diff --git a/dataset_listing.tsv b/dataset_listing.tsv index f6367d11b..710b85053 100644 --- a/dataset_listing.tsv +++ b/dataset_listing.tsv @@ -94,6 +94,7 @@ 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_toy Example microelectrode electrophysiology dataset demonstrating extracellular (ecephys) and intracellular (icephys) recordings in NWB format ecephys, icephys channels, ecephys, electrodes, events, icephys, probes, scans atlas-Destrieux n/a n/a atlas-Schaefer n/a n/a eyetracking_binocular beh events, physio diff --git a/microephys_toy/README b/microephys_toy/README new file mode 100644 index 000000000..296808fd8 --- /dev/null +++ b/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 diff --git a/microephys_toy/dataset_description.json b/microephys_toy/dataset_description.json new file mode 100644 index 000000000..3301f5e4c --- /dev/null +++ b/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": [] +} diff --git a/microephys_toy/participants.json b/microephys_toy/participants.json new file mode 100644 index 000000000..f01e219c3 --- /dev/null +++ b/microephys_toy/participants.json @@ -0,0 +1,15 @@ +{ + "age": { + "LongName": "Subject age", + "Description": "Subject postnatal age (in days)", + "Format": "number", + "Units": "day", + "Maximum": 365 + }, + "weight": { + "Description": "Weight of the subject", + "Format": "number", + "Units": "g", + "Maximum": 1000 + } +} diff --git a/microephys_toy/participants.tsv b/microephys_toy/participants.tsv new file mode 100644 index 000000000..8abe4ca3d --- /dev/null +++ b/microephys_toy/participants.tsv @@ -0,0 +1,3 @@ +participant_id species strain sex age weight +sub-mouse01 Mus musculus C57BL/6J M 90 25 +sub-mouse02 Mus musculus C57BL/6J F 85 22 diff --git a/microephys_toy/probes/customprobe1.json b/microephys_toy/probes/customprobe1.json new file mode 100644 index 000000000..8ad90cd43 --- /dev/null +++ b/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] + ] + } + ] +} diff --git a/microephys_toy/sub-mouse01/ecephys/sub-mouse01_channels.tsv b/microephys_toy/sub-mouse01/ecephys/sub-mouse01_channels.tsv new file mode 100644 index 000000000..ff59d9540 --- /dev/null +++ b/microephys_toy/sub-mouse01/ecephys/sub-mouse01_channels.tsv @@ -0,0 +1,50 @@ +name electrode_name type units sampling_frequency gain low_cutoff high_cutoff status status_description +ch001 e001 LFP uV 1000 500 0.1 300 good n/a +ch002 e002 LFP uV 1000 500 0.1 300 good n/a +ch003 e003 LFP uV 1000 500 0.1 300 good n/a +ch004 e004 LFP uV 1000 500 0.1 300 good n/a +ch005 e005 LFP uV 1000 500 0.1 300 good n/a +ch006 e006 LFP uV 1000 500 0.1 300 good n/a +ch007 e007 LFP uV 1000 500 0.1 300 good n/a +ch008 e008 LFP uV 1000 500 0.1 300 bad high_noise +ch009 e009 LFP uV 1000 500 0.1 300 good n/a +ch010 e010 LFP uV 1000 500 0.1 300 good n/a +ch011 e011 LFP uV 1000 500 0.1 300 good n/a +ch012 e012 LFP uV 1000 500 0.1 300 good n/a +ch013 e013 LFP uV 1000 500 0.1 300 good n/a +ch014 e014 LFP uV 1000 500 0.1 300 good n/a +ch015 e015 LFP uV 1000 500 0.1 300 good n/a +ch016 e016 LFP uV 1000 500 0.1 300 good n/a +ch017 e017 HP uV 30000 500 300 10000 good n/a +ch018 e018 HP uV 30000 500 300 10000 good n/a +ch019 e019 HP uV 30000 500 300 10000 good n/a +ch020 e020 HP uV 30000 500 300 10000 good n/a +ch021 e021 HP uV 30000 500 300 10000 good n/a +ch022 e022 HP uV 30000 500 300 10000 good n/a +ch023 e023 HP uV 30000 500 300 10000 good n/a +ch024 e024 HP uV 30000 500 300 10000 good n/a +ch025 e025 HP uV 30000 500 300 10000 good n/a +ch026 e026 HP uV 30000 500 300 10000 good n/a +ch027 e027 HP uV 30000 500 300 10000 good n/a +ch028 e028 HP uV 30000 500 300 10000 good n/a +ch029 e029 HP uV 30000 500 300 10000 good n/a +ch030 e030 HP uV 30000 500 300 10000 good n/a +ch031 e031 HP uV 30000 500 300 10000 good n/a +ch032 e032 HP uV 30000 500 300 10000 good n/a +ch033 e033 LFP uV 1000 500 0.1 300 good n/a +ch034 e034 LFP uV 1000 500 0.1 300 good n/a +ch035 e035 LFP uV 1000 500 0.1 300 good n/a +ch036 e036 LFP uV 1000 500 0.1 300 good n/a +ch037 e037 LFP uV 1000 500 0.1 300 good n/a +ch038 e038 LFP uV 1000 500 0.1 300 good n/a +ch039 e039 LFP uV 1000 500 0.1 300 good n/a +ch040 e040 LFP uV 1000 500 0.1 300 good n/a +ch041 e041 HP uV 30000 500 300 10000 good n/a +ch042 e042 HP uV 30000 500 300 10000 good n/a +ch043 e043 HP uV 30000 500 300 10000 good n/a +ch044 e044 HP uV 30000 500 300 10000 good n/a +ch045 e045 HP uV 30000 500 300 10000 good n/a +ch046 e046 HP uV 30000 500 300 10000 good n/a +ch047 e047 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 diff --git a/microephys_toy/sub-mouse01/ecephys/sub-mouse01_electrodes.tsv b/microephys_toy/sub-mouse01/ecephys/sub-mouse01_electrodes.tsv new file mode 100644 index 000000000..276fc852b --- /dev/null +++ b/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 diff --git a/microephys_toy/sub-mouse01/ecephys/sub-mouse01_probes.json b/microephys_toy/sub-mouse01/ecephys/sub-mouse01_probes.json new file mode 100644 index 000000000..767aab5ec --- /dev/null +++ b/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" + } + } + } +} diff --git a/microephys_toy/sub-mouse01/ecephys/sub-mouse01_probes.tsv b/microephys_toy/sub-mouse01/ecephys/sub-mouse01_probes.tsv new file mode 100644 index 000000000..911a43a6b --- /dev/null +++ b/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 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 0.07 0.02 3.84 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 0.05 0.015 2.0 tip Bregma Hippocampus CA1 CA1 Allen-CCF-2017 silicon diff --git a/microephys_toy/sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_coordsystem.json b/microephys_toy/sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_coordsystem.json new file mode 100644 index 000000000..dc2f07c65 --- /dev/null +++ b/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" +} diff --git a/microephys_toy/sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_electrodes.tsv b/microephys_toy/sub-mouse01/ecephys/sub-mouse01_space-AllenCCFv3_electrodes.tsv new file mode 100644 index 000000000..39a9fe5f6 --- /dev/null +++ b/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 diff --git a/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_ecephys.json b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_ecephys.json new file mode 100644 index 000000000..553ff7a77 --- /dev/null +++ b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_ecephys.json @@ -0,0 +1,34 @@ +{ + "TaskName": "Reach to Grasp", + "TaskDescription": "Subject reaches and grasps objects of different shapes and sizes while neural activity is recorded from motor cortex", + "CogAtlasID": "https://www.cognitiveatlas.org/task/id/trm_4c89926767870/", + "InstitutionName": "Example University", + "InstitutionAddress": "123 Main St, City, State 12345, USA", + "InstitutionalDepartmentName": "Neuroscience Department", + "PowerLineFrequency": 60, + "Manufacturer": "IMEC", + "ManufacturersModelName": "Neuropixels 1.0", + "SamplingFrequency": 30000, + "SoftwareName": "Open Ephys", + "SoftwareVersions": "0.6.0", + "SoftwareFilters": { + "LowpassFilter": { + "Half-amplitude cutoff (Hz)": 300, + "Roll-off": "6dB/Octave" + } + }, + "HardwareFilters": { + "HighpassFilter": { + "Half-amplitude cutoff (Hz)": 0.1, + "Roll-off": "6dB/Octave" + } + }, + "RecordingType": "continuous", + "RecordingDuration": 1800, + "PharmaceuticalName": "isoflurane", + "PharmaceuticalDoseAmount": [1.5], + "PharmaceuticalDoseUnits": "percent", + "BodyPart": "BRAIN", + "BodyPartDetails": "Primary Motor Cortex", + "SampleEnvironment": "in vivo" +} diff --git a/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_ecephys.nwb b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_ecephys.nwb new file mode 100644 index 000000000..e69de29bb diff --git a/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_events.json b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_events.json new file mode 100644 index 000000000..0b4a3f271 --- /dev/null +++ b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_events.json @@ -0,0 +1,21 @@ +{ + "trial_type": { + "Description": "Type of event", + "Levels": { + "cue_onset": "Visual cue presented to initiate reaching movement", + "reach": "Subject performs reaching movement" + } + }, + "success": { + "Description": "Whether the reach was successful", + "Levels": { + "true": "Successful grasp", + "false": "Failed or incomplete reach" + } + }, + "StimulusPresentation": { + "OperatingSystem": "Linux Ubuntu 20.04", + "SoftwareName": "Custom MATLAB scripts", + "SoftwareVersion": "R2021a" + } +} diff --git a/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_events.tsv b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_events.tsv new file mode 100644 index 000000000..777f6b824 --- /dev/null +++ b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-reach_events.tsv @@ -0,0 +1,21 @@ +onset duration trial_type response_time success +0.0 0.5 cue_onset n/a n/a +0.52 1.2 reach 0.52 true +2.0 0.5 cue_onset n/a n/a +2.48 1.1 reach 0.48 true +4.0 0.5 cue_onset n/a n/a +4.65 1.3 reach 0.65 false +6.0 0.5 cue_onset n/a n/a +6.55 1.0 reach 0.55 true +8.0 0.5 cue_onset n/a n/a +8.51 1.2 reach 0.51 true +10.0 0.5 cue_onset n/a n/a +10.60 1.1 reach 0.60 true +12.0 0.5 cue_onset n/a n/a +12.58 1.4 reach 0.58 true +14.0 0.5 cue_onset n/a n/a +14.72 1.2 reach 0.72 false +16.0 0.5 cue_onset n/a n/a +16.49 1.0 reach 0.49 true +18.0 0.5 cue_onset n/a n/a +18.53 1.1 reach 0.53 true diff --git a/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-rest_ecephys.json b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-rest_ecephys.json new file mode 100644 index 000000000..d9788b12c --- /dev/null +++ b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-rest_ecephys.json @@ -0,0 +1,34 @@ +{ + "TaskName": "Resting State", + "TaskDescription": "Spontaneous neural activity recording during quiet wakefulness", + "CogAtlasID": "https://www.cognitiveatlas.org/task/id/trm_4c8a834779883/", + "InstitutionName": "Example University", + "InstitutionAddress": "123 Main St, City, State 12345, USA", + "InstitutionalDepartmentName": "Neuroscience Department", + "PowerLineFrequency": 60, + "Manufacturer": "IMEC", + "ManufacturersModelName": "Neuropixels 1.0", + "SamplingFrequency": 30000, + "SoftwareName": "Open Ephys", + "SoftwareVersions": "0.6.0", + "SoftwareFilters": { + "LowpassFilter": { + "Half-amplitude cutoff (Hz)": 300, + "Roll-off": "6dB/Octave" + } + }, + "HardwareFilters": { + "HighpassFilter": { + "Half-amplitude cutoff (Hz)": 0.1, + "Roll-off": "6dB/Octave" + } + }, + "RecordingType": "continuous", + "RecordingDuration": 600, + "PharmaceuticalName": "isoflurane", + "PharmaceuticalDoseAmount": [1.5], + "PharmaceuticalDoseUnits": "percent", + "BodyPart": "BRAIN", + "BodyPartDetails": "Primary Motor Cortex", + "SampleEnvironment": "in vivo" +} diff --git a/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-rest_ecephys.nwb b/microephys_toy/sub-mouse01/ses-01/ecephys/sub-mouse01_ses-01_task-rest_ecephys.nwb new file mode 100644 index 000000000..e69de29bb diff --git a/microephys_toy/sub-mouse01/ses-01/sub-mouse01_ses-01_scans.tsv b/microephys_toy/sub-mouse01/ses-01/sub-mouse01_ses-01_scans.tsv new file mode 100644 index 000000000..5be7e3a6a --- /dev/null +++ b/microephys_toy/sub-mouse01/ses-01/sub-mouse01_ses-01_scans.tsv @@ -0,0 +1,3 @@ +filename acq_time +ecephys/sub-mouse01_ses-01_task-reach_ecephys.nwb 2024-03-15T09:30:00 +ecephys/sub-mouse01_ses-01_task-rest_ecephys.nwb 2024-03-15T10:15:00 diff --git a/microephys_toy/sub-mouse02/icephys/sub-mouse02_channels.tsv b/microephys_toy/sub-mouse02/icephys/sub-mouse02_channels.tsv new file mode 100644 index 000000000..44e9f193d --- /dev/null +++ b/microephys_toy/sub-mouse02/icephys/sub-mouse02_channels.tsv @@ -0,0 +1,5 @@ +name electrode_name type units sampling_frequency recording_mode gain ground status +patch01_vm patch01 VM mV 20000 current-clamp 10 AgCl good +patch01_im patch01 IM pA 20000 current-clamp 5 AgCl good +patch02_vm patch02 VM mV 20000 voltage-clamp 10 AgCl good +patch02_im patch02 IM pA 20000 voltage-clamp 5 AgCl good diff --git a/microephys_toy/sub-mouse02/icephys/sub-mouse02_electrodes.tsv b/microephys_toy/sub-mouse02/icephys/sub-mouse02_electrodes.tsv new file mode 100644 index 000000000..fa07e0467 --- /dev/null +++ b/microephys_toy/sub-mouse02/icephys/sub-mouse02_electrodes.tsv @@ -0,0 +1,3 @@ +name probe_name x y z hemisphere impedance pipette_solution internal_pipette_diameter external_pipette_diameter material location +patch01 pipette01 0 0 0 L 5.2 K-gluconate 1.5 2.5 borosilicate-glass VISp2/3 +patch02 pipette02 0 0 0 R 4.8 K-gluconate 1.5 2.5 borosilicate-glass VISp2/3 diff --git a/microephys_toy/sub-mouse02/icephys/sub-mouse02_probes.tsv b/microephys_toy/sub-mouse02/icephys/sub-mouse02_probes.tsv new file mode 100644 index 000000000..e75651efc --- /dev/null +++ b/microephys_toy/sub-mouse02/icephys/sub-mouse02_probes.tsv @@ -0,0 +1,3 @@ +probe_name type AP ML DV AP_angle ML_angle rotation_angle hemisphere manufacturer electrode_count coordinate_reference_point associated_brain_region associated_brain_region_id reference_atlas +pipette01 patch-pipette -1.8 0.5 -2.2 30 0 0 L Sutter 1 tip Visual Cortex Layer 2/3 VISp2/3 Allen-CCF-2017 +pipette02 patch-pipette -1.8 -0.5 -2.2 30 0 0 R Sutter 1 tip Visual Cortex Layer 2/3 VISp2/3 Allen-CCF-2017 diff --git a/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_events.json b/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_events.json new file mode 100644 index 000000000..b3269a416 --- /dev/null +++ b/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_events.json @@ -0,0 +1,17 @@ +{ + "trial_type": { + "Description": "Type of event", + "Levels": { + "sweep": "Current injection sweep" + } + }, + "current_injection_pA": { + "Description": "Amount of current injected in picoamperes", + "Units": "pA" + }, + "StimulusPresentation": { + "OperatingSystem": "Windows 10", + "SoftwareName": "pClamp", + "SoftwareVersion": "11.0" + } +} diff --git a/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_events.tsv b/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_events.tsv new file mode 100644 index 000000000..cd3701bd0 --- /dev/null +++ b/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_events.tsv @@ -0,0 +1,11 @@ +onset duration trial_type current_injection_pA +0.0 0.5 sweep -100 +1.0 0.5 sweep -50 +2.0 0.5 sweep 0 +3.0 0.5 sweep 50 +4.0 0.5 sweep 100 +5.0 0.5 sweep 150 +6.0 0.5 sweep 200 +7.0 0.5 sweep 250 +8.0 0.5 sweep 300 +9.0 0.5 sweep 350 diff --git a/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_icephys.json b/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_icephys.json new file mode 100644 index 000000000..f0499d3f4 --- /dev/null +++ b/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_icephys.json @@ -0,0 +1,29 @@ +{ + "TaskName": "IV Curve Characterization", + "TaskDescription": "Current injection protocol to characterize intrinsic membrane properties and generate current-voltage curves", + "InstitutionName": "Example University", + "InstitutionAddress": "123 Main St, City, State 12345, USA", + "InstitutionalDepartmentName": "Neuroscience Department", + "PowerLineFrequency": 60, + "Manufacturer": "Molecular Devices", + "ManufacturersModelName": "MultiClamp 700B", + "SamplingFrequency": 20000, + "SoftwareName": "pClamp", + "SoftwareVersions": "11.0", + "HardwareFilters": { + "BesselFilter": { + "Half-amplitude cutoff (Hz)": 10000, + "Roll-off": "12dB/Octave" + } + }, + "SoftwareFilters": "n/a", + "RecordingType": "epoched", + "RecordingDuration": 300, + "BodyPart": "BRAIN", + "BodyPartDetails": "Visual Cortex", + "SampleEnvironment": "ex vivo", + "SliceThickness": 300, + "SliceThicknessUnits": "um", + "TissueOrigin": "Primary Visual Cortex", + "CellType": "pyramidal" +} diff --git a/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_icephys.nwb b/microephys_toy/sub-mouse02/icephys/sub-mouse02_task-IVcurve_icephys.nwb new file mode 100644 index 000000000..e69de29bb diff --git a/microephys_toy/sub-mouse02/sub-mouse02_scans.tsv b/microephys_toy/sub-mouse02/sub-mouse02_scans.tsv new file mode 100644 index 000000000..c66e54856 --- /dev/null +++ b/microephys_toy/sub-mouse02/sub-mouse02_scans.tsv @@ -0,0 +1,2 @@ +filename acq_time +icephys/sub-mouse02_task-IVcurve_icephys.nwb 2024-03-16T14:00:00