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, 451.17it/s]

compute_waveforms (no parallelization):   0%|          | 0/10 [00:00<?, ?it/s]
compute_waveforms (no parallelization): 100%|██████████| 10/10 [00:00<00:00, 327.91it/s]

noise_level (no parallelization):   0%|          | 0/20 [00:00<?, ?it/s]
noise_level (no parallelization): 100%|██████████| 20/20 [00:00<00:00, 257.39it/s]

Fitting PCA:   0%|          | 0/10 [00:00<?, ?it/s]
Fitting PCA: 100%|██████████| 10/10 [00:00<00:00, 189.60it/s]

Projecting waveforms:   0%|          | 0/10 [00:00<?, ?it/s]
Projecting waveforms: 100%|██████████| 10/10 [00:00<00:00, 2679.90it/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   9.600041                   0.0  ...     0.751761      0.039179
1  16.282774                   0.0  ...     0.795620      0.014684
2   4.411443                   0.0  ...     0.791667      0.019707
3  20.588416                   0.0  ...     0.822848      0.014275
4  13.778447                   0.0  ...     0.812112      0.019304
5  17.610207                   0.0  ...     0.887725      0.012357
6   9.690949                   0.0  ...     0.782680      0.034989
7  41.206242                   0.0  ...     0.948333      0.005818
8   5.177965                   0.0  ...     0.720930      0.027901
9  27.964112                   0.0  ...     0.885563      0.009701

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

['3' '4' '5' '7' '9']

Annotations

• name : GroundTruthSorting

Properties

gt_unit_locations
[[22.295021 10.09109 15.0156355] [ 7.717033 -6.3216424 5.2143984] [-3.4058156 -6.2532897 34.16219 ] [-1.9566299 12.11982 10.352691 ] [20.22455 -9.183319 21.168097 ]]

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