Measure object shape

Measures various spatial metrics for each object in a specified object collection from the workspace.

Description

Measures various spatial metrics for each object in a specified object collection from the workspace. Measurements are associated with the relevant input object. When dealing with 3D objects (those with coordinates spanning multiple Z-slices) a 2D projection into the XY plane will be used. 3D metrics are calculated using the "MorphoLibJ" plugin.

Parameters

Parameter Description
Input objects Input objects from workspace. Shape metrics will be calculated for each object and stored as measurements associated with that object.
Measure volume When selected, 3D volume metrics will be calculated for each input object. Metrics are: volume (px³), volume (calibrated_units³), number of voxels, base area (px²), base area (calibrated_units²), height (n_slices) and height (calibrated_units).
Measure projected area When selected, 2D area metrics will be calculated for each input object. For 3D objects, a 2D projection in the XY plane is used for measurements. This projection includes all XY coordinates present in any Z-slice. Metrics are: area (px²) and area (calibrated_units²).
Measure projected diameter When selected, the diameter of 2D objects will be calculated for each input object. For 3D objects, a 2D projection in the XY plane is used for measurements. This projection includes all XY coordinates present in any Z-slice. Metrics are: diameter (px) and diameter (calibrated_units).
Measure projected perimeter When selected, the perimeter and circularity of 2D objects will be calculated for each input object. For 3D objects, a 2D projection in the XY plane is used for measurements. This projection includes all XY coordinates present in any Z-slice. Metrics are: perimeter (px), perimeter (calibrated_units) and circularity.
Measure 3D metrics
Connectivity
Surface area method
Enable multithreading Process multiple input objects simultaneously. This can provide a speed improvement when working on a computer with a multi-core CPU.