Diameter Analysis¶

Diameter analysis estimates vessel diameter from line scan kymographs using intensity-profile measurements on a rectangular ROI.

Input data¶

Expects a line-scan kymograph. The ROI should cover the spatial region used to estimate vessel width. Diameter is reported in physical units when X calibration is correct (see AcqImage physical units).

Programmatic use¶

from acqstore.acq_image import AcqImage
from acqstore.acq_image.analysis import DiameterAnalysis
from acqstore.sample_data import ensure_sample_file

acq = AcqImage(str(ensure_sample_file('kymograph-diameter')))

channel = acq.images.channel_indices[0]
roi_ids = acq.rois.get_roi_ids()
roi_id = roi_ids[0] if roi_ids else acq.rois.create_rect_roi(name='diameter').roi_id

diameter = acq.analysis_set.create_and_run(
    DiameterAnalysis,
    channel=channel,
    roi_id=roi_id,
    detection_params={'diameter_method': 'threshold_width'},
    replace_existing=True,
)
print(diameter.result.summary)
acq.save()

Detection parameters¶

Parameters control profile aggregation, polarity, thresholding, gradient-based edge detection, motion gating, and post-filtering.

name	display_name	type	default	choices	editable	visible	methods	description
window_rows_odd	Window Rows (Odd)	int	5		True	True	('threshold_width', 'gradient_edges')	Odd number of time rows aggregated into each spatial profile.
stride	Stride	int	1		True	True	('threshold_width', 'gradient_edges')	Center-row increment between successive measurements.
binning_method	Binning Method	enum	mean	('mean', 'median')	True	True	('threshold_width', 'gradient_edges')	Window reducer across rows before edge detection.
polarity	Polarity	enum	bright_on_dark	('bright_on_dark', 'dark_on_bright')	True	True	('threshold_width', 'gradient_edges')	Intensity polarity; dark_on_bright inverts the profile.
diameter_method	Detection Method	enum	threshold_width	('threshold_width', 'gradient_edges')	True	True		Core detector implementation.
post_filter_kernel_size	Post-Filter Kernel Size	int	3		True	True		Odd median kernel applied to diameter after detection. Post-detection smoothing; re-run analysis to apply changes.
threshold_mode	Threshold Mode	enum	half_max	('half_max', 'absolute')	True	True	('threshold_width',)	Threshold rule for threshold_width.
threshold_value	Threshold Value	float	0.0		True	True	('threshold_width',)	Absolute threshold when threshold_mode='absolute'.
gradient_sigma	Gradient Sigma	float	1.5		True	True	('gradient_edges',)	Gaussian smoothing sigma for gradient edge finding.
gradient_kernel	Gradient Kernel	enum	central_diff	('central_diff',)	True	True	('gradient_edges',)	Derivative kernel for gradient_edges.
gradient_min_edge_strength	Min Edge Strength	float	0.02		True	True	('gradient_edges',)	Minimum derivative magnitude for a confident edge.
enable_motion_gating	Enable Motion Gating	bool	True		True	True	('gradient_edges',)	Apply frame-to-frame motion constraints for gradient_edges.
max_edge_shift_um	Max Edge Shift (um)	float	2.0		True	True	('gradient_edges',)	Maximum allowed per-frame left/right edge shift.
max_diameter_change_um	Max Diameter Change (um)	float	2.0		True	True	('gradient_edges',)	Maximum allowed per-frame diameter jump.
max_center_shift_um	Max Center Shift (um)	float	2.0		True	True	('gradient_edges',)	Maximum allowed per-frame center shift.

Results¶

For a source file my_file.tif:

my_file.tif.json
my_file.tif.diameter.csv

Typical summary fields include diameter_um_mean, diameter_um_median, diameter_um_cv, num_rows, qc_score_mean, and quality-control violation counts.

See the Diameter Analysis API and the Diameter Analysis notebook.