Object Measurement Workflow

This workflow demonstrates the core value of the measurement package: take a label image and an aligned intensity image, produce per-object measurements, and summarize them per sample or image.

Analysis Question

What are the size, shape, count, and intensity summaries of segmented objects in a microscopy image, and are those measurements stable enough to aggregate per sample?

Data

Use a generated 2D label image with two non-zero labels and an aligned float-valued intensity image. The expected output is small enough to assert exact object counts, areas, and intensity means.

Expected Results

  • RegionProperties returns one row per non-zero label.

  • IntensityProperties returns one row per non-zero label and raises if image shapes differ.

  • CountLabels returns object and pixel counts.

  • SummarizeTable can aggregate numeric outputs by a grouping column.

from bioimageflow_measurement_tools import CountLabels, RegionProperties
from bioimageflow_core import Arguments

regions = RegionProperties().process_row(Arguments(label_image="labels.tif"))
counts = CountLabels().process_row(Arguments(label_image="labels.tif"))