Mar 062017

Recently during meditation at home just before bed, I have noticed that I sometimes start feeling sleepy midway through the period and start losing count of my breaths. To monitor this, I made it a practice to clench my jaw briefly whenever I lost count and had to return to “1”. The jaw clench serves as a convenient way to register an event in the EEG signal, as the Muse headband automatically records jaw clench events. In addition to recording EEG, I also recorded my breathing and synced the two signals together. The spectrogram below shows the EEG signal from the left front sensor. Superimposed are the (blue) breath and (red) jaw clench signals.

Highly rhythmical breath, alpha band signal (8.3 Hz) and no loss of breath count during the first 10 minutes.; irregular breathing, missing alpha band signal and loss of breath count (indicated by jaw clenches) during the final 10 minutes.

This same phenomenon occurred on four different dates, recorded just before 9:00 pm on February 9, 10, 11 and 15, 2017. I had been looking for correlates in the EEG signal to the experience of losing my focus on counting the breath. I was surprised to find such a dramatic change in breathing pattern whenever I began to lose count. The graphs below show the alpha power at the left back sensor (TP9) in green, the respiration signal in blue and jaw clench events in red.

To examine the EEG signal differences between sleepiness and zazen, we average the absolute power values of the five standard bands for the corresponding segments at locations lf, rf, lb and rb. Results are as follows:


First we notice that at the rear sensors lb and rb, the alpha signal is stronger during zazen compared to sleepiness. At the front sensors, the story is different: beta and gamma power is stronger during sleepiness compared to during zazen, but interestingly this only seems to be happening at on the left side, at sensor lf.

Mar 082016

For a long time, I have wondered whether my brain waves change with the rhythm of my breath. Can we observe characteristics of the EEG signal that correlate with the pattern of inhalations and exhalations during zazen?

I wanted to test this during the February 2016 osesshin at the Tahoma Zen Monastery. But first I needed to make sure that data in the EEG signal were synchronized with the respiration data. Since these two signals were coming from two separate devices, I needed to devise a system (which I describe at the end of this post) to insure that the two data streams were in sync.

Let us take a look at a 25-minute recording made on Day 6 of the sesshin. Following instructions from my teacher, Shodo Harada Roshi, I have been working on extending the exhalation as long as possible. Here is a spectrogram for the left back (lb) sensor.

spectrogram for lb sensor during zazen

The most prominent feature is the strong alpha oscillation at around 8 Hz, which we can verify by looking at the PSD spectrum for this interval.

PSD spectrum for lb sensor during zazen

At the lb sensor, we see a strong oscillation at 8.3 Hz. Now compare this with the spectrum for the left front sensor, lf.


PSD spectrum for sensor lf during zazen

The Power Spectral Density graph for sensor lf shows an alpha peak at the same frequency 8.3 Hz but at much less intensity (about 2.4 dB/Hz) compared to sensor lb (about 100 dB/Hz). In addition, there is considerably more power in the higher frequencies (beta and gamma) than we saw for lb.

Now let’s take a closer look at the spectrogram for sensor lf.

spectrogram for sensor lf during zazen

The alpha band is diminished (faint yellow horizontal strip near frequency 8 Hz). The frequencies from about 15-50 Hz are more prominent– note the orange smear centered from about 20-30 Hz.

But this spectrogram shows something else that is very interesting: the vertical bands with a semi-regular spacing. What could be the cause of these bands? At first, I thought maybe they were some kind of mathematical artifact. But when I took a look at the time intervals between successive bands, another idea came to me.

annotated spectrogram for lf

There are about 11 bands in an interval of 200 seconds, which is equivalent to about 3.3 bands per minute. But 3.3 per minute is a typical zazen breathing rate for me on the latter days of a sesshin. Could these bands be correlated with breathing?

To test this hypothesis I added a new feature to the Physiology Viewer 2.0 program, making it possible to superimpose the respiration signal on the EEG signal.  Let’s first zoom in on an interval, say from 880 – 1030 seconds. This is the spectrogram we get.

spectrogram for a short interval

We see the bands clearly in the EEG. Now let us add an overlay of the breath signal.

breath overlay on EEG signal

Remember that the respiration and EEG signals have been synchronized. So we see that the growth in high frequency power (left side of yellow bands) begins with the inhalation, continues during the exhalation and then drops off (right side of yellow bands) during the extended exhalation.

Below are spectrograms for a recording done two days earlier (Day 4 of the osesshin).

spectrogram for a segment of zazen

spectrogram with breath overlay

We see the same pattern as before. In fact, when I go back and look at other recordings of the February 2016 sesshin, I see these bands in nearly every case. The bands are most pronounced in the left front sensor, lf, relatively weak in rf and often altogether missing in sensors lb and rb.

Looking back at other recordings from the February 2016 sesshin, I find that MOST of them show the high frequency bands at sensor lf. It is harder to find evidence in the recordings of other subjects, but I did find one case. Subject S12 has 21,000 hours of meditation experience. In this recording he is practicing shikantaza with his eyes closed.

spectrogram for subject S12

Vertical yellow bands indicating changes in intensity of high frequency oscillations (from about 20 – 40 Hz) are evident and correlate with his breathing, becoming less intense during the long exhalations.

Synchronization of EEG and Respiration Signals

Our EEG signal comes from the Muse Headband where each data point is time-stamped using the system clock. Elapsed time is computed by subtracting the initial time when the Record button is pressed. The respiration signal, on the other hand, comes from the Respiration Monitor connected to the LabQuest recorder where timestamps start at zero when the Record button is pressed. Therefore, to ensure that the two signals are in sync, we need to start the recording in each program by pressing their respective Record buttons as close to the same time as possible. An automatic mouse clicker program fit the bill.

Auto Mouse clicker is available from Murgee Softwares. We set up a script that automatically clicked the Record buttons on the two recording programs within a millisecond or so.

Auto Mouse Click from Murgee Softwares



Respiration and heart rate during meditation and reading

 ECG, heartbeat, respiration  Comments Off on Respiration and heart rate during meditation and reading
Aug 102015

To explore the physiology of zazen, we began by recording respiration and heart rhythms using a respiration monitor and an electrocardiographic (ECG) sensor.

Eight subjects participated in the study. Some had training in zazen; others had experience with other meditative traditions (Vipassana, Yogic). Electrocardiogram and respiration data were collected for both meditative (counting the breath) and non-meditative (reading) conditions. Sessions were about 20 minutes long.

A Cardiorespiratory Viewer computer program was developed to aid in the display and analysis of the breath and heart data.

Cardiorespiratory Viewer

Program for displaying and analyzing ECG and respiration signals

Results were as follows:

breathing rates for meditative vs. non-meditative conditions

Breathing rate among eight subjects for meditative vs. non-meditative conditions. Rates during reading were typically double or greater compared to meditation.

At least among these eight subjects, trained in Zen, Vipassana and Yoga, breath rate was substantially slower (by at least a factor of two) during meditation than during reading. This is not surprising, given that these ancient traditions have a common origin.


In addition, we noted that heart rate did not vary appreciatively between the meditation condition and non-meditative reading. Again, this is expected as our heart rate is not usually under our conscious control and it is generally not part of meditation training.

heart rates for counting vs. reading

Heart rate among eight subjects under meditative and non-meditative conditions. Rates were not significantly different during counting, following the breath or reading.


Jul 182015

We have seen examples where the respiration rates for experienced meditators are lower than those for novices. What about patterns of inhalations and exhalations? Plotting the average respiration waveform for a novice (<200 hrs) and an expert meditator (>5,000 hrs), we see that the exhalation time is 50% longer than the inhalation time for novice and 70% longer for the expert.


comparison of respiration waveforms

Ratio of exhalation to inhalation time for novice is 1.5 while for expert is 1.7.

Furthermore, the expert breathes much more deeply than the novice, as indicated by the difference in pressure from the bottom of the exhalation to the top of the inhalation.


Jul 172015

The plots below show electrocardiogram and respiration signals for a 20-second segment of meditation.

Heartbeat and respiration

Heartbeat and Respiration during meditation. Note the increase in amplitude of the ECG signal during exhalations.

During exhalations, the amplitude of the waves in the upper plot (the sharp spikes in the electrocardiogram, known as R-waves) increase while they decrease during inhalations.

A comparison of ECG signals for a novice and an experienced meditator are shown below.

novice meditator

Heartbeat and respiration for Subject 8, a relatively inexperienced meditator. Amplitude of R-wave increases by ~10% during exhalations.


experienced meditotor

Heartbeat and respiration for a highly trained meditator. Amplitude of R-wave increases by ~50% during exhalations.


For novice meditators, this effect was small (roughly 10% change in R-wave amplitude, as shown in the upper figure, above). For highly trained meditators the effect was quite pronounced (roughly 50% as shown in the lower figure, above).

The amplitude of the R-wave is an indicator of the strength of the signal from the heart when the left ventricle is forcing blood out to the rest of the body. The electrical resistance of the body between the heart and the ECG electrode on the surface of the skin changes as the lungs fill with air and then collapse. After consulting with a cardiorespiratory expert (an anesthesiologist), I have concluded that this dramatic change in R-wave magnitude reflects the deeper breathing of the trained meditator—as the intrathoracic cavity collapses during exhalation, the gap between the heart and the outer surface of the body (where the ECG signal is measured) shrinks, thereby reducing electrical resistance and resulting in an increased amplitude of the R-wave.

Jul 162015

In the following plot of respiration during meditation, we see a regular repetition of inhalations and exhalations with a wave-like quality.

Recording of breath during Zazen meditation

My breath recorded on the 7th day of a meditation retreat.

Selecting a range of cycles, we can average the values centered around the peaks to extract a waveform that represents the entire range. Averaging over 12 cycles, we get the following:

Respiration waveform

Average waveform of the breath for subject S1 (myself) at the end of a 7-day meditation retreat

An interesting aspect of this waveform is that the exhalations are almost twice as long as the inhalations. Here, one complete cycle is 19 seconds long which corresponds to 3.2 breaths/minute. Compare this with the waveform for reading:

Reading waveform

Average waveform of the breath for subject S1 quietly reading

Jul 152015

To compare respiration rates for meditation and non-meditative activities, I recorded my breath using a Vernier LabQuest device connected to a gas pressure sensor and a respiration monitor belt. the first plot below shows my respiration sitting quietly and reading. The second plot is a recording of meditation during the 7th day of a meditation retreat.

Respiration while reading

Respiration while sitting quietly and reading. Breath rhythm was variable. Occasionally I took a deep breath. Average breathing rate was 14.6 breaths/min.


Recording of breath during Zazen meditation

Breath recorded on the 7th day of a meditation retreat. Breathing rate was 2.85 breaths per minute.

Below is a comparison of breathing rates for various other activities.

Respiration Rates

Comparison of respiration rates for various activities, including meditation.

Clearly my zazen practice is characterized by a slower breath rate compared to other activities during the day.


Jun 162015

In September 2014 I enrolled in an online course Exploring Neural Data offered by Brown University via The basic premise of the course was that students would be able to access data coming from various neuroscience labs around the country and learn techniques for analyzing that data, forming hypotheses and testing them. Participation in the course required learning the Python programming language. It sounded like an opportunity I couldn’t pass up. I had already completed two coursera online courses, Duke University’s Medical Neuroscience and Hebrew University of Jerusalem’s Synapses, Neurons and Brains, which gave me a bit of orientation to neuroscience (my background is physics and astronomy). I also discovered some good online tutorials on Python, so I could start familiarizing myself with a new language.

The final project for the Exploring Neural Data course was to apply some of our programming skills to a new data set. I chose to collect respiration and and electrocardiogram (ECG) data for subjects during meditation and reading. I chose to develop a new application I called the Cardiorespiratory Viewer. Written in Python, using the Anaconda Spyder programming environment, it imports program modules from the Tkinter, numpy, scipy and matplotlib libraries. The application reads data files generated by the LabQuest recorder, displays simultaneous plots of EKG voltage and breath pressure, and enables the user to specify time segments and signal threshold levels for analysis.

Cardiorespiratory Viewer

Program for displaying and analyzing ECG and respiration signals

PDF for final project, Exploratory Investigation of Cardiorespiratory System during Meditation


Jun 132015

A few years ago I realized that during Zen meditation, while paying attention to my breath, I was also aware of my heart beating. I started counting heartbeats during my inhalations and exhalations and found that during an inhalation, there were about four beats and during the exhalation roughly 8-10 beats. I thought it would be interesting to match a fixed number of beats, say ten with each exhalation, and maintain the synchronization during the meditation period. The synchronized rhythm felt pleasurable—having both the heart and lungs involved seemed to help me to maintain a clear mind. This experience was my motivation for recording an electrocardiogram (ECG) of heart rhythm simultaneously with respiration.


Jun 112015

For the past 15 years or so, I have maintained a daily meditation practice. My morning routine includes yoga stretching and 20-25 minutes of sitting meditation. During meditation, I usually start by counting my breaths. If and when my mind quiets down, I transition to following my inhalations and exhalations, and being aware of bodily sensations and sounds in the environment. Some days I’ll sit again just before bed. I find this routine is good for maintaining perspective on the concerns that come up during the day. It helps reduce frenetic mental activity and brings me to a place of calm.

In addition to daily practice, for several years I have participated in 7-day intensive meditation retreats, or sesshins, three or four times a year at the Tahoma Zen Monastery in Freeland, Washington. The daily schedule of sesshins includes about 7 hours of formal sitting zazen meditation plus “applied” zazen in activities such as chanting, silent meals, work, exercise and listening to a dharma talk by the Roshi, or Zen teacher. I find that after several days of meditation, such as during sesshin, my mind grows distinctly more calm. Generally, by the 3rd or 4th day, I experience periods of clarity in which the usual random jumping from one thought to another ceases and gives way to simple awareness free from internal dialog.

When I am not meditating, I tend to identify with my thoughts and feelings. The desire for a cup of coffee is MY desire. The insomnia is MY regret. The cramp in my leg is MY pain. Opinions about presidential politics are MY opinions. For me, counting breaths is a tool for disengaging from the identification process: desires, aversions, pain and opinions are what they are but the additional step of making them mine is optional. Meditation seems to reduce the feeling of drivenness of mental activity. If I find myself unable to maintain the count of breaths, it’s usually because I have become hooked on some random thought and caught on following a chain of connections from one thing to the next, far removed from the present moment. By gently returning to the awareness of the breath over and over again, these excursions gradually become less enticing.

Each day of a sesshin at Tahoma has a Golden Hour from 6:00 – 7:00 pm in which participants sit without changing posture for the full hour. Typically, I find that during Golden Hour the first 2-3 days, my practice is rather disrupted—I am pulled around by all kinds of thoughts. But by the 4th or 5th day, I can sometimes experience a clear mind. Occasionally I try to monitor this quality, by starting my count at the beginning of the hour and trying to maintain it for the full hour. Usually for the first few days of a sesshin, this is impossible—I frequently lose track of the count. But toward the end of a sesshin, I can sometimes count my breaths without interruption. The advantage of this technique is that I am less able to tell myself I am meditating when in fact I’m engaged in reverie.

I was surprised to find that I was having only 170-190 breaths in 60 minutes, or about 3 breaths per minute. It seemed much less than when I’m doing other things and not meditating.

One aspect of zazen instruction is deep breathing—on each exhalation to expel all the air from the lungs before taking an inhalation. Naturally, the inhalation brings in more air after a complete exhalation than it would during shallow breathing. I was interested in this experience of deep breathing at a slower rate and wanted to measure it with a recording device and see the data in a graph.