Ilastik, getting orientation of objects

Im quite new to Ilastik so these questions might seem stupid.
I would like to to the following:
Segment actin fibres in cells and get their major axis orientation.
Just getting the fibres already works quite well with simple pixel classification, however I find the object features within Ilastik quite cryptic and I cannot really make out how I could get the orientation of objects.

So I would see each object as being 1 dimensional and would want to know what the axis in degrees is, if you were to draw a line between its two furthest away points. In addition I would want to know what cell the fibres belong. So of course, in addition to the fibres I would have to segment the cells aswell. But I am unsure how I can relate two objects to each other in Ilastik.

Hi @Snizl,

Did you hear about OrientationJ , an ImageJ plugin. :smiley:

original image

I’ll let @ilastik_team comment about existing feature that I don’t (yet) in ilastik :sweat_smile:



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Hello @Snizl,

you are on the right track! We have something in object classification that might be of help. The object features need to be better documented for a long time - but there seems to always be something else that gets a higher priority.

In the object features there is the one that goes by Principle componentes of the object. If you hover over this feature you get the below explanation. The principle components of the pca of the object are vectors. I would choose those when I wanted t classify objects solely on their principle orientation

When you export the feature table you’ll get (among other colums) these for the case of 2D:

Principal components of the object_0 Principal components of the object_1 Principal components of the object_2 Principal components of the object_3
0.9984875 0.05497945 0.05497945 -0.9984875
0.996085 0.0884006 0.0884006 -0.996085
0.9996252 -0.027376171 -0.027376171 -0.9996252
0.9999983 -0.0018601075 -0.0018601075 -0.9999983

So in 2D we have 2 vectors, so there are 4 columns. The first two are the x and y component of the major axis, the second two are the x and y component of the minor axis.

With those you can calculate, e.g. the angle if you are interested in that.

Thanks for your help, I’ll try out the FIJI plugin aswell, looks like it might be even easier than using ilastik for this problem.