Methods

Detection Parameters

To detect action potentials, SanPy uses a number of parameters. These can all be configured using the detection parameter plugin or programmatically with the bDetection API.

Generated on 20261026 with SanPy version 0.3.0.post76.

Parameter	Category	Default	Type	Units	Human name	Description
detectionName	presets	default	str		Detection Preset	The name of detection preset
userSaveName	presets		str		Save User Name	The name of saved user detection params
detectionType	detection	dvdt	detection type		Detection Type	Detect using derivative (dvdt) or membrane potential (mV)
dvdtThreshold	detection	20	float | None	mV/ms	dV/dt Threshold	Minimum dV/dt used to detect a spike threshold
mvThreshold	detection	-20	float	mV	mV Threshold	mV threshold for spike AND minimum spike mV when detecting with dV/dt
startSeconds	windows	None	float | None	s	Start(s)	Start seconds of analysis, set from the visible x-range when detecting
stopSeconds	windows	None	float | None	s	Stop(s)	Stop seconds of analysis, set from the visible x-range when detecting
dvdt_percentOfMax	detection	0.1	float	Percent	dV/dt Percent of max	For dV/dt detection, the final TOP is when dV/dt drops to this percent from dV/dt AP peak
onlyPeaksAbove_mV	waveform	None	float | None	mV	Accept Peaks Above (mV)	Only accept APs with peaks above this value (mV)
onlyPeaksBelow_mV	waveform	None	float | None	mV	Accept Peaks Below (mV)	Only accept APs below this value (mV)
doBackupSpikeVm	advanced	False	bool	Boolean	Backup Vm Spikes	If true, APs detected with just mV will be backed up until Vm falls to xxx
refractory_ms	windows	170	float	ms	Minimum AP interval (ms)	APs with interval (wrt previous AP) less than this will be removed
peakWindow_ms	windows	100	float	ms	Peak Window (ms)	Window after TOP (ms) to seach for AP peak (mV)
dvdtPreWindow_ms	windows	10	float	ms	dV/dt Pre Window (ms)	Window (ms) to search before each TOP for real threshold crossing
dvdtPostWindow_ms	windows	20	float	ms	dV/dt Post Window (ms)	Window (ms) to search after each AP peak for minimum in dv/dt
mdp_ms	windows	250	float	ms	Pre AP MDP window (ms)	Window (ms) before an AP to look for MDP
avgWindow_ms	windows	5	float	ms	MDP averaging window (ms)	Window (ms) to calculate MDP (mV) as a mean rather than mV at single point for MDP
lowEddRate_warning	advanced	8	float	EDD slope	EDD slope warning	Generate warning when EED slope is lower than this value.
halfWidthWindow_ms	windows	200	float	ms	Half Width Window (ms)	Window (ms) after TOP to look for AP widths
preSpikeClipWidth_ms	spike clips	4	float	ms	Pre AP Clip Width (ms)	The pre duration of generated AP clips (Before AP)
postSpikeClipWidth_ms	spike clips	8	float	ms	Post AP Clip Width (ms)	The post duration of generated AP clips (After AP)
fastAhpWindow_ms	windows	8	float	ms	Fast AHP Window (ms)	Window (ms) after peak to look for a fast AHP
medianFilter	filtering	0	int | None	points	Median Filter Points	Number of points in median filter, must be odd, 0 for no filter
SavitzkyGolay_pnts	filtering	5	int | None	points	SavitzkyGolay Points	Number of points in SavitzkyGolay filter, must be odd, 0 for no filter
SavitzkyGolay_poly	filtering	2	int		SavitzkyGolay Poly Deg	The degree of the polynomial for Savitzky-Golay filter
verbose	advanced	False	bool	Boolean	Verbose	Verbose Detection Reporting

Detection Errors

When SanPy encounters errors during spike detection, they are stored for each spike in errors. Each error has a name like dvdtPercent, as follows:

• dvdtPercent: Error searching for percent (10%) of dV/dt max. When this occurs, the TOP (mV) of a spike will be more depolarized than it should be.
• preMin: Error searching for spike pre-minimum, the MDP before a spike. This can occur on the first spike if it is close to the beginning of the recording.
• postMin:
• fitEDD: Error while fitting the slope of EDD.
• preSpikeDvDt: Error while searching for peak AP upstroke (dV/dt) between spike threshold (TOP) and the peak in the first derivative of Vm (dV/dt).
• cycleLength: Usually occurs on the last spike when looking for the next MDP.
• spikeWidth: Error finding a particular spike width (AP duration). This usually occurs when spikes are too broad; increase the halfWidthWindow_ms detection parameter.

Analysis results

Once spikes are detected, SanPy exposes the following analysis results in its plotting interfaces. Name is the internal variable name and CSV column name, while Axis label is the human-readable label.

Generated on 20261026 with SanPy version 0.3.0.post76.

Name	Category	Axis label	Type	Default	Units	Plot menu	Categorical	Detection dependency	Error	Description
sweep	acquisition	Sweep	int	None		True	True			Zero-based analyzed sweep number.
epoch	acquisition	Epoch	int | None	None		True	True			Zero-based stimulus epoch containing the spike.
epochLevel	acquisition	Epoch level (pA)	float | None	None	pA	True	True			DAC stimulus level during the spike.
spike_include	metadata	Spike included	str	yes		True	True			Whether this spike is included.
file_number	metadata	File Number	int	0		True	True			File number used when pooling analyses.
sweepCondition	identity	Sweep condition	str			True	True			User-assigned sweep condition.
spikeNumber	identity	Spike number	int	None		True	False			Zero-based spike number across all sweeps.
sweepSpikeNumber	identity	Sweep spike number	int	None		True	False			Zero-based spike number within the sweep.
userType	identity	User type	int	0		True	True			User-assigned integer spike type.
spike_condition	identity	Spike condition	str			True	True			User-assigned condition for this spike.
thresholdSec	peak detection	Threshold time (s)	float | None	None	sec	True	False			Action-potential threshold time.
thresholdVal	peak detection	Threshold voltage (mV)	float | None	None	mV	True	False			Voltage at threshold.
peakVal	peak detection	Peak voltage (mV)	float | None	None	mV	True	False			Voltage at the peak.
peakHeight	peak detection	Spike height (mV)	float | None	None	mV	True	False			Peak voltage minus threshold voltage.
timeToPeak_ms	peak detection	Time to peak (ms)	float | None	None	ms	True	False			Time from threshold to peak.
fastAhpValue	peak detection	Fast AHP voltage (mV)	float | None	None	mV	True	False			Voltage at the fast AHP.
preMinVal	peak detection	Pre-spike minimum voltage (mV)	float | None	None	mV	True	False			Minimum voltage before the spike.
earlyDiastolicDuration_ms	peak detection	Early diastolic duration (ms)	float | None	None	ms	True	False			Duration of the early-diastolic fit.
earlyDiastolicDurationRate	peak detection	Early diastolic rate (mV/s)	float | None	None	mV/s	True	False			Slope of the early-diastolic fit.
preSpike_dvdt_max_val	peak detection	Voltage at pre-spike maximum dV/dt (mV)	float | None	None	mV	True	False			Voltage at maximum pre-spike dV/dt.
preSpike_dvdt_max_val2	peak detection	Pre-spike maximum dV/dt (mV/ms)	float | None	None	dV/dt	True	False			Maximum pre-spike dV/dt.
postSpike_dvdt_min_val	peak detection	Voltage at post-spike minimum dV/dt (mV)	float | None	None	mV	True	False			Voltage at minimum post-spike dV/dt.
isi_ms	timing	Interspike interval (ms)	float | None	None	ms	True	False			Time since the previous threshold.
spikeFreq_hz	timing	Spike frequency (Hz)	float | None	None	Hz	True	False			Instantaneous frequency from the previous spike.
cycleLength_ms	timing	Cycle length (ms)	float | None	None	ms	True	False			Time between successive pre-spike minima.
diastolicDuration_ms	timing	Diastolic duration (ms)	float | None	None	ms	True	False			Time from pre-spike minimum to threshold.
width_10_ms	widths	Spike width at 10% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 10 percent of spike height.
width_20_ms	widths	Spike width at 20% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 20 percent of spike height.
width_50_ms	widths	Spike width at 50% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 50 percent of spike height.
width_80_ms	widths	Spike width at 80% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 80 percent of spike height.
width_90_ms	widths	Spike width at 90% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 90 percent of spike height.

Analysis results (full)

The complete analysis-result registry includes stored results that are not offered by plotting menus.

Generated on 20261026 with SanPy version 0.3.0.post76.

Name	Category	Axis label	Type	Default	Units	Plot menu	Categorical	Detection dependency	Error	Description
file	acquisition	File	str			False	False			Name of the analyzed raw-data file.
sweep	acquisition	Sweep	int	None		True	True			Zero-based analyzed sweep number.
epoch	acquisition	Epoch	int | None	None		True	True			Zero-based stimulus epoch containing the spike.
epochLevel	acquisition	Epoch level (pA)	float | None	None	pA	True	True			DAC stimulus level during the spike.
detectionType	detection	Detection type	detectionTypes_	None		False	False			Spike-detection algorithm.
dvdtThreshold	detection	dV/dt threshold (mV/ms)	float | None	None	dvdt	False	False	dvdtThreshold		Derivative threshold used for detection.
mvThreshold	detection	Voltage threshold (mV)	float | None	None	mV	False	False	mvThreshold		Membrane-potential detection threshold.
medianFilter	detection	Median filter	int | None	0		False	False	medianFilter		Median-filter width in points.
analysisDate	detection	Analysis date	str			False	False			Analysis date in YYYYMMDD format.
analysisTime	detection	Analysis time	str			False	False			Analysis time in 24-hour HH:MM:SS format.
modDate	detection	Modification date	str			False	False			Date of a post-detection edit.
modTime	detection	Modification time	str			False	False			Time of a post-detection edit.
sanpy_version	detection	Sanpy Version	str			False	False			SanPy version used for analysis.
sanpy_git_commit	detection	Sanpy Git Commit	str			False	False			SanPy Git commit used for analysis.
sanpy_git_dirty	detection	Sanpy Git Dirty	bool | str			False	False			Whether the checkout had changes.
spike_include	metadata	Spike included	str	yes		True	True			Whether this spike is included.
file_number	metadata	File Number	int	0		True	True			File number used when pooling analyses.
sweepCondition	identity	Sweep condition	str			True	True			User-assigned sweep condition.
spikeNumber	identity	Spike number	int	None		True	False			Zero-based spike number across all sweeps.
sweepSpikeNumber	identity	Sweep spike number	int	None		True	False			Zero-based spike number within the sweep.
userType	identity	User type	int	0		True	True			User-assigned integer spike type.
spike_condition	identity	Spike condition	str			True	True			User-assigned condition for this spike.
errors	identity	Errors	list	[]		False	False			Detection errors for this spike.
thresholdPnt	peak detection	Threshold point	int	None	point	False	False			Action-potential threshold point.
thresholdSec	peak detection	Threshold time (s)	float | None	None	sec	True	False			Action-potential threshold time.
thresholdVal	peak detection	Threshold voltage (mV)	float | None	None	mV	True	False			Voltage at threshold.
thresholdVal_dvdt	peak detection	Threshold dV/dt (mV/ms)	float | None	None	dvdt	False	False			dV/dt at threshold.
peakPnt	peak detection	Peak point	int	None	point	False	False	(onlyPeaksAbove_mV, peakWindow_ms)		Action-potential peak point.
peakSec	peak detection	Peak time (s)	float | None	None	sec	False	False			Action-potential peak time.
peakVal	peak detection	Peak voltage (mV)	float | None	None	mV	True	False			Voltage at the peak.
peakHeight	peak detection	Spike height (mV)	float | None	None	mV	True	False			Peak voltage minus threshold voltage.
timeToPeak_ms	peak detection	Time to peak (ms)	float | None	None	ms	True	False			Time from threshold to peak.
fastAhpPnt	peak detection	Fast AHP point	int | None	None	point	False	False	fastAhpWindow_ms		Fast afterhyperpolarization point.
fastAhpSec	peak detection	Fast AHP time (s)	float | None	None	sec	False	False			Fast AHP time.
fastAhpValue	peak detection	Fast AHP voltage (mV)	float | None	None	mV	True	False			Voltage at the fast AHP.
preMinPnt	peak detection	Pre-spike minimum point	int | None	None	point	False	False	mdp_ms		Minimum point before the spike.
preMinVal	peak detection	Pre-spike minimum voltage (mV)	float | None	None	mV	True	False			Minimum voltage before the spike.
preLinearFitPnt0	peak detection	Early diastolic fit start point	int	None	point	False	False			Start point for the early-diastolic fit.
preLinearFitPnt1	peak detection	Early diastolic fit end point	int	None	point	False	False			End point for the early-diastolic fit.
earlyDiastolicDuration_ms	peak detection	Early diastolic duration (ms)	float | None	None	ms	True	False			Duration of the early-diastolic fit.
preLinearFitVal0	peak detection	Early diastolic fit start voltage (mV)	float | None	None	mV	False	False			Voltage at the fit start.
preLinearFitVal1	peak detection	Early diastolic fit end voltage (mV)	float | None	None	mV	False	False			Voltage at the fit end.
earlyDiastolicDurationRate	peak detection	Early diastolic rate (mV/s)	float | None	None	mV/s	True	False			Slope of the early-diastolic fit.
lateDiastolicDuration	peak detection	Late diastolic duration	float | None	None		False	False			Deprecated late-diastolic duration.
preSpike_dvdt_max_pnt	peak detection	Pre-spike maximum dV/dt point	int | None	None	point	False	False			Point of maximum dV/dt before the peak.
preSpike_dvdt_max_val	peak detection	Voltage at pre-spike maximum dV/dt (mV)	float | None	None	mV	True	False			Voltage at maximum pre-spike dV/dt.
preSpike_dvdt_max_val2	peak detection	Pre-spike maximum dV/dt (mV/ms)	float | None	None	dV/dt	True	False			Maximum pre-spike dV/dt.
postSpike_dvdt_min_pnt	peak detection	Post-spike minimum dV/dt point	int	None	point	False	False	dvdtPostWindow_ms		Point of minimum dV/dt after the peak.
postSpike_dvdt_min_val	peak detection	Voltage at post-spike minimum dV/dt (mV)	float | None	None	mV	True	False			Voltage at minimum post-spike dV/dt.
postSpike_dvdt_min_val2	peak detection	Post-spike minimum dV/dt (mV/ms)	float | None	None	dV/dt	False	False			Minimum post-spike dV/dt.
isi_pnts	timing	Interspike interval (points)	int | None	None	point	False	False	refractory_ms		Points since the previous threshold.
isi_ms	timing	Interspike interval (ms)	float | None	None	ms	True	False			Time since the previous threshold.
spikeFreq_hz	timing	Spike frequency (Hz)	float | None	None	Hz	True	False			Instantaneous frequency from the previous spike.
cycleLength_pnts	timing	Cycle length (points)	int | None	None	point	False	False			Points between successive pre-spike minima.
cycleLength_ms	timing	Cycle length (ms)	float | None	None	ms	True	False			Time between successive pre-spike minima.
diastolicDuration_ms	timing	Diastolic duration (ms)	float | None	None	ms	True	False			Time from pre-spike minimum to threshold.
width_10_ms	widths	Spike width at 10% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 10 percent of spike height.
width_10_rising_pnt	widths	Spike width 10% rising point	int | None	None	point	False	False	halfWidthWindow_ms		Rising-phase crossing point at 10 percent of spike height.
width_10_falling_pnt	widths	Spike width 10% falling point	int | None	None	point	False	False	halfWidthWindow_ms		Falling-phase crossing point at 10 percent of spike height.
width_20_ms	widths	Spike width at 20% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 20 percent of spike height.
width_20_rising_pnt	widths	Spike width 20% rising point	int | None	None	point	False	False	halfWidthWindow_ms		Rising-phase crossing point at 20 percent of spike height.
width_20_falling_pnt	widths	Spike width 20% falling point	int | None	None	point	False	False	halfWidthWindow_ms		Falling-phase crossing point at 20 percent of spike height.
width_50_ms	widths	Spike width at 50% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 50 percent of spike height.
width_50_rising_pnt	widths	Spike width 50% rising point	int | None	None	point	False	False	halfWidthWindow_ms		Rising-phase crossing point at 50 percent of spike height.
width_50_falling_pnt	widths	Spike width 50% falling point	int | None	None	point	False	False	halfWidthWindow_ms		Falling-phase crossing point at 50 percent of spike height.
width_80_ms	widths	Spike width at 80% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 80 percent of spike height.
width_80_rising_pnt	widths	Spike width 80% rising point	int | None	None	point	False	False	halfWidthWindow_ms		Rising-phase crossing point at 80 percent of spike height.
width_80_falling_pnt	widths	Spike width 80% falling point	int | None	None	point	False	False	halfWidthWindow_ms		Falling-phase crossing point at 80 percent of spike height.
width_90_ms	widths	Spike width at 90% (ms)	float | None	None	ms	True	False	halfWidthWindow_ms		Width at 90 percent of spike height.
width_90_rising_pnt	widths	Spike width 90% rising point	int | None	None	point	False	False	halfWidthWindow_ms		Rising-phase crossing point at 90 percent of spike height.
width_90_falling_pnt	widths	Spike width 90% falling point	int | None	None	point	False	False	halfWidthWindow_ms		Falling-phase crossing point at 90 percent of spike height.

What spike parameters are detected?

For cardiac myocyte analysis, SanPy follows the nomenclature from this paper:

Larson, et al. (2013), “Depressed pacemaker activity of sinoatrial node myocytes contributes to the age-dependent decline in maximum heart rate,” PNAS 110(44):18011–18016.

• MDP and Vmax were defined as the most negative and positive membrane potentials, respectively.
• Take-off potential (TOP) was defined as the membrane potential when the first derivative of voltage with respect to time (dV/dt) reached 10% of its maximum value.
• Cycle length was defined as the interval between MDPs in successive APs.
• The maximum rates of the AP upstroke and repolarization were taken as the maximum and minimum values of the first derivative (dV/dtmax and dV/dtmin, respectively).
• Action potential duration (APD) was formerly defined as the interval between the TOP and the subsequent MDP; this definition was removed in 2021.
• APD_50 and APD_90 were defined as the interval between the TOP and 50% and 90% repolarization, respectively.
• The diastolic duration was defined as the interval between MDP and TOP.
• The early diastolic depolarization rate was estimated as the slope of a linear fit between 10% and 50% of the diastolic duration, and the early diastolic duration was the corresponding time interval.
• The nonlinear late diastolic depolarization phase was estimated as the duration between 1% and 10% dV/dt.