Ilastik : Object Classification Table

Hi everyone,

I’m sorry in advance if this kind of questions have already been answered.

I’m a PhD student working on particles analysis in 3D, I use the FIB-SEM 3D technique to analyse nanocomposites. In this sample, I have one type of spherical particles of different size, and I need to analyse size distribution, coordination etc…

I’m working with Ilastik to segment my particles with Pixel Classification then I do Object Classification to do some measurements: Size in pixels, Radii of the Object, Object Centre. I need some precisions on the measurement made.

Is the size in pixels the measurement of the projected diameter of the object?
Is the “Radii of the object_0”, “Radii of the object_1”, “Radii of the object_2” correspond to the X, Y, Z directions of the radii for the ellipse?

Best regards,

Hi @MgTomo3D,

welcome to the community!

  • Size in pixels: Total size of the object in pixels. No correction for anisotropic resolution or anything else.
  • Center of the object: Average of the coordinates of this object’s pixels.
  • Radii of the object: Eigenvalues of the PCA on the coordinates of the object’s pixels. Very roughly, this corresponds to the radii of an ellipse fit to the object. The radii are ordered, with the largest value as first. So please first bear in mind that this is not an ellipse fit, but a principle component analysis of the object voxel/pixel coordinates. The radii are then to be interpreted in the direction of the principle components, which are 3 vectors with 3 values each, ordered descending from the one that explains the most variance of the data.

@Sith pointed out that they use the result of object classification in Fiji to compute ellipse fits using MorphoLibJ: Object size underestimated by the Radii - #3 by Sith