Processing defaults

This page lists the default settings of the EIT, EMG and ventilator processing in one place. It also lists the settings where two places use different values for the same thing.

M3Resp gets most of its processing from eitprocessing (EIT) and resurfemg (EMG and part of the ventilator processing). Each package has its own defaults. M3Resp shows some of them as step settings. Others are fixed in the code of the package.

Checked versions

The values come from the code on 2026-10-01. Both packages come from the m3resp-integration branch of the M3RESP copies, at the commits in uv.lock:

• eitprocessing 1.8.7, commit 6d6da6a825a08201ad01c0a7b68f4de07d4501f3

• ReSurfEMG 1.1.1.dev47, commit c63668689030e4581d5f985e7d09d3a8c01e7a77

Check the values again after an update of either package.

The “Set by” column

Value	Meaning
m3resp	A step setting. It shows in a workflow file and in the GUI.
m3resp (undeclared)	M3Resp gives it to the package, but the step does not list it as a setting. You can set it in a workflow file, but the GUI does not show it.
m3resp (fixed)	A value in the M3Resp code. You cannot change it.
eitprocessing, ReSurfEMG	A value in the code of the package. You cannot change it from a workflow file.

1. Open points

Each point is one kind of value with different values in two places. The last column is a proposal for the team.

#	What	Current values	Proposal
D1	Butterworth filter order	EIT eit.butterworth_filter: 4 (m3resp’s own choice; eitprocessing has no default). EMG band-pass: 3 (ReSurfEMG, cannot be changed).	One default order for all band filters, and make the EMG order a setting.
D2	Shortest breath accepted	EIT eit.detect_breaths and eit.pixel_breaths: 0.67 s. EMG emg.detect_breaths: 0.5 s (undeclared). ReSurfEMG’s own EMG class: 0.2 s. Ventilator ventilator.detect_breaths and ventilator.normalize_breaths: 0.5 s. Occlusions in ventilator.find_occluded_breaths: 0.1 s (m3resp, fixed).	One value in seconds for all three modalities, as a setting of each breath detection step.
D3	Highest breathing rate allowed	EIT rate search, adult: 60 /min (neonate 85 /min). Ventilator ventilator.detect_pressure_breaths: shortest gap 2 s, so 30 /min. Occlusions in ventilator.find_occluded_breaths: shortest gap 0.5 s (m3resp, fixed). A 0.67 s shortest breath (D2) allows 90 /min.	Take the limits from subject_type (adult/neonate), as EIT already does.
D4	Highest heart rate allowed	EIT rate search, adult: 200 /min (neonate 210 /min). EMG emg.ecg_detect_peaks: shortest gap between beats is a third of a second, so 180 /min. It can be changed with peak_distance_seconds.	Same heart-rate range for both devices, taken from subject_type.
D5	ECG gate width, when not set	emg.ecg_gating takes gate_width_seconds or gate_width_samples. When neither is set it uses 205 samples (ReSurfEMG function default). That is 0.1 s only at 2048 Hz; at 4000 Hz it is 0.05 s. ReSurfEMG’s own EMG class falls back to 0.1 s at any sampling rate.	Fall back to 0.1 s instead of 205 samples.
D6	How a gate is filled	emg.ecg_gating: 1 (straight line between the gate edges; ReSurfEMG function default). ReSurfEMG’s own EMG class and ECG-removal workflow: 3 (running RMS).	Choose one method. ReSurfEMG uses method 3 in its own workflow.
D7	Slope window for breath onset/offset	emg.onoffpeak_slope_extrapolation: 0.5 s. ReSurfEMG’s peak-set class: 0.2 s.	Choose one value. ReSurfEMG uses 0.2 s.
D8	Same step, different default from Python	ventilator.detect_breaths: the step setting says 0.5 s, but calling the Python function directly uses 0.25 s, so the same data gives different breath counts. emg.ecg_detect_peaks: the step setting is empty (ReSurfEMG then uses a third of a second), while the Python function says 0.33 s. Same result today, but written in two places.	Make the Python default and the step setting the same value.

All EMG and ventilator baselines use a window of 7.5 s, a step of 0.2 s and the 33rd percentile, as in ReSurfEMG: emg.moving_baseline, emg.slopesum_baseline, the "emg" preset, M3Session.postprocess_emg without a baseline, and ventilator.pocc_intervals. The EIT breath detection uses a moving average of 15 s.

2. Values that M3Resp chose

The packages give no default for these settings, so M3Resp chose the values. Each value needs a reason or a reference in the docs.

Step	Setting	Value
eit.butterworth_filter	mode / lowpass_hz / highpass_hz / order	lowpass / 1.0 Hz / 0.05 Hz / 4
emg.detect_breaths	shortest breath (min_breath_width_seconds)	0.5 s
ventilator.detect_breaths	breath_width_seconds	0.5 s
ventilator.detect_pressure_breaths	smoothing_seconds / min_depth / min_interval_seconds	0.2 s / 0.15 / 2.0 s
ventilator.find_occluded_breaths	peep	median airway pressure
emg.envelope in the "emg" preset	envelope window and method after ECG gating	the ones recorded by session.preprocess_emg (0.25 s / RMS unless set)

3. All defaults, by modality

EIT (eitprocessing)

Step	Setting	Value	Set by
eit.detect_breaths	shortest breath	0.67 s	m3resp (same as eitprocessing)
	moving-average window	15 s, Blackman shape	eitprocessing
	smallest breath, as a fraction of the typical breath	0.25	eitprocessing
	removal of bad data: window / percentile / factor	0.5 s / 5th / ×4	eitprocessing
eit.detect_rates	subject_type	adult	m3resp
	Welch window	30 s (shortest allowed 10 s)	eitprocessing, can be set with welch_window_seconds
	Welch overlap	0.5	eitprocessing
	breathing rate, adult / neonate	6 to 60 /min / 15 to 85 /min	eitprocessing
	heart rate, adult / neonate	40 to 200 /min / 90 to 210 /min	eitprocessing
eit.mdn_filter	upper noise limit	220 /min	eitprocessing
	notch distance	10 /min	eitprocessing
	filter order	10	eitprocessing
eit.butterworth_filter	see section 2		m3resp
eit.pixel_breaths	phase_correction_mode	negative amplitude	m3resp (same as eitprocessing)
	minimum_duration_seconds	0.67 s	m3resp (same as eitprocessing)
eit.pixel_tiv	tiv_timing	continuous	m3resp
eit.roi_tiv_lungspace, eit.roi_amplitude_lungspace	threshold	0.15	m3resp (same as eitprocessing)
eit.roi_watershed	threshold_fraction	0.15	m3resp (same as eitprocessing)
eit.roi_filter_by_size	min_region_size / connectivity	10 pixels / 1 (4 neighbours)	m3resp (same as eitprocessing)

EMG (ReSurfEMG)

Step	Setting	Value	Set by
emg.preprocess, emg.select_channel	channel	picked from the channel labels	m3resp
emg.preprocess, emg.bandpass_filter	band-pass edges	20 Hz to the lower of 500 Hz and 0.95 × half the sampling rate	m3resp, same as ReSurfEMG
	band-pass order	3	ReSurfEMG
emg.preprocess, emg.notch_filter	harmonic notch (EIT frame-rate comb)	off in emg.preprocess unless a base frequency is given	m3resp
	notch quality factor / upper limit / applied	30 / half the sampling rate / after the band-pass	m3resp
emg.envelope	envelope window / method	0.25 s / RMS	m3resp, same as ReSurfEMG
emg.detect_breaths	shortest breath	0.5 s	m3resp (undeclared)
	prominence: factor × (75th + 50th percentile of the envelope above baseline)	0.5	m3resp (undeclared), same as ReSurfEMG
	merge peaks closer than the shortest breath	no	m3resp (undeclared)
emg.moving_baseline	window / step / percentile	7.5 s / 0.2 s / 33	m3resp
emg.slopesum_baseline	window / step / percentile / extra percentile	7.5 s / 0.2 s / 33 / 25	m3resp
	smoothing window / percentile window	0.5 s / 1.0 s	m3resp
emg.ecg_detect_peaks	peak_fraction	0.4	m3resp (same as ReSurfEMG)
	band-pass before detection	1 to 500 Hz	ReSurfEMG
	shortest peak width / shortest gap between peaks	1 ms / 0.33 s	ReSurfEMG, can be set
emg.ecg_gating	gate width / fill method	205 samples / 1	m3resp (same as the ReSurfEMG function)
emg.ecg_wavelet_denoising	levels / wavelet / threshold / hard thresholding	4 / db2 / 4.5 / yes	m3resp (same as ReSurfEMG)
emg.onoffpeak_slope_extrapolation	slope_window_seconds	0.5 s	m3resp
emg.area_under_baseline	window_seconds	5 s	m3resp (same as ReSurfEMG)
emg.percentage_under_baseline	window / limit	the breath’s own onset to offset / 40 %	m3resp (limit same as ReSurfEMG)
emg.detect_local_high_aub	percentile / factor	75 / ×4	m3resp (same as ReSurfEMG)
emg.detect_extreme_time_products	upper percentile and factor / lower percentile and factor	95, ×10 / 5, ×0.1	m3resp (same as ReSurfEMG)
emg.evaluate_respiratory_rates	minimum_fraction	0.1	m3resp (same as ReSurfEMG)
emg.interpeak_dist	threshold	1.1	m3resp (same as ReSurfEMG)
emg.evaluate_bell_curve_error	largest bell-curve error for a valid breath	40 %	m3resp (fixed), same as ReSurfEMG
emg.evaluate_event_timing	how far the EMG peak may come before the ventilator peak: least / most	−0.5 s / 2.0 s	m3resp (fixed)
emg.snr_pseudo	minimum_snr	none (measure only)	m3resp
respiratory rate	outlier percentile / factor	33 / ×3	m3resp (fixed), same as ReSurfEMG

Ventilator

Step	Setting	Value	Set by
ventilator.detect_breaths	breath_width_seconds	0.5 s (0.25 s from Python, see D8)	m3resp
	height / prominence, first pass (× 90th percentile of volume)	0.25 / 0.10	m3resp (fixed)
	height / prominence, second pass (× 90th percentile of volume)	0.5 / 0.5	m3resp (fixed)
ventilator.normalize_breaths	breath_width_seconds	0.5 s	m3resp
ventilator.detect_pressure_breaths	see section 2		m3resp
ventilator.find_occluded_breaths	prominence: factor × (PEEP − lowest pressure)	0.8	m3resp (fixed), same as ReSurfEMG
	shortest occlusion / shortest gap between occlusions	0.1 s / 0.5 s	m3resp (fixed)
ventilator.pocc_intervals	window / step / percentile	7.5 s / 0.2 s / 33	m3resp
ventilator.pocc_quality	dP thresholds at 10 % / 90 % / 90 % scaled	0.0 / 2.0 / 0.8	m3resp (same as ReSurfEMG)
ventilator.pocc_time_product	add area under baseline / its window	yes / 5 s	m3resp

4. Other findings

• emg.preprocess and emg.detect_breaths list only variant as a setting. You can set their filter limits, envelope window, channel and shortest breath in a workflow file, but the GUI does not show them.

• Some default values are numbers of samples, for example the gate width in D5. So their duration in seconds depends on the sampling rate.

Continue with Migration guide.