Analysis¶
Analysis modules take detection parameters as input and produce summary values
(and optional tabular CSV outputs) on an AcqImage for a given
(channel, ROI).
All current quantitative workflows operate on line scan kymographs: repeated sampling along a spatial line over time (typically Y = time, X = distance along the line). Correct physical units and a proper rectangular ROI are required for meaningful results.
Kymograph analysis¶
| Analysis | What it measures |
|---|---|
| Velocity | Blood flow velocity (Radon transform) |
| Diameter | Vessel diameter from intensity profiles |
| Sum intensity | Normalized line intensity + peak detection (e.g. GCaMP) |
| Heart rate | Periodic rate from a velocity time series |
Common pattern¶
Load one sample file, ensure a rectangular ROI, then create_and_run:
from acqstore.acq_image import AcqImage
from acqstore.acq_image.analysis import RadonVelocityAnalysis
from acqstore.sample_data import ensure_sample_file
acq = AcqImage(str(ensure_sample_file('kymograph-flow')))
channel = acq.get_default_channel()
roi_id = acq.get_default_roi()
if roi_id is None:
roi_id = acq.rois.create_rect_roi(name='analysis').roi_id
analysis = acq.analysis_set.create_and_run(
RadonVelocityAnalysis,
channel=channel,
roi_id=roi_id,
detection_params={'window_width': 64},
replace_existing=True,
execution_options={'use_multiprocessing': False},
)
print(analysis.result.summary)
Batch, pools, and event analysis remain documented under API.