Curation Tutorial

After spike sorting and computing quality metrics, you can automatically curate the spike sorting output using the quality metrics that you have calculated.

Import the modules and/or functions necessary from spikeinterface

import spikeinterface.core as si

Let’s generate a simulated dataset, and imagine that the ground-truth sorting is in fact the output of a sorter.

recording, sorting = si.generate_ground_truth_recording()
print(recording)
print(sorting)

GroundTruthRecording (InjectTemplatesRecording): 4 channels - 25.0kHz - 1 segments
                      250,000 samples - 10.00s - float32 dtype - 3.81 MiB
GroundTruthSorting (NumpySorting): 10 units - 1 segments - 25.0kHz

Create SortingAnalyzer

For this example, we will need a SortingAnalyzer and some extensions to be computed first

analyzer = si.create_sorting_analyzer(sorting=sorting, recording=recording, format="memory")
analyzer.compute(["random_spikes", "waveforms", "templates", "noise_levels"])

analyzer.compute("principal_components", n_components=3, mode="by_channel_local")
print(analyzer)

estimate_sparsity (no parallelization):   0%|          | 0/10 [00:00<?, ?it/s]
estimate_sparsity (no parallelization): 100%|██████████| 10/10 [00:00<00:00, 364.79it/s]

compute_waveforms (no parallelization):   0%|          | 0/10 [00:00<?, ?it/s]
compute_waveforms (no parallelization): 100%|██████████| 10/10 [00:00<00:00, 256.71it/s]

noise_level (no parallelization):   0%|          | 0/20 [00:00<?, ?it/s]
noise_level (no parallelization): 100%|██████████| 20/20 [00:00<00:00, 257.20it/s]

Fitting PCA:   0%|          | 0/10 [00:00<?, ?it/s]
Fitting PCA: 100%|██████████| 10/10 [00:00<00:00, 140.01it/s]

Projecting waveforms:   0%|          | 0/10 [00:00<?, ?it/s]
Projecting waveforms: 100%|██████████| 10/10 [00:00<00:00, 1328.53it/s]
SortingAnalyzer: 4 channels - 10 units - 1 segments - memory - sparse - has recording
Loaded 5 extensions: random_spikes, waveforms, templates, noise_levels, principal_components

Then we compute some quality metrics:

metrics_ext = analyzer.compute("quality_metrics", metric_names=["snr", "isi_violation", "nearest_neighbor"])
metrics = metrics_ext.get_data()
print(metrics)

         snr  isi_violations_ratio  ...  nn_hit_rate  nn_miss_rate
0  35.330805                   0.0  ...     0.939355      0.007732
1  12.653011                   0.0  ...     0.751678      0.023094
2  15.026809                   0.0  ...     0.808284      0.030053
3   8.378558                   0.0  ...     0.764103      0.030506
4  20.095183                   0.0  ...     0.824675      0.018574
5  11.003163                   0.0  ...     0.768831      0.029421
6  45.898795                   0.0  ...     0.979856      0.002792
7  14.637378                   0.0  ...     0.784375      0.017347
8   5.273214                   0.0  ...     0.762857      0.021618
9  29.340620                   0.0  ...     0.833333      0.017708

[10 rows x 5 columns]

We can now threshold each quality metric and select units based on some rules.

The easiest and most intuitive way is to use boolean masking with a dataframe.

Then create a list of unit ids that we want to keep

keep_mask = (metrics["snr"] > 7.5) & (metrics["isi_violations_ratio"] < 0.2) & (metrics["nn_hit_rate"] > 0.80)
print(keep_mask)

keep_unit_ids = keep_mask[keep_mask].index.values
keep_unit_ids = [unit_id for unit_id in keep_unit_ids]
print(keep_unit_ids)

0     True
1    False
2     True
3    False
4     True
5    False
6     True
7    False
8    False
9     True
dtype: bool
['0', '2', '4', '6', '9']

And now let’s create a sorting that contains only curated units and save it.

curated_sorting = sorting.select_units(keep_unit_ids)
print(curated_sorting)


curated_sorting.save(folder="curated_sorting", overwrite=True)

GroundTruthSorting (UnitsSelectionSorting): 5 units - 1 segments - 25.0kHz

NumpyFolder (NumpyFolderSorting): 5 units - 1 segments - 25.0kHz

Unit IDs

['0' '2' '4' '6' '9']

Annotations

• name : GroundTruthSorting

Properties

gt_unit_locations
[[ 3.7012112 -2.5791025 7.4028034] [19.811974 3.9781427 39.108723 ] [29.059048 25.829254 45.021927 ] [16.323465 22.91235 6.7904286] [20.05267 1.1883203 19.221003 ]]

We can also save the analyzer with only theses units

clean_analyzer = analyzer.select_units(unit_ids=keep_unit_ids, format="zarr", folder="clean_analyzer")

print(clean_analyzer)

SortingAnalyzer: 4 channels - 5 units - 1 segments - zarr - sparse - has recording
Loaded 6 extensions: random_spikes, waveforms, templates, noise_levels, principal_components, quality_metrics