Internal axes order of N-D datasets in Ilastik

what is the order of axes of N-D dataset in Ilastik?
Is it [time, depth, height, width, color]?


Hi @Ilya_Belevich,

internally we use [time, color, depth, height, width] most of the places. But for writing output we take the original axisorder into consideration. You can also fully customize the axisorder in the export applet (or via command line options in headless mode). Furthermore, the ilastik plugin will import (and export) data per default as [time, depth, height, width, color]. Side note, we use z, y, x for depth, height, width.


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Hi @k-dominik ,
thank you!
Is there any specific reason of having the internal organization as [time, color, depth, height, width]?
Why for example it is not as [width, height, depth, color, time]?
in this case it is quite straight forward to get original 3D dataset as a[:,:,:,colorId, timeId] for processing and it won’t require any transposition?
Or is it just faster to access 2D data, when the last two dimensions are height and width?