"Goodness" of ellipse fit in MeasureObjectSizeShape

Hi,

When using MeasureObjectSizeShape, I understand that the parameters “Major” and “Minor axis” refer to an ellipse that best describe the object.

Is there also a value that describes how well the object fits to an ellipse in the first place, i.e. some R^2 or chi value?

The reason for me asking this is that I am trying to identify bacterial cells which usually have a very nice elliptical shape.

However the images also show many artefacts with objects that are “fuzzy” ore “edgy” and do not fit to an ellipse that well.

Thanks!

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In the meantime I found out that the parameter “Solidity” is very helpful in this case, see here:

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Yes, and in CellProfiler’s MeasureObjectSizeShape, there are multiple measures that might work for you:

  • FormFactor: Calculated as 4πArea/Perimeter2. Equals 1 for a perfectly circular object.
  • Solidity: The proportion of the pixels in the convex hull that are also in the object, i.e. ObjectArea/ConvexHullArea. Equals 1 for a solid object (i.e., one with no holes or has a concave boundary), or <1 for an object with holes or possessing a convex/irregular boundary.
  • MinFeretDiameter, MaxFeretDiameter: The Feret diameter is the distance between two parallel lines tangent on either side of the object (imagine taking a caliper and measuring the object at various angles). The minimum and maximum Feret diameters are the smallest and largest possible diameters, rotating the calipers along all possible angles.

None directly measure how well objects fit into an ellipse, but these might provide the filter thresholds you need as well.

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