Skip to content

Commit 1773e23

Browse files
author
Thinh Nguyen
committed
add QC metrics
1 parent 4ab2a6c commit 1773e23

File tree

2 files changed

+146
-0
lines changed

2 files changed

+146
-0
lines changed

‎element_array_ephys/ephys.py

Lines changed: 73 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@
44
import numpy as np
55
import inspect
66
import importlib
7+
import pandas as pd
78

89
from .readers import spikeglx, kilosort, openephys
910
from . import probe, find_full_path, find_root_directory, dict_to_uuid
@@ -646,6 +647,78 @@ def yield_unit_waveforms():
646647
self.Waveform.insert(unit_electrode_waveforms, ignore_extra_fields=True)
647648

648649

650+
@schema
651+
class QualityMetric(dj.Imported):
652+
definition = """
653+
# Clusters and waveforms metrics
654+
-> CuratedClustering
655+
"""
656+
657+
class Cluster(dj.Part):
658+
definition = """
659+
# Cluster metrics for a particular unit
660+
-> master
661+
-> CuratedClustering.Unit
662+
---
663+
firing_rate=null: float # (Hz) firing rate for a unit
664+
snr=null: float # signal-to-noise ratio for a unit
665+
presence_ratio=null: float # fraction of time in which spikes are present
666+
isi_violation=null: float # rate of ISI violation as a fraction of overall rate
667+
number_violation=null: int # total number of ISI violations
668+
amplitude_cutoff=null: float # estimate of miss rate based on amplitude histogram
669+
isolation_distance=null: float # distance to nearest cluster in Mahalanobis space
670+
l_ratio=null: float #
671+
d_prime=null: float # Classification accuracy based on LDA
672+
nn_hit_rate=null: float # Fraction of neighbors for target cluster that are also in target cluster
673+
nn_miss_rate=null: float # Fraction of neighbors outside target cluster that are in target cluster
674+
silhouette_score=null: float # Standard metric for cluster overlap
675+
max_drift=null: float # Maximum change in spike depth throughout recording
676+
cumulative_drift=null: float # Cumulative change in spike depth throughout recording
677+
contamination_rate=null: float #
678+
"""
679+
680+
class Waveform(dj.Part):
681+
definition = """
682+
# Waveform metrics for a particular unit
683+
-> master
684+
-> CuratedClustering.Unit
685+
---
686+
amplitude: float # (uV) absolute difference between waveform peak and trough
687+
duration: float # (ms) time between waveform peak and trough
688+
halfwidth=null: float # (ms) spike width at half max amplitude
689+
pt_ratio=null: float # absolute amplitude of peak divided by absolute amplitude of trough relative to 0
690+
repolarization_slope=null: float # the repolarization slope was defined by fitting a regression line to the first 30us from trough to peak
691+
recovery_slope=null: float # the recovery slope was defined by fitting a regression line to the first 30us from peak to tail
692+
spread=null: float # (um) the range with amplitude above 12% of the maximum amplitude along the probe
693+
velocity_above=null: float # (s/m) inverse velocity of waveform propagation from the soma toward the top of the probe
694+
velocity_below=null: float # (s/m) inverse velocity of waveform propagation from the soma toward the bottom of the probe
695+
"""
696+
697+
def make(self, key):
698+
output_dir = (ClusteringTask & key).fetch1('clustering_output_dir')
699+
kilosort_dir = find_full_path(get_ephys_root_data_dir(), output_dir)
700+
701+
metric_fp = kilosort_dir / 'metrics.csv'
702+
703+
if not metric_fp.exists():
704+
raise FileNotFoundError(f'QC metrics file not found: {metric_fp}')
705+
706+
metrics_df = pd.read_csv(metric_fp)
707+
metrics_df.set_index('cluster_id', inplace=True)
708+
709+
# Get all units
710+
units = {u['unit']: u for u in (CuratedClustering.Unit & key).fetch(
711+
'KEY', order_by='unit')}
712+
713+
metrics_list = []
714+
for unit, unit_key in units.items():
715+
metrics_list.append({**unit_key, **dict(metrics_df.loc[unit])})
716+
717+
self.insert1(key)
718+
self.Cluster.insert(metrics_list, ignore_extra_fields=True)
719+
self.Waveform.insert(metrics_list, ignore_extra_fields=True)
720+
721+
649722
# ---------------- HELPER FUNCTIONS ----------------
650723

651724
def get_spikeglx_meta_filepath(ephys_recording_key):

‎element_array_ephys/ephys_chronic.py

Lines changed: 73 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@
44
import numpy as np
55
import inspect
66
import importlib
7+
import pandas as pd
78

89
from .readers import spikeglx, kilosort, openephys
910
from . import probe, find_full_path, find_root_directory, dict_to_uuid
@@ -649,6 +650,78 @@ def yield_unit_waveforms():
649650
self.Waveform.insert(unit_electrode_waveforms, ignore_extra_fields=True)
650651

651652

653+
@schema
654+
class QualityMetric(dj.Imported):
655+
definition = """
656+
# Clusters and waveforms metrics
657+
-> CuratedClustering
658+
"""
659+
660+
class Cluster(dj.Part):
661+
definition = """
662+
# Cluster metrics for a particular unit
663+
-> master
664+
-> CuratedClustering.Unit
665+
---
666+
firing_rate=null: float # (Hz) firing rate for a unit
667+
snr=null: float # signal-to-noise ratio for a unit
668+
presence_ratio=null: float # fraction of time in which spikes are present
669+
isi_violation=null: float # rate of ISI violation as a fraction of overall rate
670+
number_violation=null: int # total number of ISI violations
671+
amplitude_cutoff=null: float # estimate of miss rate based on amplitude histogram
672+
isolation_distance=null: float # distance to nearest cluster in Mahalanobis space
673+
l_ratio=null: float #
674+
d_prime=null: float # Classification accuracy based on LDA
675+
nn_hit_rate=null: float # Fraction of neighbors for target cluster that are also in target cluster
676+
nn_miss_rate=null: float # Fraction of neighbors outside target cluster that are in target cluster
677+
silhouette_score=null: float # Standard metric for cluster overlap
678+
max_drift=null: float # Maximum change in spike depth throughout recording
679+
cumulative_drift=null: float # Cumulative change in spike depth throughout recording
680+
contamination_rate=null: float #
681+
"""
682+
683+
class Waveform(dj.Part):
684+
definition = """
685+
# Waveform metrics for a particular unit
686+
-> master
687+
-> CuratedClustering.Unit
688+
---
689+
amplitude: float # (uV) absolute difference between waveform peak and trough
690+
duration: float # (ms) time between waveform peak and trough
691+
halfwidth=null: float # (ms) spike width at half max amplitude
692+
pt_ratio=null: float # absolute amplitude of peak divided by absolute amplitude of trough relative to 0
693+
repolarization_slope=null: float # the repolarization slope was defined by fitting a regression line to the first 30us from trough to peak
694+
recovery_slope=null: float # the recovery slope was defined by fitting a regression line to the first 30us from peak to tail
695+
spread=null: float # (um) the range with amplitude above 12% of the maximum amplitude along the probe
696+
velocity_above=null: float # (s/m) inverse velocity of waveform propagation from the soma toward the top of the probe
697+
velocity_below=null: float # (s/m) inverse velocity of waveform propagation from the soma toward the bottom of the probe
698+
"""
699+
700+
def make(self, key):
701+
output_dir = (ClusteringTask & key).fetch1('clustering_output_dir')
702+
kilosort_dir = find_full_path(get_ephys_root_data_dir(), output_dir)
703+
704+
metric_fp = kilosort_dir / 'metrics.csv'
705+
706+
if not metric_fp.exists():
707+
raise FileNotFoundError(f'QC metrics file not found: {metric_fp}')
708+
709+
metrics_df = pd.read_csv(metric_fp)
710+
metrics_df.set_index('cluster_id', inplace=True)
711+
712+
# Get all units
713+
units = {u['unit']: u for u in (CuratedClustering.Unit & key).fetch(
714+
'KEY', order_by='unit')}
715+
716+
metrics_list = []
717+
for unit, unit_key in units.items():
718+
metrics_list.append({**unit_key, **dict(metrics_df.loc[unit])})
719+
720+
self.insert1(key)
721+
self.Cluster.insert(metrics_list, ignore_extra_fields=True)
722+
self.Waveform.insert(metrics_list, ignore_extra_fields=True)
723+
724+
652725
# ---------------- HELPER FUNCTIONS ----------------
653726

654727
def get_spikeglx_meta_filepath(ephys_recording_key):

0 commit comments

Comments
 (0)