In [1]:
# install cell skipped during CI (deps preinstalled into system Python)
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Reach-related Single Unit Activity in the Parkinsonian Macaque Tutorial¶
This tutorial demonstrates how to access an NWB file from the DANDI:000947 dandiset using pynwb and dandi.
This dataset contains recordings of single-unit activity from from multiple cortical areas, including globus pallidus-internus (GPi), ventrolateral nucleus of the thalamus (VLa and VLp) and the arm-related regions of primary motor cortex, including sulcus (M1-S) and gyrus (M1-G) subregions, in monkeys performing a choice reaction time reaching task. Small numbers of recordings were also obtained from supplementary motor area (SMA), external globus pallidus (GPe), the thalamic reticular nucleus (RTN), striatum (STR) and the region between RTN and VL thalamus (R-V). It contains data from two monkeys before and after the administration of MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine), which induces Parkinsonism. The neuronal activity was recorded using 16-contact linear probes (0.5–1.0 MΩ, V-probe, Plexon) or glass-insulated tungsten microelectrodes (0.5–1.5 MΩ, Alpha Omega). The neuronal data were amplified (4×, 2 Hz–7.5 kHz) and digitized at 24.414 kHz (approx., 16-bit resolution; Tucker Davis Technologies). The neuronal data were high-pass filtered (Fpass: 200 Hz, Matlab FIRPM) and thresholded, and candidate action potentials were sorted into clusters in principal components space (Off-line Sorter, Plexon).
Contents:
Streaming NWB files ¶
This section demonstrates how to access the files on the DANDI Archive without downloading them.
Based on the Streaming NWB files tutorial from PyNWB.
The dandi.dandiapi.DandiAPIClient can be used to get the S3 URL of the NWB file stored in the DANDI Archive.
In [2]:
from dandi.dandiapi import DandiAPIClient
client = DandiAPIClient.for_dandi_instance("dandi")
dandiset_id = "000947"
file_path = "sub-Isis/sub-Isis_ses-post-MPTP-I-190118-6_ecephys.nwb"
with DandiAPIClient() as client:
asset = client.get_dandiset(dandiset_id, 'draft').get_asset_by_path(file_path)
s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)
We will use remfile for streaming the file. You can read more about remfile at this tutorial section.
In [3]:
import h5py
from pynwb import NWBHDF5IO
import remfile
# We stream the file using remfile and open it with h5py and pynwb
file = remfile.File(s3_url)
h5_file = h5py.File(file, "r")
io = NWBHDF5IO(file=h5_file, load_namespaces=True)
nwbfile = io.read()
nwbfile
Out[3]:
root (NWBFile)
session_description: This session contains raw and high-pass filtered (200 Hz) extracellular data from multiple cortical areas,
including the globus pallidus-internus (GPi) and ventrolateral nucleus of the thalamus (VLa and VLp) in
parkinsonian macaque performing a choice reaction time reaching task.
identifier: 0b60cba4-1a1a-4a01-808b-6a50a9f74e5d
session_start_time
2019-01-20 14:51:30-08:00timestamps_reference_time
2019-01-20 14:51:30-08:00file_create_date
0
2024-04-25 17:04:56.027983+02:00experimenter
('Kase, Daisuke', 'Zimnik, Andrew')related_publications
('https://doi.org/10.1101/2023.09.08.556120',)acquisition
ElectricalSeries (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: Acquisition traces for the ElectricalSeries.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | int16 |
|---|---|
| Shape | (33587200, 12) |
| Array size | 768.75 MiB |
| Chunk shape | (416666, 12) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 806092800 |
| Compressed size (bytes) | 413718193 |
| Compression ratio | 1.948410327703428 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
keywords
HDF5 dataset
['extracellular electrophysiology' 'single-unit activity' 'globus pallidus-internus' 'ventrolateral anterior nucleus' 'primary motor cortex' 'reaching task' "Parkinson's disease" 'macaque' 'MPTP']
| Data type | object |
|---|---|
| Shape | (9,) |
| Array size | 72.00 bytes |
| Chunk shape | None |
| Compression | None |
| Compression opts | None |
| Uncompressed size (bytes) | 72 |
| Compressed size (bytes) | 144 |
| Compression ratio | 0.5 |
['extracellular electrophysiology' 'single-unit activity' 'globus pallidus-internus' 'ventrolateral anterior nucleus' 'primary motor cortex' 'reaching task' "Parkinson's disease" 'macaque' 'MPTP']
processing
ecephys (ProcessingModule)
description: Intermediate data from extracellular electrophysiology recordings, e.g., LFP.
Processed (FilteredEphys)
ElectricalSeriesProcessedGPe (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: High-pass filtered traces (200 Hz) from GPe region.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | float32 |
|---|---|
| Shape | (33588268, 2) |
| Array size | 256.26 MiB |
| Chunk shape | (1250000, 2) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 268706144 |
| Compressed size (bytes) | 249582258 |
| Compression ratio | 1.0766235795494725 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
filtering: Equiripple High-pass filter designed using the FIRPM function in MATLAB with a stop-band frequency of 200 Hz, a pass-band frequency of 300 Hz, a stop-band attenuation of 0.0001 dB, a pass-band ripple of 0.057501127785 dB, and a density factor of 20.
ElectricalSeriesProcessedGPi (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: High-pass filtered traces (200 Hz) from GPi region.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | float32 |
|---|---|
| Shape | (33588268, 4) |
| Array size | 512.52 MiB |
| Chunk shape | (625000, 4) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 537412288 |
| Compressed size (bytes) | 500098920 |
| Compression ratio | 1.074611974766912 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
filtering: Equiripple High-pass filter designed using the FIRPM function in MATLAB with a stop-band frequency of 200 Hz, a pass-band frequency of 300 Hz, a stop-band attenuation of 0.0001 dB, a pass-band ripple of 0.057501127785 dB, and a density factor of 20.
ElectricalSeriesProcessedVLa (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: High-pass filtered traces (200 Hz) from VLa region.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | float32 |
|---|---|
| Shape | (33588268, 6) |
| Array size | 768.77 MiB |
| Chunk shape | (416666, 6) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 806118432 |
| Compressed size (bytes) | 748594139 |
| Compression ratio | 1.0768430982866672 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
filtering: Equiripple High-pass filter designed using the FIRPM function in MATLAB with a stop-band frequency of 200 Hz, a pass-band frequency of 300 Hz, a stop-band attenuation of 0.0001 dB, a pass-band ripple of 0.057501127785 dB, and a density factor of 20.
electrodes (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
electrode_groups
Group GPe (ElectrodeGroup)
description: Group vp16 electrodes.
location: GPe
device (Device)
description: TDT recording
manufacturer: Tucker-Davis Technologies (TDT)
Group GPi (ElectrodeGroup)
description: Group vp16 electrodes.
location: GPi
device (Device)
description: TDT recording
manufacturer: Tucker-Davis Technologies (TDT)
Group VLa (ElectrodeGroup)
description: Group vp16 electrodes.
location: VLa
device (Device)
description: TDT recording
manufacturer: Tucker-Davis Technologies (TDT)
devices
DeviceEcephys (Device)
description: TDT recording
manufacturer: Tucker-Davis Technologies (TDT)
intervals
trials (TimeIntervals)
description: experimental trials
columns
start_time
Start time of epoch, in seconds
stop_time
Stop time of epoch, in seconds
error_onset_time
The times of the error onset.
reward_start_time
The times of the reward onset.
reward_stop_time
The times of the reward offset.
movement_start_time
The times of the hand sensor at the home-position off (= onset of the movement).
movement_stop_time
The times of the hand sensor at the reach target on (= end of the movement).
return_start_time
The times of the hand sensor at the reach target off (= onset of the return movement)
return_stop_time
The times of the hand sensor at the home-position on (= end of the return movement)
cue_onset_time
The times of the target and go-cue instruction (reach target and go-cue were instructed simulatneously in this task).
target
Defines whether the target was on the left or right side.
table
| start_time | stop_time | error_onset_time | reward_start_time | reward_stop_time | movement_start_time | movement_stop_time | return_start_time | return_stop_time | cue_onset_time | target | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 0 | 50.992620 | 60.075663 | NaN | 53.932647 | 54.212239 | 53.702328 | 53.919293 | 58.726072 | 60.075663 | 53.478851 | Left |
| 1 | 60.086641 | 70.747259 | NaN | 63.636644 | 63.962071 | 63.347057 | 63.622390 | 69.581988 | 70.747259 | 63.103672 | Right |
| 2 | 70.757294 | 87.668572 | NaN | 75.166679 | 75.442340 | 74.939474 | 75.144356 | 85.597430 | 87.668572 | 74.664960 | Left |
| 3 | 87.680328 | 102.365225 | NaN | 90.649436 | 90.927391 | 90.407362 | 90.637189 | 93.556941 | 102.365225 | 90.165125 | Left |
... and 82 more row(s).
subject (Subject)
age__reference: birth
description: USDA registration number RQ7513
sex: F
species: Macaca mulatta
subject_id: Isis
date_of_birth
2005-06-14 00:00:00-07:00lab_meta_data
MPTPMetaData (TurnerLabMetaData)
MPTP_status: post_MPTP
trials (TimeIntervals)
description: experimental trials
columns
start_time
Start time of epoch, in seconds
stop_time
Stop time of epoch, in seconds
error_onset_time
The times of the error onset.
reward_start_time
The times of the reward onset.
reward_stop_time
The times of the reward offset.
movement_start_time
The times of the hand sensor at the home-position off (= onset of the movement).
movement_stop_time
The times of the hand sensor at the reach target on (= end of the movement).
return_start_time
The times of the hand sensor at the reach target off (= onset of the return movement)
return_stop_time
The times of the hand sensor at the home-position on (= end of the return movement)
cue_onset_time
The times of the target and go-cue instruction (reach target and go-cue were instructed simulatneously in this task).
target
Defines whether the target was on the left or right side.
table
| start_time | stop_time | error_onset_time | reward_start_time | reward_stop_time | movement_start_time | movement_stop_time | return_start_time | return_stop_time | cue_onset_time | target | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 0 | 50.992620 | 60.075663 | NaN | 53.932647 | 54.212239 | 53.702328 | 53.919293 | 58.726072 | 60.075663 | 53.478851 | Left |
| 1 | 60.086641 | 70.747259 | NaN | 63.636644 | 63.962071 | 63.347057 | 63.622390 | 69.581988 | 70.747259 | 63.103672 | Right |
| 2 | 70.757294 | 87.668572 | NaN | 75.166679 | 75.442340 | 74.939474 | 75.144356 | 85.597430 | 87.668572 | 74.664960 | Left |
| 3 | 87.680328 | 102.365225 | NaN | 90.649436 | 90.927391 | 90.407362 | 90.637189 | 93.556941 | 102.365225 | 90.165125 | Left |
... and 82 more row(s).
units (Units)
description: The curated single-units from the Plexon Offline Sorter v3, selected based on the quality of spike sorting.
waveform_unit: volts
columns
spike_times
the spike times for each unit
unit_name
Unique reference for each unit.
sort_label
The sorting label for each unit.
location
The brain region for each unit.
channel_ids
The electrode channel ids for each unit.
unit_quality_post_sorting
The quality of the unit after sorting.
table
| spike_times | unit_name | sort_label | location | channel_ids | unit_quality_post_sorting | |
|---|---|---|---|---|---|---|
| id | ||||||
| 0 | [0.03395584, 0.0520192, 0.12259328, 0.16719872, 0.19607552, 0.21151744, 0.36909056, 0.44445696, 0.46055424, 0.47939584, 0.48775168, 0.5031936, 0.78553088, 0.79757312, 0.83361792, 0.89706496, 0.98656256, 0.99344384, 1.07515904, 1.10252032, 1.11804416, 1.2115968, 1.22527744, 1.27184896, 1.28659456, 1.42753792, 1.5904768, 1.62676736, 1.72642304, 1.75443968, 1.93019904, 2.02985472, 2.2228992, 2.4510464, 2.7342848, 2.86711808, 2.89046528, 2.96071168, 3.12057856, 3.2503808, 3.53796096, 3.60906752, 3.65293568, 3.77167872, 3.796992, 3.81042688, 3.92081408, 3.95710464, 4.02116608, 4.13827072, 4.20352, 4.25009152, 4.27429888, 4.4945408, 4.5316096, 4.548608, 4.59091968, 4.7407104, 4.88955904, 4.99183616, 5.04446976, 5.06875904, 5.08706816, 5.10345216, 5.1546112, 5.26483456, 5.35212032, 5.43256576, 5.57236224, 5.61278976, 5.7071616, 5.71592704, 5.87923456, 6.14813696, 6.27634176, 6.660096, 6.77240832, 6.82733568, 6.88144384, 6.94411264, 7.04090112, 7.06527232, 7.28875008, 7.48212224, 7.64379136, 7.70658304, 7.79976704, 8.17238016, 8.18610176, 8.19703808, 8.23238656, 8.26540032, 8.29820928, 8.76212224, 8.91154432, 8.99690496, 9.0750976, 9.71460608, 9.75147008, 10.30488064, ...] | 0 | 1.0 | VLa | 1 | excellent |
| 1 | [1.32456448, 5.83467008, 5.99814144, 6.02116096, 15.63148288, 16.39100416, 16.41283584, 16.46559232, 16.49328128, 16.57708544, 16.768, 16.98430976, 19.10030336, 20.29195264, 21.95042304, 26.56559104, 27.19920128, 27.4956288, 29.77763328, 29.86262528, 32.86622208, 32.93057024, 32.9586688, 33.02817792, 33.05426944, 33.17383168, 33.27492096, 33.30183168, 33.37101312, 34.98360832, 42.9602816, 43.01000704, 43.22230272, 43.92722432, 43.96404736, 43.99071232, 44.86832128, 46.98796032, 47.09302272, 49.16609024, 49.24596224, 51.69487872, 52.31542272, 53.00736, 53.09816832, 56.83044352, 57.51701504, 58.42190336, 61.02679552, 61.08434432, 61.18670336, 61.28615424, 61.32785152, 61.40145664, 61.4969344, 61.86897408, 62.05079552, 62.17977856, 62.50524672, 62.53776896, 64.51310592, 64.6074368, 65.12910336, 69.98552576, 70.00055808, 70.0700672, 70.10062336, 70.17680896, 70.281216, 70.38824448, 70.49183232, 70.66529792, 76.27505664, 76.34714624, 76.41739264, 76.490752, 76.51639296, 76.55026688, 76.62862336, 76.6826496, 76.7985664, 77.99177216, 85.37202688, 85.4822912, 88.73467904, 94.46719488, 95.07278848, 95.0933504, 95.12046592, 95.1631872, 95.8234624, 95.8558208, 95.9168512, 95.98943232, 96.02183168, 96.05414912, 96.0796672, 96.2822144, 97.45874944, 98.34668032, ...] | 1 | 1.0 | VLa | 5 | excellent |
| 2 | [0.00217088, 0.10825728, 0.1626112, 0.23588864, 0.25718784, 0.32731136, 0.33878016, 0.42225664, 0.57561088, 0.61906944, 0.72536064, 0.86720512, 0.88600576, 0.9095168, 0.93646848, 1.05345024, 1.09727744, 1.12254976, 1.17059584, 1.22994688, 1.32608, 1.34754304, 1.37744384, 1.47009536, 1.51760896, 1.5826944, 1.61251328, 1.63893248, 1.70614784, 2.08207872, 2.10497536, 2.16113152, 2.17481216, 2.19734016, 2.24182272, 2.25800192, 2.31329792, 2.32706048, 2.3422976, 2.3783424, 2.38911488, 2.397184, 2.40406528, 2.41119232, 2.47902208, 2.5061376, 2.51895808, 2.63970816, 2.71835136, 2.74251776, 2.77295104, 2.81071616, 2.81649152, 2.86662656, 2.88694272, 2.9437952, 2.96648704, 3.01375488, 3.08146176, 3.10525952, 3.12705024, 3.18631936, 3.216384, 3.25402624, 3.2772096, 3.3314816, 3.38571264, 3.41327872, 3.44182784, 3.45526272, 3.4955264, 3.5719168, 3.59763968, 3.66096384, 3.80076032, 3.88112384, 3.93793536, 4.0071168, 4.04529152, 4.06368256, 4.12409856, 4.135936, 4.18787328, 4.20192256, 4.21773312, 4.32320512, 4.34454528, 4.39853056, 4.41348096, 4.42355712, 4.43695104, 4.47696896, 4.49220608, 4.5666304, 4.72363008, 4.77032448, 4.78629888, 4.83520512, 7.6396544, 7.65456384, ...] | 2 | 2.0 | VLa | 5 | excellent |
| 3 | [0.8450048, 1.18214656, 4.81329152, 6.4045056, 6.88902144, 14.77070848, 15.03469568, 16.40460288, 16.6404096, 17.9027968, 20.76770304, 20.86875136, 21.528576, 24.46430208, 26.62887424, 27.620352, 27.94758144, 28.82420736, 32.07344128, 35.23567616, 38.63687168, 42.9334528, 48.71999488, 57.26445568, 57.69117696, 60.53122048, 65.47550208, 69.2355072, 69.32226048, 86.80718336, 86.87230976, 89.06375168, 91.63358208, 111.40050944, 113.17383168, 129.0668032, 129.25403136, 133.05331712, 133.111808, 134.119424, 138.52418048, 149.84736768, 150.75373056, 156.43283456, 163.57081088, 172.46830592, 175.8111744, 176.93904896, 178.23481856, 181.43096832, 189.31818496, 196.29600768, 199.11081984, 199.5220992, 202.27018752, 203.3983488, 203.95024384, 205.3746688, 205.81228544, 213.09988864, 213.27429632, 214.46377472, 215.56494336, 221.08823552, 233.19158784, 239.9827968, 241.12099328, 241.81825536, 244.18983936, 249.94287616, 250.08717824, 250.3870464, 251.6434944, 253.19796736, 254.05513728, 266.18310656, 267.80983296, 269.43811584, 270.2864384, 276.42318848, 286.30728704, 286.37728768, 300.37479424, 300.5018112, 303.80158976, 311.92567808, 320.44531712, 320.61005824, 322.33193472, 327.83781888, 328.9356288, 338.1700608, 338.87801344, 340.72670208, 344.551424, 345.44173056, 346.63038976, 347.0450688, 348.81175552, 359.39926016, ...] | 3 | 1.0 | VLa | 7 | good |
... and 13 more row(s).
experiment_description: This dataset contains recordings of single-unit activity from from multiple cortical areas,
including globus pallidus-internus (GPi), ventrolateral nucleus of the thalamus (VLa and VLp) and
the arm-related regions of primary motor cortex, including sulcus (M1-S) and gyrus (M1-G) subregions, in MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine)-induced parkinsonian monkeys performing a choice
reaction time reaching task. Small numbers of recordings were also obtained from supplementary motor area (SMA),
external globus pallidus (GPe), the thalamic reticular nucleus (RTN), striatum (STR) and the region between RTN
and VL thalamus (R-V).
The neuronal activity was recorded using 16-contact linear probes (0.5–1.0 MΩ, V-probe, Plexon) or glass-insulated
tungsten microelectrodes (0.5–1.5 MΩ, Alpha Omega). The neuronal data were amplified (4×, 2 Hz–7.5 kHz) and
digitized at 24.414 kHz (approx., 16-bit resolution; Tucker Davis Technologies).
The neuronal data were high-pass filtered (Fpass: 200 Hz, Matlab FIRPM) and thresholded, and candidate action
potentials were sorted into clusters in principal components space (Off-line Sorter, Plexon).
session_id: post-MPTP-I-190118-6
lab: Turner
institution: University of Pittsburgh
pharmacology: MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; the chemical compound that induces parkinsonism) administration date 2017-10-27 (ICA; internal carotid artery injection), 2017-11-28 (IM; intramuscular injection), 2017-12-01 (IM), 2018-06-08 (ICA), 2018-07-05 (IM), 2018-07-19 (IM), 2018-08-27 (IM)
In [4]:
nwbfile.subject
Out[4]:
subject (Subject)
age__reference: birth
description: USDA registration number RQ7513
sex: F
species: Macaca mulatta
subject_id: Isis
date_of_birth
2005-06-14 00:00:00-07:00The MPTP status is stored in a TurnerLabMetaData container which extends pynwb.file.LabMetaData, and can be accessed as nwbfile.lab_meta_data["MPTPMetaData"].
In [5]:
nwbfile.lab_meta_data["MPTPMetaData"]
Out[5]:
MPTPMetaData (TurnerLabMetaData)
MPTP_status: post_MPTP
Access trials ¶
Behavior trials are stored in nwbfile.trials. The start_time denotes the start time of each trial in seconds relative to the global session start time.
The stop_time denotes the end time of each trial in seconds relative to the global session start time.
nwbfile.trials can be converted to a pandas DataFrame for convenient analysis using nwbfile.trials.to_dataframe().
In [6]:
trials = nwbfile.trials.to_dataframe()
trials.head(10)
Out[6]:
| start_time | stop_time | error_onset_time | reward_start_time | reward_stop_time | movement_start_time | movement_stop_time | return_start_time | return_stop_time | cue_onset_time | target | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||
| 0 | 50.992620 | 60.075663 | NaN | 53.932647 | 54.212239 | 53.702328 | 53.919293 | 58.726072 | 60.075663 | 53.478851 | Left |
| 1 | 60.086641 | 70.747259 | NaN | 63.636644 | 63.962071 | 63.347057 | 63.622390 | 69.581988 | 70.747259 | 63.103672 | Right |
| 2 | 70.757294 | 87.668572 | NaN | 75.166679 | 75.442340 | 74.939474 | 75.144356 | 85.597430 | 87.668572 | 74.664960 | Left |
| 3 | 87.680328 | 102.365225 | NaN | 90.649436 | 90.927391 | 90.407362 | 90.637189 | 93.556941 | 102.365225 | 90.165125 | Left |
| 4 | 102.381896 | 118.222643 | NaN | 105.212150 | 105.524838 | 104.894423 | 105.200640 | 115.487580 | 118.222643 | 104.665498 | Right |
| 5 | 118.241034 | 133.235917 | NaN | 121.586442 | 121.857434 | 121.264620 | 121.573253 | 126.400512 | 133.235917 | 121.009603 | Right |
| 6 | 133.241979 | 148.448256 | NaN | 136.416051 | 136.696095 | 136.139940 | 136.393155 | 146.674319 | 148.448256 | 135.913800 | Left |
| 7 | 148.459520 | 165.340938 | NaN | 152.901140 | 153.242665 | 152.581325 | 152.887132 | 162.919014 | 165.340938 | 152.366694 | Right |
| 8 | 165.350031 | 180.914258 | NaN | 169.070920 | 169.386926 | 168.770929 | 169.049989 | 173.979689 | 180.914258 | 168.523612 | Left |
| 9 | 180.927775 | 197.386732 | NaN | 184.650588 | 184.983347 | 184.306893 | 184.624456 | 194.873057 | 197.386732 | 184.101397 | Right |
Access Recording ¶
This section demonstrates how to access the raw ElectricalSeries data.
NWB organizes data into different groups depending on the type of data. Groups can be thought of as folders within the file. Here are some of the groups within an NWBFile and the types of data they are intended to store:
acquisition: raw, acquired data that should never changeprocessing: processed data, typically the results of preprocessing algorithms and could change
Raw ElectricalSeries¶
The raw ElectricalSeries data is stored in an pynwb.ecephys.ElectricalSeries object which is added to nwbfile.acquisition. The data can be accessed as nwbfile.acquisition["ElectricalSeries"].
The data in ElectricalSeries is stored as a two dimensional array: the first dimension is time, the second dimension represents electrodes/channels.
In [7]:
electrical_series = nwbfile.acquisition["ElectricalSeries"]
In [8]:
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
# Prepare data for plotting
data = electrical_series.data[:1000, :10]
timestamps = electrical_series.get_timestamps()[:1000]
df = pd.DataFrame(data)
df["Time (s)"] = timestamps
df.set_index("Time (s)", inplace=True)
df.columns.name = "electrodes"
channel_name_mapper = dict(zip(df.columns, electrical_series.electrodes["channel_name"][:]))
df.rename(channel_name_mapper, axis=1, inplace=True)
fig, axes = plt.subplots(nrows=len(df.columns), sharex=True, sharey=True, dpi=200)
lines = df.plot(subplots=True, ax=axes, legend=False, linewidth=0.8)
# Hide y-axis labels
for ax in axes:
ax.yaxis.set_visible(False)
# Remove box around the plots
for ax in axes:
ax.set_frame_on(False)
# Get handles and labels for all lines
handles, labels = [], []
for line in lines:
h, l = line.get_legend_handles_labels()
handles.extend(h)
labels.extend(l)
# Create a single legend box
fig.legend(handles, labels, loc='upper right', bbox_to_anchor=(1.2, 0.8), frameon=False)
plt.xlabel('Time (s)')
plt.tight_layout()
plt.show()
The electrodes table describe the electrodes that generated this data. Extracellular electrodes are stored in an "electrodes" table, which is a DynamicTable and can be can be converted to a pandas DataFrame for convenient analysis using nwbfile.electrodes.to_dataframe().
In [9]:
nwbfile.electrodes.to_dataframe().head()
Out[9]:
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x14... | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x14... | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x14... | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x14... | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
| 4 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x14... | Group VLa | Conx 12 | 1.0 | 0.0 | 12 | vp16 | Sagittal | 4.0 | 2.0 | 41.90 | -3.954138 | -5.019382 | 4.834319 |
Filtered ElectricalSeries¶
The processed ecephys data is stored in "processing/ecephys" which can be accessed as nwbfile.processing["ecephys"].
Within this processing module we can access the container of filtered traces as nwbfile.processing["ecephys"]["Processed"] which can hold multiple processed ElectricalSeries objects.
In [10]:
nwbfile.processing["ecephys"]
Out[10]:
ecephys (ProcessingModule)
description: Intermediate data from extracellular electrophysiology recordings, e.g., LFP.
Processed (FilteredEphys)
ElectricalSeriesProcessedGPe (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: High-pass filtered traces (200 Hz) from GPe region.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | float32 |
|---|---|
| Shape | (33588268, 2) |
| Array size | 256.26 MiB |
| Chunk shape | (1250000, 2) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 268706144 |
| Compressed size (bytes) | 249582258 |
| Compression ratio | 1.0766235795494725 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
filtering: Equiripple High-pass filter designed using the FIRPM function in MATLAB with a stop-band frequency of 200 Hz, a pass-band frequency of 300 Hz, a stop-band attenuation of 0.0001 dB, a pass-band ripple of 0.057501127785 dB, and a density factor of 20.
ElectricalSeriesProcessedGPi (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: High-pass filtered traces (200 Hz) from GPi region.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | float32 |
|---|---|
| Shape | (33588268, 4) |
| Array size | 512.52 MiB |
| Chunk shape | (625000, 4) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 537412288 |
| Compressed size (bytes) | 500098920 |
| Compression ratio | 1.074611974766912 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
filtering: Equiripple High-pass filter designed using the FIRPM function in MATLAB with a stop-band frequency of 200 Hz, a pass-band frequency of 300 Hz, a stop-band attenuation of 0.0001 dB, a pass-band ripple of 0.057501127785 dB, and a density factor of 20.
ElectricalSeriesProcessedVLa (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: High-pass filtered traces (200 Hz) from VLa region.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | float32 |
|---|---|
| Shape | (33588268, 6) |
| Array size | 768.77 MiB |
| Chunk shape | (416666, 6) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 806118432 |
| Compressed size (bytes) | 748594139 |
| Compression ratio | 1.0768430982866672 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
filtering: Equiripple High-pass filter designed using the FIRPM function in MATLAB with a stop-band frequency of 200 Hz, a pass-band frequency of 300 Hz, a stop-band attenuation of 0.0001 dB, a pass-band ripple of 0.057501127785 dB, and a density factor of 20.
In [11]:
processed_ecephys = nwbfile.processing["ecephys"]["Processed"]
filtered_electrical_series = processed_ecephys["ElectricalSeriesProcessedGPi"]
filtered_electrical_series
Out[11]:
ElectricalSeriesProcessedGPi (ElectricalSeries)
starting_time: 9.5367431640625e-07
rate: 24414.0625
resolution: -1.0
comments: no comments
description: High-pass filtered traces (200 Hz) from GPi region.
conversion: 1e-06
offset: 0.0
unit: volts
data
HDF5 dataset
| Data type | float32 |
|---|---|
| Shape | (33588268, 4) |
| Array size | 512.52 MiB |
| Chunk shape | (625000, 4) |
| Compression | gzip |
| Compression opts | 4 |
| Uncompressed size (bytes) | 537412288 |
| Compressed size (bytes) | 500098920 |
| Compression ratio | 1.074611974766912 |
starting_time_unit: seconds
electrodes (DynamicTableRegion)
description: electrode_table_region
table (ElectrodesTable)
description: metadata about extracellular electrodes
columns
location
the location of channel within the subject e.g. brain region
group
a reference to the ElectrodeGroup this electrode is a part of
group_name
the name of the ElectrodeGroup this electrode is a part of
channel_name
The channel names from TDT.
gain_to_uV
The gain to apply to the traces to convert to microvolts.
offset_to_uV
The offset to apply to the traces to convert to microvolts.
channel_ids
The identifier of the channels.
electrode_type
The type of electrode.
chamber_type
The type of the chamber (either Sagittal or Coronal).
chamber_x
The medio-lateral coordinate relative to the chamber center, lateral positive, in millimeters.
chamber_y
The antero-posterior coordinate relative to the chamber center, posterior negative, in millimeters.
chamber_z
The dorso-ventral coordinate relative to the chamber center, ventral positive, in millimeters.
acx_x
Medio-lateral coordinate relative to the anterior commissure crossing, lateral positive, in millimeters.
acx_y
Antero-posterior coordinate relative to the anterior commissure crossing, posterior negative, in millimeters.
acx_z
Dorso-ventral coordinate relative to the anterior commissure crossing, ventral positive, in millimeters.
table
| location | group | group_name | channel_name | gain_to_uV | offset_to_uV | channel_ids | electrode_type | chamber_type | chamber_x | chamber_y | chamber_z | acx_x | acx_y | acx_z | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 0 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 1 | 1.0 | 0.0 | 1 | vp16 | Sagittal | 4.0 | 2.0 | 42.50 | -3.920903 | -5.335591 | 4.325490 |
| 1 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 5 | 1.0 | 0.0 | 5 | vp16 | Sagittal | 4.0 | 2.0 | 43.10 | -3.887668 | -5.651801 | 3.816661 |
| 2 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 7 | 1.0 | 0.0 | 7 | vp16 | Sagittal | 4.0 | 2.0 | 43.40 | -3.871051 | -5.809906 | 3.562247 |
| 3 | VLa | Group VLa pynwb.ecephys.ElectrodeGroup at 0x140185594470288\nFields:\n description: Group vp16 electrodes.\n device: DeviceEcephys pynwb.device.Device at 0x140185593143248\nFields:\n description: TDT recording\n manufacturer: Tucker-Davis Technologies (TDT)\n\n location: VLa\n | Group VLa | Conx 11 | 1.0 | 0.0 | 11 | vp16 | Sagittal | 4.0 | 2.0 | 42.05 | -3.945830 | -5.098434 | 4.707112 |
... and 8 more row(s).
filtering: Equiripple High-pass filter designed using the FIRPM function in MATLAB with a stop-band frequency of 200 Hz, a pass-band frequency of 300 Hz, a stop-band attenuation of 0.0001 dB, a pass-band ripple of 0.057501127785 dB, and a density factor of 20.
Access Units ¶
Spike times are stored in the Units table, which is a DynamicTable and can be can be converted to a pandas DataFrame for convenient analysis using nwbfile.units.to_dataframe().
In [12]:
nwbfile.units[:]
Out[12]:
| spike_times | unit_name | sort_label | location | channel_ids | unit_quality_post_sorting | |
|---|---|---|---|---|---|---|
| id | ||||||
| 0 | [0.03395584, 0.0520192, 0.12259328, 0.16719872... | 0 | 1.0 | VLa | 1 | excellent |
| 1 | [1.32456448, 5.83467008, 5.99814144, 6.0211609... | 1 | 1.0 | VLa | 5 | excellent |
| 2 | [0.00217088, 0.10825728, 0.1626112, 0.23588864... | 2 | 2.0 | VLa | 5 | excellent |
| 3 | [0.8450048, 1.18214656, 4.81329152, 6.4045056,... | 3 | 1.0 | VLa | 7 | good |
| 4 | [0.09691136, 0.1282048, 0.15757312, 0.25923584... | 4 | 1.0 | VLa | 11 | good |
| 5 | [0.04907008, 0.116736, 0.15835136, 0.18751488,... | 5 | 1.0 | VLa | 12 | excellent |
| 6 | [0.01056768, 0.08716288, 0.09531392, 0.1458585... | 6 | 1.0 | VLa | 15 | excellent |
| 7 | [2.70639104, 9.90437376, 10.7485184, 25.959055... | 7 | 1.0 | GPi | 20 | F |
| 8 | [0.02125824, 0.09744384, 0.17870848, 0.2081587... | 8 | 1.0 | GPi | 22 | excellent |
| 9 | [0.01036288, 0.055296, 0.09613312, 0.1349632, ... | 9 | 2.0 | GPi | 22 | good |
| 10 | [0.10190848, 0.13770752, 0.1859584, 0.26558464... | 10 | 3.0 | GPi | 22 | good |
| 11 | [0.063488, 0.0784384, 0.72880128, 1.0031104, 1... | 11 | 4.0 | GPi | 22 | good |
| 12 | [0.1062912, 0.19480576, 0.33542144, 0.34828288... | 12 | 1.0 | GPi | 23 | excellent |
| 13 | [0.00405504, 0.00933888, 0.0514048, 0.06397952... | 13 | 2.0 | GPi | 23 | good |
| 14 | [0.00131072, 0.00364544, 0.0063488, 0.00970752... | 14 | 1.0 | GPi | 26 | excellent |
| 15 | [0.34803712, 1.18255616, 1.44543744, 1.4502707... | 15 | 1.0 | GPe | 28 | excellent |
| 16 | [0.03166208, 0.05963776, 0.0618496, 0.07155712... | 16 | 1.0 | GPe | 31 | excellent |
In [13]:
from matplotlib import pyplot as plt
import pynapple as nap
movement_onset_ts = nap.Ts(nwbfile.trials["movement_start_time"][:], time_units="s")
spike_times_group = nap.TsGroup({unit_ind: nap.Ts(spikes) for unit_ind, spikes in enumerate(nwbfile.units["spike_times"])})
perievent_histogram = nap.compute_perievent(
data=spike_times_group,
tref=movement_onset_ts,
minmax=(-0.5, 1),
time_unit="s",
)
fig, ax = plt.subplots(nrows=2, ncols=1, figsize=(8, 6), dpi=200, sharex=True, sharey=True)
ax[0].plot(
perievent_histogram[0].to_tsd(),
"|",
color="black",
markersize=2,
)
ax[0].set_title(nwbfile.units[0]["location"].values[0])
ax[0].axvline(0.0)
ax[1].plot(
perievent_histogram[11].to_tsd(),
"|",
color="black",
markersize=2,
)
ax[1].set_title(nwbfile.units[11]["location"].values[0])
ax[1].axvline(0.0)
plt.xlabel("Time from Movement onset (s)")
plt.ylabel("Trials")
plt.xlim(-0.5, 1)
plt.show()
We can also use Neurosift for this visualization:
