Bombcell integration #4306

Julie-Fabre · 2026-01-08T11:36:27Z

This PR ports bombcell-style unit classification to SpikeInterface.

Template metrics

Rewrote peak/trough detection with a new get_trough_and_peak_idx() function that uses scipy.signal.find_peaks(). Since SpikeInterface stores templates based on raw data rather than the heavily smoothed templates used in template matching, the waveforms can be noisy—so you can optionally apply Savitzky-Golay smoothing before detection. The function returns dicts for troughs, peaks before, and peaks after, each containing indices, values, prominences, and widths.

from spikeinterface.postprocessing import get_trough_and_peak_idx

troughs, peaks_before, peaks_after = get_trough_and_peak_idx(
    templates,
    sampling_frequency,
    smooth=True,
    min_thresh_detect_peaks_troughs=0.4,
)

New metrics: peak_before_to_trough_ratio, peak_after_to_trough_ratio, waveform_baseline_flatness, peak_before_width, trough_width, main_peak_to_trough_ratio.
Renamed peak_to_valley to peak_to_trough_duration.

analyzer.compute("template_metrics", metric_names=[
    "peak_before_to_trough_ratio",
    "waveform_baseline_flatness",
    "trough_width",
])

Quality metrics

Added snr_bombcell—peak amplitude over baseline MAD.

analyzer.compute("quality_metrics", metric_names=["snr_bombcell"])

amplitude_cutoff now has parameters for controlling the histogram fitting:

analyzer.compute("quality_metrics", metric_names=["amplitude_cutoff"], qm_params={
    "amplitude_cutoff": {
        "num_histogram_bins": 100,
        "histogram_smoothing_value": 3,
    }
})

Unit classification

New in spikeinterface.curation:

import spikeinterface.comparison as sc

thresholds = sc.bombcell_get_default_thresholds()
unit_type, unit_type_string = sc.bombcell_classify_units(
    quality_metrics,
    thresholds=thresholds,
    classify_non_somatic=True,
)
summary = sc.get_classification_summary(unit_type, unit_type_string)

Units get classified as NOISE → MUA → GOOD based on successive threshold checks. Optional NON_SOMA category for non-somatic waveforms.

Plots

Added plots for classification summaries, metric histograms with threshold lines, waveform overlays by category, and UpSet plots.

from spikeinterface.widgets import (
    plot_unit_classification,
    plot_classification_histograms,
    plot_waveform_overlay,
    plot_upset,
)

plot_unit_classification(analyzer, unit_type, unit_type_string)
plot_classification_histograms(quality_metrics, thresholds=thresholds)
plot_waveform_overlay(analyzer, unit_type, unit_type_string)
plot_upset(quality_metrics, unit_type, unit_type_string)

or a wrapper for all plots:

plots = plot_unit_classification_all(
    sorting_analyzer,
    unit_type,
    unit_type_string,
    quality_metrics=quality_metrics,  # optional, will try to get from analyzer
    thresholds=thresholds,            # optional, uses defaults
    split_non_somatic=False,
    include_upset=True,
)

TODO:

Add documentation tutorial

…s and add more template metrics

…ault params

…verlay and histograms

…uration, add amplitude_median, bombcell_snr and fix non-somatic classification rules

for more information, see https://pre-commit.ci

into bombcell

… for name changes

…ell_

for more information, see https://pre-commit.ci

into bombcell

for more information, see https://pre-commit.ci

…ve template and quality metrics (this way it is clear what to input)

into bombcell

for more information, see https://pre-commit.ci

into bombcell

… into unitrefine-actor

Co-authored-by: Chris Halcrow <57948917+chrishalcrow@users.noreply.github.com>

…bombcell

src/spikeinterface/core/analyzer_extension_core.py

samuelgarcia · 2026-02-03T15:38:00Z

src/spikeinterface/metrics/template/metrics.py

+        Minimum prominence threshold as a fraction of the template's absolute max value
+    smooth : bool, default: True
+        Whether to apply smoothing before peak detection
+    smooth_window_frac : float, default: 0.1


I think I wowuld prefer to have this params in ms like smooth_window_ms
to avoid different smoothing when we change ms_before/ms_after

samuelgarcia · 2026-02-03T15:39:07Z

src/spikeinterface/metrics/template/metrics.py

-from collections import namedtuple
-
 from spikeinterface.core.analyzer_extension_core import BaseMetric



I would add a small and consice internal code doc string to explain the main rules for peak and trough detection concept.

samuelgarcia · 2026-02-03T15:39:54Z

src/spikeinterface/curation/bombcell_curation.py

+    unit_type_string = np.array([labels.get(int(t), "unknown") for t in unit_type], dtype=object)
+    labels = pd.DataFrame(data={"label": unit_type_string, "label_type": unit_type}, index=combined_metrics.index)
+
+    return labels


I think we should return on the unit_type_string and handle this in any downstream function.

samuelgarcia · 2026-02-03T15:40:06Z

src/spikeinterface/curation/bombcell_curation.py

+    return labels
+
+
+def get_bombcell_labeling_summary(unit_type: np.ndarray, unit_type_string: np.ndarray) -> dict:


this should work only on unit_type_string

samuelgarcia · 2026-02-03T15:41:10Z

src/spikeinterface/curation/bombcell_curation.py

+            noise_mask |= values < thresh["min"]
+        if not is_threshold_disabled(thresh["max"]):
+            noise_mask |= values > thresh["max"]
+    unit_type[noise_mask] = 0


I think I would do directly

Suggested change

unit_type[noise_mask] = 0

unit_type[noise_mask] = "noise"

to avoid remembering internal number.
This also would make the code super easy to read.
No ?

samuelgarcia · 2026-02-03T15:41:45Z

src/spikeinterface/core/analyzer_extension_core.py

+        if metric_names is None:
+            metric_names = [m.metric_name for m in cls.metric_list]
+        else:
+            for metric_name in metric_names:
+                if metric_name not in [m.metric_name for m in cls.metric_list]:
+                    raise ValueError(
+                        f"Metric {metric_name} not in available metrics {cls.get_available_metric_names()}"
+                    )
+        for metric_name in metric_names:
+            metric_class = cls.get_metric_by_name(metric_name)
+            default_metric_columns.extend(metric_class.metric_columns)


Can I try a small rewrite of this ?

I rewrote a bit already, but sure!

samuelgarcia · 2026-02-03T15:43:36Z

src/spikeinterface/widgets/unit_labels.py

+                [label in np.unique(unit_labels) for label in labels_order]
+            ), "All labels in labels_order must be present in unit_labels"
+        else:
+            labels_order = np.unique(unit_labels)


This will change the behavior if you have only good units for instance because it will be only on plots.
I would hard code of the possible no ?

samuelgarcia · 2026-02-03T15:45:30Z

src/spikeinterface/metrics/template/template_metrics.py

@@ -239,6 +294,9 @@ def _prepare_data(self, sorting_analyzer, unit_ids):

        tmp_data["troughs"] = troughs
        tmp_data["peaks"] = peaks


We should rename peak_after no ? to avoid the confusion

done! also added indices

…width and peak_half_width

Julie-Fabre and others added 20 commits January 7, 2026 01:15

template metrics from bombcell - use scipy findpeaks() to detect peak…

98de1f9

…s and add more template metrics

template denoising - SVD option and bombcell baseline flatness metric

71d35a4

woops remove kilosort4_output folder

788e8be

woops remove kilosort4_output folder

4b79f55

remove SVD option - was not performing well - and add sane tested def…

b391456

…ault params

bombcell unit type classification logic and output plots - waveform o…

c9306df

…verlay and histograms

bombcell unit type classification logic and output plots - waveform o…

44d8192

…verlay and histograms

bombcell snr

a29d3e1

fix: use peak_valley code to get duration, rename to peak_to_trough_d…

4514a51

…uration, add amplitude_median, bombcell_snr and fix non-somatic classification rules

upset plots

5b4cafb

[pre-commit.ci] auto fixes from pre-commit.com hooks

515ed36

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cleanup

8467177

Merge branch 'bombcell' of https://github.com/Julie-Fabre/spikeinterface

41fde99

into bombcell

cleanup

2e8d6ea

cleanup

ed770bb

cleanup old template metric functions and ensure backward compaiblity…

c81898f

… for name changes

move bombcell functions to curation and rename bombcell ones to bombc…

71063dc

…ell_

remove upset plot warnings for now

5a2416e

bombcell plot wrapper

afe4e1b

[pre-commit.ci] auto fixes from pre-commit.com hooks

6fb5b13

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alejoe91 added the curation Related to curation module label Jan 8, 2026

Julie-Fabre and others added 9 commits January 8, 2026 15:25

users can input bombcell parameters as JSON

52a58b2

Merge branch 'bombcell' of https://github.com/Julie-Fabre/spikeinterface

103ba7a

into bombcell

[pre-commit.ci] auto fixes from pre-commit.com hooks

aa35ac8

for more information, see https://pre-commit.ci

optionally save plots and metrics, explicit inputs to functions to ha…

eb130e9

…ve template and quality metrics (this way it is clear what to input)

Merge branch 'bombcell' of https://github.com/Julie-Fabre/spikeinterface

3b609b5

into bombcell

[pre-commit.ci] auto fixes from pre-commit.com hooks

01480b3

for more information, see https://pre-commit.ci

example jupyter notebook

af36259

example jupyter notebook

7045c43

Merge branch 'bombcell' of https://github.com/Julie-Fabre/spikeinterface

91a333e

into bombcell

alejoe91 and others added 16 commits February 2, 2026 12:28

Add warnings if wrong labels and extend to local models

d89a1e3

Merge branch 'unitrefine-actor' of github.com:alejoe91/spikeinterface…

d5d0482

… into unitrefine-actor

Update src/spikeinterface/curation/__init__.py

f9600e7

Co-authored-by: Chris Halcrow <57948917+chrishalcrow@users.noreply.github.com>

Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …

7de1b4e

…bombcell

wip merging

87bffa6

Solve conflicts

3b3edaa

Fix how_to/README

a2550d2

Add qualitymetrics_based curation

c797a49

Add qualitymetrics curation

b50d1a5

Merge branch 'main' into qualitymetrics_curation

5116b08

Add to __init__

d395c43

Solve conflicts

9c4f745

rename function

57616d0

Merge branch 'qualitymetrics_curation' into bombcell

42d9945

bombcell returns dataframe and docs

4c9d32d

Use rst note

1d9dfb8

samuelgarcia reviewed Feb 3, 2026

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src/spikeinterface/core/analyzer_extension_core.py Show resolved Hide resolved

samuelgarcia added this to the 0.104.0 milestone Feb 3, 2026

Clean up BaseMetricExtension

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samuelgarcia reviewed Feb 3, 2026

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alejoe91 added 3 commits February 3, 2026 17:29

Use smooth_window_ms, rename variable unambiguously, add trough_half_…

9d115c4

…width and peak_half_width

Update and clarify template_metrics documentation and docstring

e7bf88a

Add new template metrics figure

a37186f

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edited by alejoe91

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		from collections import namedtuple

		from spikeinterface.core.analyzer_extension_core import BaseMetric

		return labels


		def get_bombcell_labeling_summary(unit_type: np.ndarray, unit_type_string: np.ndarray) -> dict:

		@@ -239,6 +294,9 @@ def _prepare_data(self, sorting_analyzer, unit_ids):

		tmp_data["troughs"] = troughs
		tmp_data["peaks"] = peaks

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Julie-Fabre commented Jan 8, 2026 • edited by alejoe91 Loading Uh oh! There was an error while loading. Please reload this page.

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Template metrics

Quality metrics

Unit classification

Plots

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Julie-Fabre commented Jan 8, 2026 •

edited by alejoe91

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