spacr.plaque_growth

Experimental plaque growth approximations with explicit provenance.

The anchor is the median, across three independent RH/HFF vehicle-control experiments, of the median equivalent diameter of the largest quarter of plaques. Kelsen et al. (2023), PLOS Biology 21(5): e3002110, S20 Data, CC BY. https://doi.org/10.1371/journal.pbio.3002110

528 measured plaques support a seven-day size anchor, not a temporal growth curve. Linear diameter growth through zero is an assumption. Leave-one- experiment-out endpoint time error averages 39.73 hours (range 29.69–54.34). The reproducible extraction and assessment live in tools/build_plaque_growth_reference.py.

Functions

estimate_page(wells, *[, reference_diameter_um, ...])

Suggest missing scale/time using an explicitly assumed growth relation.

estimates_from_settings(wells, settings)

Return per-well suggestions and complete JSON provenance when enabled.

largest_quarter(areas)

Median equivalent diameter of the largest ceil(N/4) positive areas.

Module Contents

spacr.plaque_growth.estimate_page(wells, *, reference_diameter_um=REFERENCE_DIAMETER_UM, reference_hours=REFERENCE_HOURS)[source]

Suggest missing scale/time using an explicitly assumed growth relation.

Parameters:

  • wells – mappings with unique well identifiers, areas_px and optional measured pixels_per_um and formation_hours. A scale must be positive; time may be zero. Do not pass earlier estimates as measured input. Different resolutions are converted before pooling.

  • reference_diameter_um – largest-quarter reference diameter in µm.

  • reference_hours – its positive elapsed time in hours.

Returns:

report with per-well estimated_* values, sources, counts, observed page descriptor and assumptions. Measured inputs are never overwritten. With neither scale nor time, reference duration is an explicitly labelled assumption; pixel scale follows from that choice.

The whole-page descriptor assumes a common formation time. Conflicting known times disable page pooling; each calibrated well is then evaluated separately. Unknown-scale wells use their own pixel descriptor. Physical measurements are never computed from these suggestions automatically.

spacr.plaque_growth.estimates_from_settings(wells, settings)[source]

Return per-well suggestions and complete JSON provenance when enabled.

Parameters:

  • wells – estimate_page() input mappings.

  • settings – plaque_estimate_growth (default False), optional plaque_growth_reference_um and plaque_growth_reference_hours.

Returns:

mapping by well identifier. Empty when estimation is disabled.

spacr.plaque_growth.largest_quarter(areas)[source]

Median equivalent diameter of the largest ceil(N/4) positive areas.

Parameters:

areas – finite positive plaque areas, all in the same squared unit.

Returns:

diameter, total count and selected count; diameter is None for fewer than four plaques. Invalid/nonpositive areas raise ValueError.