View volumetric (3D) medical images in Jupyter notebooks

CTViewer

This tiny, but very useful utility enables interactive slice-by-slice viewing of 3D images in ipython notebooks. It builds upon ImageSliceViewer3D and is specifically designed for viewing CT images. Key features:

• Change orientation of 3D images to view them along any of the three possible axes
• Window CT images. All major presets for window level and window width provided. See the table below for the complete list of presets
• Window CT images using custom values for window level and window width

Installation

CTViewer can be installed from PyPI with the following command:

  pip install ctviewer

Usage

CTViewer takes as input a 3-dimensional numpy array. For windowing to work as intended, the voxel values should be in Hounsfield Units (HU). Typical usage:

  from ctviewer import CTViewer
  # assuming that volumetric_image is the 3-dimensional numpy array
  CTViewer(volumetric_image)

For a more detailed example of loading a stack of dicom images from disk, converting to HU, and then viewing using CTViewer, check the sample_run.ipynb inside the examples folder

Windowing

The following windows are available as presets, along with custom inputs for window level and window width:

Window Name	Window Level	Window Width
Bone	500	2000
Lung	-600	1600
Abdomen	40	400
Brain	30	70
Soft Tissue	50	350
Liver	60	160
Mediastinum	50	500
Stroke	30	30
CTA	170	600

Example

Support

Reach out to me at one of the following places!

Twitter: @vibhuagrawal
Email: vibhu[dot]agrawal14[at]gmail