3D Shepp-Logan Phantom

This page illustrates the 3D Shepp-Logan phantom(s) in the Julia package ImagePhantoms.

This page comes from a single Julia file: 37-shepp3.jl.

You can access the source code for such Julia documentation using the 'Edit on GitHub' link in the top right. You can view the corresponding notebook in nbviewer here: 37-shepp3.ipynb, or open it in binder here: 37-shepp3.ipynb.

Setup

Packages needed here.

using ImagePhantoms: ellipsoid_parameters, ellipsoid, phantom
using ImageGeoms: ImageGeom, axes
using MIRTjim: jim, prompt
using Unitful: g, cm

The following line is helpful when running this file as a script; it prompts user to hit a key after each figure is displayed.

isinteractive() ? jim(:prompt, true) : prompt(:draw);

Overview

Currently this package provides one version of a 3D Shepp-Logan phantom consisting of ellipsoids.

For completeness, we illustrate it using units, though units are not required.

We use cm for the spatial units and g/cm³ (density) for the tissue values.

fovs = (24cm, 24cm, 20cm)
u = (1, 1, 1*g/cm^3)
params = ellipsoid_parameters( ; fovs, u)
ob = ellipsoid(params); # Vector of Ellipsoid objects

To visualize this phantom, we sample it with the help of ImageGeoms, using over-sampling to account for partial volume effects.

dims = (128,130,30)
ig = ImageGeom( ; dims, deltas = fovs ./ dims )

oversample = 3
image = phantom(axes(ig)..., ob, oversample)
clim = (0.95, 1.05)
jim(axes(ig)[1:2]..., image; title = "3D Shepp-Logan phantom slices", clim)

This page was generated using Literate.jl.