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

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into bombcell

… for name changes

…ell_

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into bombcell

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

into bombcell

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into bombcell

Julie-Fabre · 2026-01-18T00:11:06Z

Regarding the 'spikeInterface' vs 'bombcell' SNR:

spikeInterace SNR: |peak(mean_template)| / MAD(recording_noise), is that right?
Bombcell SNR: |peak(median_waveform)| / MAD(waveform_baseline). Uses median waveform and baseline noise from extracted spikes.

The do agree mostly:

Here's a correlation plot:

And some example units where they don't agree (top row = high spikeInterface SNR and low bombcell SNR; second row: low SI and high BC; third row: both high and fourth row: both low). I am plotting the median waveform +/- m.a.d. here.

Based on this very quick look at these examples, I would say:
(1) I think the spikeInterface way of choosing the extreme value doesn't work for non-somatic units (basically all the ones in the second row - blue ones). we should update that.
(2) for the top row (spikeInterface high, bombcell low), it's a mixed bag (some fine, others noisy) but I might tend to prefer the bombcell one (is does seem to seperate better what visually I would say are noisier units from less noisy ones), so I would like keep it at least for the bombcell pipeline.

I would really like to get your input on this! What do you think? And also what was the rationale for using the full recording to calculate noise?

…_metrics in bombcell functions

…n.dump()/json.load() since None serializes directly to JSON null.

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samuelgarcia · 2026-01-19T08:08:52Z

Thanks Julie for this plot this is really cool. lets have a call to discuss no ?
I suspect that some difference may also be due to the fact that we measurign the negative peak only.
lets check this.

Julie-Fabre · 2026-01-19T18:36:00Z

Yes, absolutely I agree! I think that's what's responsible for all the cases where the SI metric < BC metric (blue guys) but maybe not for the cases where SI metric > BC metric (red guys)? Curious to hear what you think

Great idea, let's have a call. Sent you a message on slack :)

…refine

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… bombcell

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…

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…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

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cleanup

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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…

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…ell_

remove upset plot warnings for now

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bombcell plot wrapper

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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

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

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

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

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into bombcell

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example jupyter notebook

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example jupyter notebook

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

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into bombcell

Julie-Fabre and others added 15 commits January 17, 2026 20:14

labelling -> labeling and unit_labeling.py -> bombcell_curation.py

adac68e

WAVEFORM_METRICS -> NOISE_METRICS

291bca4

use sorting analyzer rather than inputing template_metrics and qualty…

6b21830

…_metrics in bombcell functions

remove unused apply_thresholds() function

8673ebc

get_labeling_summary -> get_bombcell_labeling_summary

e55cde7

Removed save_thresholds and load_thresholds. can now use standard jso…

b04ff26

…n.dump()/json.load() since None serializes directly to JSON null.

get_labeling_results -> get_bombcell_results

5383728

woops, that was tracked and committed too early - reverting

7491a6a

removed debugging plots

3b1d819

imports to individual functions

02c9a53

remove more debugging plots

96d8bb6

rename waveform_duration

0e7fb40

more combine -> sorting_analyzer

a5ab4a6

converted all durations (and defualt thresholds) to seconds

a345e42

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Julie-Fabre mentioned this pull request Jan 18, 2026

spikeinterface sorting object as input Julie-Fabre/bombcell#368

Open

alejoe91 and others added 11 commits January 21, 2026 12:24

Use external metrics and remove json

e596493

clean up imports

90b5a51

Add polarity inversion for old peak to trough

7d4747d

ported general label widhet to unit labels and backward comp for unit…

81dc7d6

…refine

labels to lower case

702f5c7

Use peak_sign='both' as default for SNR

2983204

Merge conflicts and use SNR in bombcell by default

bbab79a

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Lazy import of pandas and basic tests

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

241a6cb

… bombcell

fix docs and tests

6af9617

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Bombcell integration #4306

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edited by alejoe91

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Template metrics

Quality metrics

Unit classification

Plots

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