_name	x	y	z	hemisphere	impedance	shank_id	size	material	location
+e001	probe01	0	0	0	L	1.2	0	12	iridium-oxide	MOp
+e002	probe01	0	0	25	L	1.1	0	12	iridium-oxide	MOp
+e003	probe01	32	0	0	L	1.3	0	12	iridium-oxide	MOp
+e004	probe01	32	0	25	L	1.4	0	12	iridium-oxide	MOp
+e005	probe01	0	0	50	L	1.2	0	12	iridium-oxide	MOp
+e006	probe01	0	0	75	L	1.1	0	12	iridium-oxide	MOp
+e007	probe01	32	0	50	L	1.3	0	12	iridium-oxide	MOp
+e008	probe01	32	0	75	L	1.2	0	12	iridium-oxide	MOp
+e009	probe01	0	0	100	L	1.1	0	12	iridium-oxide	MOp
+e010	probe01	0	0	125	L	1.2	0	12	iridium-oxide	MOp
+e011	probe01	32	0	100	L	1.1	0	12	iridium-oxide	MOp
+e012	probe01	32	0	125	L	1.3	0	12	iridium-oxide	MOp
+e013	probe01	0	0	150	L	1.2	0	12	iridium-oxide	MOp
+e014	probe01	0	0	175	L	1.1	0	12	iridium-oxide	MOp
+e015	probe01	32	0	150	L	1.2	0	12	iridium-oxide	MOp
+e016	probe01	32	0	175	L	1.1	0	12	iridium-oxide	MOp
+e017	probe01	0	0	200	L	1.3	0	12	iridium-oxide	MOp
+e018	probe01	0	0	225	L	1.2	0	12	iridium-oxide	MOp
+e019	probe01	32	0	200	L	1.1	0	12	iridium-oxide	MOp
+e020	probe01	32	0	225	L	1.2	0	12	iridium-oxide	MOp
+e021	probe01	0	0	250	L	1.1	0	12	iridium-oxide	MOp
+e022	probe01	0	0	275	L	1.3	0	12	iridium-oxide	MOp
+e023	probe01	32	0	250	L	1.2	0	12	iridium-oxide	MOp
+e024	probe01	32	0	275	L	1.1	0	12	iridium-oxide	MOp
+e025	probe01	0	0	300	L	1.2	0	12	iridium-oxide	MOp
+e026	probe01	0	0	325	L	1.1	0	12	iridium-oxide	MOp
+e027	probe01	32	0	300	L	1.3	0	12	iridium-oxide	MOp
+e028	probe01	32	0	325	L	1.2	0	12	iridium-oxide	MOp
+e029	probe01	0	0	350	L	1.1	0	12	iridium-oxide	MOp
+e030	probe01	0	0	375	L	1.2	0	12	iridium-oxide	MOp
+e031	probe01	32	0	350	L	1.1	0	12	iridium-oxide	MOp
+e032	probe01	32	0	375	L	1.3	0	12	iridium-oxide	MOp
+e033	probe02	0	0	0	R	1.5	0	12	iridium-oxide	CA1
+e034	probe02	0	0	25	R	1.4	0	12	iridium-oxide	CA1
+e035	probe02	0	0	50	R	1.6	0	12	iridium-oxide	CA1
+e036	probe02	0	0	75	R	1.3	0	12	iridium-oxide	CA1
+e037	probe02	0	0	100	R	1.5	0	12	iridium-oxide	CA1
+e038	probe02	0	0	125	R	1.4	0	12	iridium-oxide	CA1
+e039	probe02	0	0	150	R	1.6	0	12	iridium-oxide	CA1
+e040	probe02	0	0	175	R	1.3	0	12	iridium-oxide	CA1
+e041	probe02	0	0	200	R	1.5	0	12	iridium-oxide	CA1
+e042	probe02	0	0	225	R	1.4	0	12	iridium-oxide	CA1
+e043	probe02	0	0	250	R	1.6	0	12	iridium-oxide	CA1
+e044	probe02	0	0	275	R	1.3	0	12	iridium-oxide	CA1
+e045	probe02	0	0	300	R	1.5	0	12	iridium-oxide	CA1
+e046	probe02	0	0	325	R	1.4	0	12	iridium-oxide	CA1
+e047	probe02	0	0	350	R	1.6	0	12	iridium-oxide	CA1
+e048	probe02	0	0	375	R	1.3	0	12	iridium-oxide	CA1

microephys_toy/sub-mouse01/ecephys/sub-mouse01_probes.json

@@ -0,0 +1,14 @@
+{
+  "model": {
+    "Levels": {
+      "A1x32-Poly3-10mm-50-177": {
+        "Description": "NeuroNexus A1x32-Poly3-10mm-50-177, a 1-shank 32-channel polytrode probe with contacts arranged in a Poly3 configuration",
+        "TermURL": "https://raw.githubusercontent.com/SpikeInterface/probeinterface_library/refs/heads/main/neuronexus/A1x32-Poly3-10mm-50-177/A1x32-Poly3-10mm-50-177.json"
+      },
+      "customprobe1": {
+        "Description": "Custom experimental 16-channel linear silicon probe designed for hippocampal recordings",
+        "TermURL": "bids::probes/customprobe1.json"
+      }
+    }
+  }
+}

microephys_toy/sub-mouse01/ecephys/sub-mouse01_probes.tsv

@@ -0,0 +1,3 @@
+probe_name	type	AP	ML	DV	AP_angle	ML_angle	rotation_angle	hemisphere	manufacturer	model	device_serial_number	electrode_count	width	height	depth	dimension_unit	coordinate_reference_point	anatomical_reference_point	associated_brain_region	associated_brain_region_id	reference_atlas	material
+probe01	silicon-probe	-2.5	1.5	-4.0	15	0	0	L	NeuroNexus	A1x32-Poly3-10mm-50-177	NP1100-2205	32	70	20	3840	um	tip	Bregma	Primary Motor Cortex	MOp	Allen-CCF-2017	silicon
+probe02	silicon-probe	-1.8	2.0	-3.5	10	5	0	R	Custom Lab	customprobe1	CUSTOM-001	16	50	15	2000	um	tip	Bregma	Hippocampus CA1	CA1	Allen-CCF-2017	silicon

microephys_toy/sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_coordsystem.json

@@ -0,0 +1,7 @@
+{
+    "MicroephysCoordinateSystem": "AllenCCFv3",
+    "MicroephysCoordinateUnits": "um",
+    "MicroephysCoordinateSystemDescription": "Allen Mouse Brain Common Coordinate Framework version 3. The origin is at the anterior commissure. X is anterior-posterior (anterior positive), Y is inferior-superior (superior positive), Z is left-right (right positive). Coordinates are in micrometers.",
+    "MicroephysCoordinateProcessingDescription": "Electrode positions were registered to the Allen CCF using anatomical landmarks and histological verification.",
+    "MicroephysCoordinateProcessingReference": "https://doi.org/10.1016/j.cell.2020.04.007"
+}

microephys_toy/sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_electrodes.tsv

@@ -0,0 +1,49 @@
+name	probe_name	x	y	z	hemisphere	impedance	shank_id	size	material	location
+e001	probe01	5700	4200	3800	L	1.2	0	12	iridium-oxide	MOp
+e002	probe01	5700	4200	3775	L	1.1	0	12	iridium-oxide	MOp
+e003	probe01	5732	4200	3800	L	1.3	0	12	iridium-oxide	MOp
+e004	probe01	5732	4200	3775	L	1.4	0	12	iridium-oxide	MOp
+e005	probe01	5700	4200	3750	L	1.2	0	12	iridium-oxide	MOp
+e006	probe01	5700	4200	3725	L	1.1	0	12	iridium-oxide	MOp
+e007	probe01	5732	4200	3750	L	1.3	0	12	iridium-oxide	MOp
+e008	probe01	5732	4200	3725	L	1.2	0	12	iridium-oxide	MOp
+e009	probe01	5700	4200	3700	L	1.1	0	12	iridium-oxide	MOp
+e010	probe01	5700	4200	3675	L	1.2	0	12	iridium-oxide	MOp
+e011	probe01	5732	4200	3700	L	1.1	0	12	iridium-oxide	MOp
+e012	probe01	5732	4200	3675	L	1.3	0	12	iridium-oxide	MOp
+e013	probe01	5700	4200	3650	L	1.2	0	12	iridium-oxide	MOp
+e014	probe01	5700	4200	3625	L	1.1	0	12	iridium-oxide	MOp
+e015	probe01	5732	4200	3650	L	1.2	0	12	iridium-oxide	MOp
+e016	probe01	5732	4200	3625	L	1.1	0	12	iridium-oxide	MOp
+e017	probe01	5700	4200	3600	L	1.3	0	12	iridium-oxide	MOp
+e018	probe01	5700	4200	3575	L	1.2	0	12	iridium-oxide	MOp
+e019	probe01	5732	4200	3600	L	1.1	0	12	iridium-oxide	MOp
+e020	probe01	5732	4200	3575	L	1.2	0	12	iridium-oxide	MOp
+e021	probe01	5700	4200	3550	L	1.1	0	12	iridium-oxide	MOp
+e022	probe01	5700	4200	3525	L	1.3	0	12	iridium-oxide	MOp
+e023	probe01	5732	4200	3550	L	1.2	0	12	iridium-oxide	MOp
+e024	probe01	5732	4200	3525	L	1.1	0	12	iridium-oxide	MOp
+e025	probe01	5700	4200	3500	L	1.2	0	12	iridium-oxide	MOp
+e026	probe01	5700	4200	3475	L	1.1	0	12	iridium-oxide	MOp
+e027	probe01	5732	4200	3500	L	1.3	0	12	iridium-oxide	MOp
+e028	probe01	5732	4200	3475	L	1.2	0	12	iridium-oxide	MOp
+e029	probe01	5700	4200	3450	L	1.1	0	12	iridium-oxide	MOp
+e030	probe01	5700	4200	3425	L	1.2	0	12	iridium-oxide	MOp
+e031	probe01	5732	4200	3450	L	1.1	0	12	iridium-oxide	MOp
+e032	probe01	5732	4200	3425	L	1.3	0	12	iridium-oxide	MOp
+e033	probe02	7800	3500	2800	R	1.2	0	15	iridium	CA1
+e034	probe02	7800	3500	2750	R	1.1	0	15	iridium	CA1
+e035	probe02	7800	3500	2700	R	1.3	0	15	iridium	CA1
+e036	probe02	7800	3500	2650	R	1.2	0	15	iridium	CA1
+e037	probe02	7800	3500	2600	R	1.4	0	15	iridium	CA1
+e038	probe02	7800	3500	2550	R	1.1	0	15	iridium	CA1
+e039	probe02	7800	3500	2500	R	1.2	0	15	iridium	CA1
+e040	probe02	7800	3500	2450	R	1.3	0	15	iridium	CA1
+e041	probe02	7800	3500	2400	R	1.2	0	15	iridium	CA1
+e042	probe02	7800	3500	2350	R	1.1	0	15	iridium	CA1
+e043	probe02	7800	3500	2300	R	1.4	0	15	iridium	CA1
+e044	probe02	7800	3500	2250	R	1.2	0	15	iridium	CA1
+e045	probe02	7800	3500	2200	R	1.3	0	15	iridium	CA1
+e046	probe02	7800	3500	2150	R	1.1	0	15	iridium	CA1
+e047	probe02	7800	3500	2100	R	1.2	0	15	iridium	CA1
+e048	probe02	7800	3500	2050	R	1.3	0	15	iridium	CA1