Viewing Voxels Using ITK Widgets

dylanmendonca · January 27, 2020, 5:50pm

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?

jianxu_chen · January 29, 2020, 7:44am

I think this example will be helpful:

github.com

InsightSoftwareConsortium/itkwidgets/blob/master/examples/ImageWithAnisotropicPixelSpacing.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Install dependencies for this example\n",
    "# Note: This does not include itkwidgets, itself\n",
    "import sys\n",
    "!{sys.executable} -m pip install itk-io imageio"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [

This file has been truncated. show original

dylanmendonca · January 31, 2020, 5:16pm

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?

jianxu_chen · February 12, 2020, 9:20pm

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.

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Viewing Voxels Using ITK Widgets

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