Viewing NIB or Imaging Data in Jupyter notebooks

jupyter
neuroimaging
viewer
niwidgets

#1

Is anyone aware of any libraries that can display 2-D or 3-D imaging data in a jupyter notebook?

The nibabel viewer comes close in functionality, but the interactors don’t work currently in Jupyter notebooks.

http://nipy.org/nibabel/reference/nibabel.viewers.html#orthoslicer3d

I also found a “papaya” viewer that can potentially integrate with Jupyter Notebooks as well… and I have done some basic MATPLOTLIB + Numpy stuff in the past, but it was usually kind of cloogy.

I also found some stuff here that might do it… but wanted to see if anyone had any recommendations…


#2

Have you taken a look at niwidgets? I think from your description, niwidgets should do what you want it to do.


#3

I was also just struggeling with using nibabel’s orthoview(). If you use %matplotlib notebook before using img.orthoview(), you can interactively investigate your 2-D, 3-D and 4-D files.


#4

i would highly recommend niwidgets for notebook visualization.