Allen Cell Discussion Forum

Viewing Voxels Using ITK Widgets

Hi,

My cell images are distorted in the sense that the aspect ratios are all off. How do I incorporate the voxel size in python?

When I use 3D viewer in ImageJ with the specified size, it interpolates just fine. How could I do this in Python and visualize the results using the view function in itkwidgets?

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I think this example will be helpful:

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Thanks for that!

I was curious, when using Otsu’s method to threshold 3D cell images, should we perform the Otsu thresholding on the image that has been interpolated along the z slices?

Not necessarily. The Otsu method can be applied on the anisotropic image, after proper pre-processing, like smoothing. When you interprete or analyze your results, you can decide if you need to interpolate along z or not.