simple-slice-viewer

README

Overview

A viewer to scroll through slices of 2D, 3D and 4D medical data sets (CT, PET, MRI...)

Supports files than can be read by SimpleITK:

• Nifti: .nii .nii.gz .nia .img .img.gz .hdr
• Nrrd: .nrrd .nhdr
• Meta Image: .mhd .mha

And probably some more types as long as they are supported by the SimpleITK file reader.

In addition there is support for reading folders with dicom data. Sorting dicom data into 3D volume is tricky and may depend on modality, vendor and model of the imaging device. Basic support is offered that works well with CT, PET and MRI. For Siemens PET the PET data is read in SUV.

A second image can be loaded and is displayed as fusion on top of the first. Works well with PET/CT and PET/MRI data.

##Usage

pip install simple-slice-viewer

Command Line

simple-slice-viewer
simple-slice-viewer ct.nii
simple-slice-viewer ct.nii --fusion pet.nii

or use ssv as shorthand: ssv ssv ct.nii ssv ct.nii --fusion pet.nii ssv --image ct.nii --fusion pet.nii

Inside Python

In Python images should be read to SimpleITK Image objects first.

import simple_slice_viewer as ssv
import SimpleITK as sikt

image = sitk.ReadImage('ct.nii')
fusion = sitk.ReadImage('pet.nii')

ssv.display(image=image, fusion=fusion)

To display a numpy array convert it to SimpleITK first

import SimpleITK as sitk
import simple_slice_viewer as ssv
image = sitk.GetImageFromArray(np_array)
ssv.display(image)