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Calibration

Until an image is calibrated, every measurement it produces is in pixels. A pixel area is not a quantity anyone can compare across setups, publish, or reason about physically. Calibration maps image space to a physical length unit so that areas come out in mm², distances in mm, and ratios stay ratios.

How it works

Calibration establishes a scale — how many physical units one pixel spans — and an associated unit for the image. Once set, metrics are computed in that unit rather than in pixels.

Internally, measurements are also stored in pixel-native form, so a re-calibration does not require re-deriving geometry from scratch and a dataset whose images share a unit can be aggregated consistently.

Per image, per dataset

Setting a scale on every image by hand does not scale, and for a consistent acquisition setup it is also redundant. Calibration therefore supports per-dataset defaults: when every image was captured at the same working distance with the same optics, calibrate once and let the dataset supply it.

Images captured differently can still override the default individually.

Measuring a scale

Scale measurement belongs to Calibrate mode, and is started from that calibration's drawer button — not from the annotation tool rail.

That is a deliberate placement: on the rail it invited an annotator to recalibrate an image in the middle of annotating it, which silently rescales every measurement already taken. Setting a scale is a calibration, so it lives with the other calibrations and behind the curator permission.

You draw a known distance across a reference in the image — a scale bar, a ruler, a calibration target — and enter what that distance is in physical units. Press Esc to cancel a measurement in progress.

Units

The image's unit is what every length- and area-kind metric is reported in. See the unit_kind column in the metric reference:

  • length metrics (perimeter, max diameter, neighbour distances) come out in the unit
  • area metrics come out in the unit squared
  • ratio, count, colour and intensity metrics are unaffected by calibration
Measure-scale tool across a scale bar → enter the real distance → object stats flip from px to mm.

Calibrate before you quantify at scale

Metrics computed before calibration are in pixels. Calibrating afterwards is supported, but it is far less confusing to establish the scale first.