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name eye-tracking-analysis description Use this Skill to analyze eye-tracking data: IVT fixation detection, AOI dwell time, scanpath similarity, heatmap generation, and pupillometry baseline correction.
tags ["psychology","eye-tracking","fixations","AOI","scanpath","pupillometry"] version 1.0.0 authors [{"name":"awesome-rosetta-skills contributors","github":"@xjtulyc"}] license MIT platforms ["claude-code","codex","gemini-cli","cursor"] dependencies {"python":["pandas>=1.5","numpy>=1.23","scipy>=1.9","matplotlib>=3.6","sklearn>=1.2"]} last_updated 2026-03-18 status stable
Eye-Tracking Analysis
TL;DR — Complete eye-tracking pipeline: blink detection and interpolation,
IVT velocity-based fixation detection, AOI assignment with dwell-time metrics,
Levenshtein scanpath similarity, Gaussian kernel density heatmaps, and
event-locked pupillometry with baseline correction.
When to Use
Use this Skill when you need to:
Process raw gaze samples (x, y, timestamp, pupil diameter) from Tobii, SR Research,
or SMI eye trackers
Detect fixations using the I-VT (velocity threshold) algorithm
Define AOIs as rectangles or polygons and extract per-AOI metrics
(first fixation latency, dwell time, fixation count, proportion dwell)
Compare scanpath sequences across participants or conditions using edit distance
Generate fixation heatmaps for visual attention analysis
Preprocess pupillometry data: blink removal, interpolation, and event-locked
baseline correction
Background
Gaze Data Format
Raw gaze files typically have these columns:
Column Description timestamp_msSample time in milliseconds gaze_xHorizontal gaze coordinate (pixels from left) gaze_yVertical gaze coordinate (pixels from top) pupil_diamPupil diameter (mm or arbitrary units; 0 = blink)
IVT Fixation Detection
The I-VT algorithm classifies each sample as a fixation or saccade:
velocity_i = distance(sample_i, sample_{i-1}) / (t_i - t_{i-1})
Samples with velocity < threshold (~50 °/s or ~30 px/ms) are fixations.
Adjacent fixation samples are merged into fixation events.
Pupillometry Preprocessing
Detect blinks (pupil_diam = 0 or NaN; ± 100 ms margin)
Linear interpolation for blinks < 150 ms
Baseline correction: subtract mean pupil diameter in a pre-stimulus window
Z-scoring across the trial or session
Environment Setup
conda create -n eyetrack_env python=3.11 -y
conda activate eyetrack_env
pip install pandas>=1.5 numpy>=1.23 scipy>=1.9 matplotlib>=3.6 scikit-learn>=1.2
pip install shapely>=2.0
python -c "import pandas, numpy, scipy, matplotlib, sklearn; print('All OK')"
Core Workflow
Step 1 — Blink Detection and Interpolation import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy import stats, ndimage
from typing import Optional , Dict , List , Tuple , Union
DEFAULT_SAMPLE_RATE_HZ = 1000
def detect_and_interpolate_blinks (
df: pd.DataFrame,
pupil_col: str = "pupil_diam" ,
time_col: str = "timestamp_ms" ,
max_blink_ms: float = 150.0 ,
margin_ms: float = 50.0 ,
) -> pd.DataFrame:
"""
Detect blinks (pupil_diam = 0 or NaN) and linearly interpolate short blinks.
Blinks > max_blink_ms are left as NaN (genuine data loss).
A margin is applied around each blink to remove partial blink artifacts.
Args:
df: DataFrame sorted by timestamp with one row per gaze sample.
pupil_col: Pupil diameter column name.
time_col: Timestamp column (milliseconds).
max_blink_ms: Maximum blink duration to interpolate (default 150 ms).
margin_ms: Samples within this margin of a blink are also marked invalid.
Returns:
DataFrame with 'pupil_clean' column (interpolated) and 'is_blink' bool.
"""
df = df.copy().reset_index(drop=True )
pupil = df[pupil_col].copy().astype(float )
time = df[time_col].values.astype(float )
blink_mask = (pupil == 0 ) | pupil.isna()
blink_indices = np.where(blink_mask)[0 ]
sample_dur = np.median(np.diff(time)) if len (time) > 1 else 1.0
margin_samples = int (np.ceil(margin_ms / sample_dur))
expanded_mask = blink_mask.copy()
for idx in blink_indices:
start = max (0 , idx - margin_samples)
end = min (len (pupil), idx + margin_samples + 1 )
expanded_mask.iloc[start:end] = True
df["is_blink" ] = expanded_mask
pupil_clean = pupil.copy()
pupil_clean[expanded_mask] = np.nan
labeled, n_blinks = ndimage.label(expanded_mask.values)
for blink_id in range (1 , n_blinks + 1 ):
blink_indices_seg = np.where(labeled == blink_id)[0 ]
if len (blink_indices_seg) == 0 :
continue
blink_duration_ms = (
time[blink_indices_seg[-1 ]] - time[blink_indices_seg[0 ]]
)
if blink_duration_ms <= max_blink_ms:
start_idx = max (0 , blink_indices_seg[0 ] - 1 )
end_idx = min (len (pupil_clean) - 1 , blink_indices_seg[-1 ] + 1 )
if not np.isnan(pupil_clean.iloc[start_idx]) and not np.isnan(pupil_clean.iloc[end_idx]):
interp_vals = np.interp(
blink_indices_seg,
[start_idx, end_idx],
[pupil_clean.iloc[start_idx], pupil_clean.iloc[end_idx]],
)
pupil_clean.iloc[blink_indices_seg] = interp_vals
df["pupil_clean" ] = pupil_clean
n_blinks_detected = int (n_blinks)
pct_blink = expanded_mask.mean() * 100
print (
f"Blink detection: {n_blinks_detected} blinks, "
f"{pct_blink:.1 f} % of samples invalid"
)
return df
Step 2 — IVT Fixation Detection def detect_fixations_ivt (
df: pd.DataFrame,
x_col: str = "gaze_x" ,
y_col: str = "gaze_y" ,
time_col: str = "timestamp_ms" ,
velocity_threshold: float = 30.0 ,
min_fixation_ms: float = 80.0 ,
screen_width_px: int = 1920 ,
screen_height_px: int = 1080 ,
screen_width_cm: float = 53.0 ,
viewing_distance_cm: float = 57.0 ,
) -> pd.DataFrame:
"""
I-VT fixation detection from raw gaze samples.
Velocity is computed in pixels/ms. An optional conversion to degrees/second
is performed if screen geometry is provided.
Fixation events are defined as contiguous runs of low-velocity samples
exceeding min_fixation_ms.
Args:
df: Gaze DataFrame sorted by timestamp.
x_col: Horizontal gaze coordinate column.
y_col: Vertical gaze coordinate column.
time_col: Timestamp column (milliseconds).
velocity_threshold: Maximum velocity for fixation classification (px/ms).
min_fixation_ms: Minimum fixation duration (ms).
screen_width_px: Screen width in pixels.
screen_height_px: Screen height in pixels.
screen_width_cm: Physical screen width (cm) for degree conversion.
viewing_distance_cm: Viewing distance (cm) for degree conversion.
Returns:
DataFrame of fixation events with columns:
fixation_id, onset_ms, offset_ms, duration_ms, x_mean, y_mean.
"""
df = df.copy().reset_index(drop=True )
x = df[x_col].values.astype(float )
y = df[y_col].values.astype(float )
t = df[time_col].values.astype(float )
dx = np.diff(x, prepend=x[0 ])
dy = np.diff(y, prepend=y[0 ])
dt = np.diff(t, prepend=t[0 ] - 1.0 )
dt[dt == 0 ] = 1.0
velocity = np.sqrt(dx**2 + dy**2 ) / dt
is_fixation = velocity < velocity_threshold
fixations = []
labeled, n_events = ndimage.label(is_fixation)
for evt_id in range (1 , n_events + 1 ):
indices = np.where(labeled == evt_id)[0 ]
duration = t[indices[-1 ]] - t[indices[0 ]]
if duration >= min_fixation_ms:
fixations.append({
"fixation_id" : len (fixations) + 1 ,
"onset_ms" : t[indices[0 ]],
"offset_ms" : t[indices[-1 ]],
"duration_ms" : round (duration, 2 ),
"x_mean" : round (np.nanmean(x[indices]), 2 ),
"y_mean" : round (np.nanmean(y[indices]), 2 ),
"n_samples" : len (indices),
})
fix_df = pd.DataFrame(fixations)
print (
f"IVT fixation detection: {len (fix_df)} fixations detected\n"
f" Mean duration: {fix_df['duration_ms' ].mean():.0 f} ms\n"
f" Median duration: {fix_df['duration_ms' ].median():.0 f} ms"
)
return fix_df
Step 3 — AOI Analysis def define_aoi_rectangles (
aoi_specs: List [Dict ],
) -> List [Dict ]:
"""
Define rectangular areas of interest.
Args:
aoi_specs: List of dicts with keys:
name (str), x_min, x_max, y_min, y_max (floats in pixels).
Returns:
List of AOI dicts with added 'type' = 'rectangle'.
Example:
aoi_specs = [
{"name": "face", "x_min": 400, "x_max": 800, "y_min": 100, "y_max": 600},
{"name": "text", "x_min": 100, "x_max": 400, "y_min": 200, "y_max": 500},
]
"""
for aoi in aoi_specs:
aoi["type" ] = "rectangle"
return aoi_specs
def assign_fixation_to_aoi (
fixation: Dict ,
aois: List [Dict ],
) -> str :
"""
Assign a fixation to an AOI by point-in-rectangle test.
Args:
fixation: Fixation dict with 'x_mean', 'y_mean'.
aois: List of AOI dicts.
Returns:
AOI name or 'outside' if not in any AOI.
"""
fx, fy = fixation["x_mean" ], fixation["y_mean" ]
for aoi in aois:
if (aoi["x_min" ] <= fx <= aoi["x_max" ] and
aoi["y_min" ] <= fy <= aoi["y_max" ]):
return aoi["name" ]
return "outside"
def compute_aoi_metrics (
fix_df: pd.DataFrame,
aois: List [Dict ],
total_duration_ms: Optional [float ] = None ,
) -> pd.DataFrame:
"""
Compute per-AOI dwell time, fixation count, and first fixation latency.
Args:
fix_df: Fixation events DataFrame from detect_fixations_ivt().
aois: List of AOI dicts (from define_aoi_rectangles()).
total_duration_ms: Total trial/stimulus duration for proportion dwell.
Returns:
DataFrame with one row per AOI and metrics columns.
"""
fix_df = fix_df.copy()
fix_df["aoi" ] = fix_df.apply(
lambda row: assign_fixation_to_aoi(row.to_dict(), aois), axis=1
)
if total_duration_ms is None :
total_duration_ms = fix_df["duration_ms" ].sum ()
rows = []
for aoi in aois:
aoi_name = aoi["name" ]
aoi_fixes = fix_df[fix_df["aoi" ] == aoi_name]
n_fix = len (aoi_fixes)
dwell_ms = aoi_fixes["duration_ms" ].sum ()
prop_dwell = dwell_ms / total_duration_ms if total_duration_ms > 0 else 0
first_fix_latency = aoi_fixes["onset_ms" ].min () if n_fix > 0 else np.nan
mean_fix_dur = aoi_fixes["duration_ms" ].mean() if n_fix > 0 else np.nan
rows.append({
"aoi" : aoi_name,
"n_fixations" : n_fix,
"total_dwell_ms" : round (dwell_ms, 2 ),
"proportion_dwell" : round (prop_dwell, 4 ),
"first_fixation_latency_ms" : round (float (first_fix_latency), 2 ) if not np.isnan(first_fix_latency) else np.nan,
"mean_fixation_duration_ms" : round (float (mean_fix_dur), 2 ) if not np.isnan(mean_fix_dur) else np.nan,
})
result_df = pd.DataFrame(rows)
print ("\nAOI Metrics:" )
print (result_df.to_string(index=False ))
return result_df
def scanpath_similarity (
seq_a: List [str ],
seq_b: List [str ],
normalize: bool = True ,
) -> float :
"""
Compute Levenshtein (edit) distance between two AOI scanpath sequences.
Args:
seq_a, seq_b: Lists of AOI labels (strings) in temporal order.
normalize: Divide by max(len(seq_a), len(seq_b)) for [0, 1] range.
Returns:
Edit distance (lower = more similar). Normalized: 0 = identical, 1 = maximally different.
"""
m, n = len (seq_a), len (seq_b)
dp = np.zeros((m + 1 , n + 1 ), dtype=int )
for i in range (m + 1 ):
dp[i][0 ] = i
for j in range (n + 1 ):
dp[0 ][j] = j
for i in range (1 , m + 1 ):
for j in range (1 , n + 1 ):
cost = 0 if seq_a[i - 1 ] == seq_b[j - 1 ] else 1
dp[i][j] = min (
dp[i - 1 ][j] + 1 ,
dp[i][j - 1 ] + 1 ,
dp[i - 1 ][j - 1 ] + cost,
)
dist = int (dp[m][n])
if normalize and max (m, n) > 0 :
return round (dist / max (m, n), 4 )
return float (dist)
Advanced Usage
Heatmap Generation and Pupillometry def generate_fixation_heatmap (
fix_df: pd.DataFrame,
screen_width: int = 1920 ,
screen_height: int = 1080 ,
bandwidth: float = 50.0 ,
weight_by_duration: bool = True ,
output_path: Optional [str ] = None ,
) -> plt.Figure:
"""
Generate a fixation density heatmap using Gaussian KDE.
Args:
fix_df: Fixation events DataFrame.
screen_width: Screen width in pixels.
screen_height: Screen height in pixels.
bandwidth: Gaussian kernel bandwidth (pixels).
weight_by_duration: Weight fixation points by their duration.
output_path: Optional path to save figure.
Returns:
Matplotlib Figure.
"""
from scipy.stats import gaussian_kde
x = fix_df["x_mean" ].values
y = fix_df["y_mean" ].values
weights = fix_df["duration_ms" ].values if weight_by_duration else None
xy = np.vstack([x, y])
kde = gaussian_kde(xy, bw_method=bandwidth / np.std(xy))
grid_x = np.linspace(0 , screen_width, 200 )
grid_y = np.linspace(0 , screen_height, 150 )
XX, YY = np.meshgrid(grid_x, grid_y)
grid_pts = np.vstack([XX.ravel(), YY.ravel()])
Z = kde(grid_pts).reshape(XX.shape)
fig, ax = plt.subplots(figsize=(10 , 7 ))
im = ax.imshow(
Z, origin="upper" , extent=[0 , screen_width, screen_height, 0 ],
cmap="hot" , alpha=0.85 , aspect="auto" ,
)
plt.colorbar(im, ax=ax, label="Fixation density" )
ax.scatter(x, y, s=5 , c="cyan" , alpha=0.3 )
ax.set_xlim(0 , screen_width)
ax.set_ylim(screen_height, 0 )
ax.set_xlabel("Screen X (px)" )
ax.set_ylabel("Screen Y (px)" )
ax.set_title("Fixation Heatmap" )
fig.tight_layout()
if output_path:
fig.savefig(output_path, dpi=150 )
plt.show()
return fig
def pupillometry_baseline_correct (
df: pd.DataFrame,
pupil_col: str = "pupil_clean" ,
time_col: str = "timestamp_ms" ,
event_onset_ms: float = 0.0 ,
baseline_window: Tuple [float , float ] = (-200.0 , 0.0 ),
analysis_window: Tuple [float , float ] = (-200.0 , 2000.0 ),
zscore: bool = True ,
) -> pd.DataFrame:
"""
Event-locked pupillometry: baseline subtraction and optional z-scoring.
Args:
df: Gaze DataFrame with cleaned pupil data.
pupil_col: Cleaned pupil diameter column.
time_col: Timestamp column (ms, absolute).
event_onset_ms: Absolute timestamp of the event of interest.
baseline_window: (start, end) relative to event onset for baseline (ms).
analysis_window: (start, end) relative to event onset to return (ms).
zscore: Whether to z-score the corrected signal.
Returns:
DataFrame with 'time_relative_ms', 'pupil_corrected', 'pupil_zscore' columns.
"""
df = df.copy()
df["time_relative_ms" ] = df[time_col] - event_onset_ms
baseline_mask = (
(df["time_relative_ms" ] >= baseline_window[0 ]) &
(df["time_relative_ms" ] <= baseline_window[1 ])
)
baseline_mean = df.loc[baseline_mask, pupil_col].mean()
df["pupil_corrected" ] = df[pupil_col] - baseline_mean
if zscore:
mu = df["pupil_corrected" ].mean()
sigma = df["pupil_corrected" ].std()
df["pupil_zscore" ] = (df["pupil_corrected" ] - mu) / sigma if sigma > 0 else 0
analysis_mask = (
(df["time_relative_ms" ] >= analysis_window[0 ]) &
(df["time_relative_ms" ] <= analysis_window[1 ])
)
result = df[analysis_mask][
["time_relative_ms" , pupil_col, "pupil_corrected" ] +
(["pupil_zscore" ] if zscore else [])
].copy()
print (
f"Pupillometry baseline correction:\n"
f" Baseline mean: {baseline_mean:.3 f} \n"
f" Analysis window: {analysis_window} ms relative to event\n"
f" Samples in analysis window: {len (result)} "
)
return result
Troubleshooting Problem Likely Cause Solution All samples classified as saccades Velocity threshold too low Increase velocity_threshold to 50–100 px/ms Very few fixations detected min_fixation_ms too largeReduce to 80 ms; check sampling rate IVT merges multiple fixations Short saccades between fixations Apply fixation merging if gap < 75 ms Heatmap appears blank Fixations outside screen bounds Check coordinate origin (top-left vs center) Pupil baseline window all NaN Event onset timestamp mismatch Verify event_onset_ms unit (ms vs seconds) Levenshtein distance is 0 for different scanpaths Same AOI sequence Check AOI assignment; some fixations may be "outside" KDE import error scipy version Use from scipy.stats import gaussian_kde
External Resources
Salvucci, D. D., & Goldberg, J. H. (2000). Identifying fixations and saccades.
ETRA 2000 , 71–78.
Holmqvist, K., et al. (2011). Eye Tracking: A Comprehensive Guide.
Mathôt, S., et al. (2018). Methods in cognitive pupillometry. Behavior Research Methods.
PyGaze (open-source eye-tracking framework): https://www.pygaze.org/
Tobii Pro SDK: https://developer.tobiipro.com/
SR Research EyeLink: https://www.sr-research.com/
Examples
Example 1 — IVT Fixation Detection from Gaze Stream import numpy as np
import pandas as pd
rng = np.random.default_rng(10 )
n_samples = 5000
time_ms = np.arange(0 , n_samples)
gaze_x = np.zeros(n_samples)
gaze_y = np.zeros(n_samples)
fixation_regions = [
(0 , 800 , 500 , 400 ),
(900 , 1800 , 1200 , 600 ),
(2000 , 3000 , 800 , 300 ),
(3100 , 4000 , 1500 , 700 ),
(4100 , 4999 , 960 , 540 ),
]
for start, end, fx, fy in fixation_regions:
gaze_x[start:end] = rng.normal(fx, 5 , end - start)
gaze_y[start:end] = rng.normal(fy, 5 , end - start)
for i in range (len (fixation_regions) - 1 ):
sac_start = fixation_regions[i][1 ]
sac_end = fixation_regions[i + 1 ][0 ]
fx_start = fixation_regions[i][2 ]
fx_end = fixation_regions[i + 1 ][2 ]
fy_start = fixation_regions[i][3 ]
fy_end = fixation_regions[i + 1 ][3 ]
n = sac_end - sac_start
if n > 0 :
gaze_x[sac_start:sac_end] = np.linspace(fx_start, fx_end, n)
gaze_y[sac_start:sac_end] = np.linspace(fy_start, fy_end, n)
pupil = rng.normal(4.5 , 0.2 , n_samples)
pupil[1500 :1600 ] = 0
pupil[3500 :3580 ] = 0
df_gaze = pd.DataFrame({
"timestamp_ms" : time_ms, "gaze_x" : gaze_x,
"gaze_y" : gaze_y, "pupil_diam" : pupil,
})
df_clean = detect_and_interpolate_blinks(df_gaze, max_blink_ms=150 , margin_ms=50 )
fix_df = detect_fixations_ivt(df_clean, velocity_threshold=30 , min_fixation_ms=80 )
print (fix_df)
aois = define_aoi_rectangles([
{"name" : "left_region" , "x_min" : 0 , "x_max" : 960 , "y_min" : 0 , "y_max" : 1080 },
{"name" : "right_region" , "x_min" : 960 , "x_max" : 1920 , "y_min" : 0 , "y_max" : 1080 },
])
aoi_metrics = compute_aoi_metrics(fix_df, aois, total_duration_ms=5000 )
generate_fixation_heatmap(fix_df, screen_width=1920 , screen_height=1080 ,
bandwidth=60 , output_path="heatmap.png" )
Example 2 — AOI Dwell Time Table and Pupillometry Baseline Correction
seq1 = ["left_region" , "right_region" , "left_region" , "right_region" , "right_region" ]
seq2 = ["left_region" , "left_region" , "right_region" , "left_region" , "right_region" ]
seq3 = ["right_region" , "right_region" , "right_region" , "left_region" , "right_region" ]
dist_12 = scanpath_similarity(seq1, seq2, normalize=True )
dist_13 = scanpath_similarity(seq1, seq3, normalize=True )
print (f"Scanpath distance seq1-seq2: {dist_12:.3 f} " )
print (f"Scanpath distance seq1-seq3: {dist_13:.3 f} " )
pupil_result = pupillometry_baseline_correct(
df_clean,
pupil_col="pupil_clean" ,
time_col="timestamp_ms" ,
event_onset_ms=1000.0 ,
baseline_window=(-200 , 0 ),
analysis_window=(-200 , 2000 ),
zscore=True ,
)
fig, ax = plt.subplots(figsize=(10 , 4 ))
ax.plot(pupil_result["time_relative_ms" ], pupil_result["pupil_zscore" ],
color="steelblue" , linewidth=1.5 )
ax.axvline(0 , color="crimson" , linestyle="--" , linewidth=1 , label="Event onset" )
ax.axvspan(-200 , 0 , alpha=0.1 , color="gray" , label="Baseline window" )
ax.set_xlabel("Time relative to event onset (ms)" )
ax.set_ylabel("Pupil diameter (z-score)" )
ax.set_title("Event-Locked Pupillometry" )
ax.legend()
ax.grid(alpha=0.3 )
fig.tight_layout()
plt.savefig("pupillometry.png" , dpi=150 )
plt.show()
print ("Eye-tracking analysis complete." )
Changelog Version Date Change 1.0.0 2026-03-18 Initial release — blink interpolation, IVT fixation detection, AOI metrics, scanpath distance, heatmap, pupillometry
