hits
# -*- coding: utf-8 -*-
'''
This module implements :class:`SpikeTrain`, an array of spike times.
:waveforms: (quantity array 3D (spike, channel_index, time))
The waveforms of each spike.
:sort: (bool) If True, the spike train will be sorted by time.
stack = np.concatenate((np.asarray(self), np.asarray(other)))
sorting = np.argsort(stack)
stack = stack[sorting]
kwargs = {}
kwargs['array_annotations'] = self.
_merge_array_annotations(other, sorting=sorting)
for name in ("name", "description", "file_origin
wfs_stack = np.vstack((self.waveforms, other.waveforms))
wfs_stack = wfs_stack[sorting
Apart from that the array_annotations need to be sorted according to the sorting of
the spikes
:return Merged array_annotations
'''
assert sorting is not None, "The order of the merged
arr_ann = np.concatenate([self_ann, other_ann])
merged_array_annotations[key] = arr_ann[sorting
hits
# -*- coding: utf-8 -*-
'''
This module implements :class:`SpikeTrain`, an array of spike times.
:waveforms: (quantity array 3D (spike, channel_index, time))
The waveforms of each spike.
:sort: (bool) If True, the spike train will be sorted by time.
stack = np.concatenate((np.asarray(self), np.asarray(other)))
sorting = np.argsort(stack)
stack = stack[sorting]
kwargs = {}
kwargs['array_annotations'] = self.
_merge_array_annotations(other, sorting=sorting)
for name in ("name", "description", "file_origin
wfs_stack = np.vstack((self.waveforms, other.waveforms))
wfs_stack = wfs_stack[sorting
Apart from that the array_annotations need to be sorted according to the sorting of
the spikes
:return Merged array_annotations
'''
assert sorting is not None, "The order of the merged
arr_ann = np.concatenate([self_ann, other_ann])
merged_array_annotations[key] = arr_ann[sorting
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
The spike sorting version is attached
to filename by a postfix '-XX', where XX is the version
, e.g.,
l101010-001-02 for spike sorting version 2 of file l101010-001.
If no odML is present, no information on the spike sorting (e.g.,
if a unit is SUA or MUA
= re.sub(os.path.extsep + ext + '$', '', filename)
if nev_override:
# check if sorting
sorting version
nev_versions = [re.sub(
os.path.extsep + 'nev$', '', p)
version, and there is an
# odML, then make sure the detected sorting version matches the odML
_print_verbose(
"Attempting to utilize the most recent "
"sorting
sorting info from the odML be matched with the odML?
detection and spike sorting
procedure.
detection and spike sorting
procedure.
hits
Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the
Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several
sorting quality metrics.
## Downloading the data
## Repository structure
Each recording and corresponding
Information about spike sorting and single units and corresponding data are available in the units group
For an easier visualization of the spike waveform in two dimensions, we have also added an array which
contains the mean spike waveform in the 32 x 4 shape of the array (‘mean_waveform_all_channels_filt_
Furthermore, the spike waveform recorded on the channel with the largest spike (i.e., peak waveform channel
times and spike count of each unit were saved in the units group.
However, if needed, potential future users can use the provided wideband recordings to redo the spike
sorting either by applying different parameters in Kilosort2 or using other spike sorting algorithms
hits
Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the
Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several
sorting quality metrics.
## Downloading the data
## Repository structure
Each recording and corresponding
Information about spike sorting and single units and corresponding data are available in the units group
For an easier visualization of the spike waveform in two dimensions, we have also added an array which
contains the mean spike waveform in the 32 x 4 shape of the array (‘mean_waveform_all_channels_filt_
Furthermore, the spike waveform recorded on the channel with the largest spike (i.e., peak waveform channel
times and spike count of each unit were saved in the units group.
However, if needed, potential future users can use the provided wideband recordings to redo the spike
sorting either by applying different parameters in Kilosort2 or using other spike sorting algorithms
hits
Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the
Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several
sorting quality metrics.
## Downloading the data
## Repository structure
Each recording and corresponding
Information about spike sorting and single units and corresponding data are available in the units group
For an easier visualization of the spike waveform in two dimensions, we have also added an array which
contains the mean spike waveform in the 32 x 4 shape of the array (‘mean_waveform_all_channels_filt_
Furthermore, the spike waveform recorded on the channel with the largest spike (i.e., peak waveform channel
times and spike count of each unit were saved in the units group.
However, if needed, potential future users can use the provided wideband recordings to redo the spike
sorting either by applying different parameters in Kilosort2 or using other spike sorting algorithms
hits
Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the
Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several
sorting quality metrics.
## Repository structure
Each recording and corresponding metadata, single
Information about spike sorting and single units and corresponding data are available in the *units*
For each unit, we included here the mean and standard deviation of their spike waveform on all channels
For an easier visualization of the multichannel spike waveform in two dimensions, we have also added
Furthermore, the spike waveform recorded on the channel with the largest spike (i.e., peak waveform channel
Several single unit properties and cluster quality metrics, as well as the spike times and spike count
Loading and plotting the mean spike waveform of a specific single unit on the peak waveform channel:
as se
2. nwbPath = 'Rat01_Insertion1_Depth1.nwb'
3. recording = se.NwbRecordingExtractor(nwbPath)
4. sorting
hits
Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the
Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several
sorting quality metrics.
## Repository structure
Each recording and corresponding metadata, single
Information about spike sorting and single units and corresponding data are available in the *units*
For each unit, we included here the mean and standard deviation of their spike waveform on all channels
For an easier visualization of the multichannel spike waveform in two dimensions, we have also added
Furthermore, the spike waveform recorded on the channel with the largest spike (i.e., peak waveform channel
Several single unit properties and cluster quality metrics, as well as the spike times and spike count
Loading and plotting the mean spike waveform of a specific single unit on the peak waveform channel:
as se
2. nwbPath = 'Rat01_Insertion1_Depth1.nwb'
3. recording = se.NwbRecordingExtractor(nwbPath)
4. sorting
hits
Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the
Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several
sorting quality metrics.
## Repository structure
Each recording and corresponding metadata, single
Information about spike sorting and single units and corresponding data are available in the *units*
For each unit, we included here the mean and standard deviation of their spike waveform on all channels
For an easier visualization of the multichannel spike waveform in two dimensions, we have also added
Furthermore, the spike waveform recorded on the channel with the largest spike (i.e., peak waveform channel
Several single unit properties and cluster quality metrics, as well as the spike times and spike count
Loading and plotting the mean spike waveform of a specific single unit on the peak waveform channel:
as se
2. nwbPath = 'Rat01_Insertion1_Depth1.nwb'
3. recording = se.NwbRecordingExtractor(nwbPath)
4. sorting