niftiwidget 0.0.1

View volumetric images in Jupyter 🧠

NiftiWidget

NiftiWidget brings the 3D image viewing capabilities of NiftiView into Jupyter notebooks 👩‍💻

NiftiWidget is build around the niftiview Python package, that allows users to

• View multiple 3D images in a beautiful layout 🧩
• Add custom image layers and overlays (crosshair, colorbar...) 📑
• Save the view as a high-quality figure or as a GIF 💾
• ...and much more...

Learn to use it via the niftiview examples and this YouTube-Tutorial 💡

Install it via pip install niftiwidget 🛠️

• In Colab, run apt install libcairo2-dev pkg-config python3-dev then pip install niftiwidget
• On other systems these tips might help to make it work

Usage 💡

To view saved files, pass the filepaths to Config which is passed to NiftiWidget

from niftiview import TEMPLATES, Config
from niftiwidget import NiftiWidget

filepaths = [[TEMPLATES['ch2']], [TEMPLATES['T1']]]
# filepaths = [['/path/to/nifti1.nii.gz'], ['/path/to/nifti2.nii.gz']]
config = Config(filepaths_view1=filepaths)
NiftiWidget(config=config)

Alternatively, one can also pass a list of nibabel images directly to NiftiWidget

import nibabel as nib
from niftiview import TEMPLATES, Config
from niftiwidget import NiftiWidget

nib_images = [[nib.load(TEMPLATES['ch2'])], [nib.load(TEMPLATES['T1'])]]
config = Config()
NiftiWidget(nib_images1=nib_images)

To avoid the widget getting to large you can limit the image width by passing a Layout

from ipywidgets import Layout
...
NiftiWidget(..., layout=Layout(max_width='1000px'))

Start exploring by pasting the below code into a cell and try different settings by changing the config...

from ipywidgets import Layout
from niftiview import TEMPLATES
from niftiview.config import Config
from niftiwidget import NiftiWidget

filepaths = [[TEMPLATES['ch2']], [TEMPLATES['T1']]]
# filepaths = [['/path/to/nifti1.nii.gz'], ['/path/to/nifti2.nii.gz']]
config = Config(filepaths_view1=filepaths, layout='all', fpath=1, crosshair=True)
NiftiWidget(config=config, layout=Layout(max_width='1000px'))

...or interacting with the widget itself!

Pitfall: Use ; at the end of filepaths!

Inside the NiftiView widget, instead of hitting Enter to confirm a filepath, write ; at the end of it. If you write

/path/to/figures/figure1.pdf

in the Save image or GIF textbox and hit Enter, nothing will happen. Write ; at the end of it

/path/to/figures/figure1.pdf;

and the figure will be saved 🎉 This also applies to the Filepattern textboxes!

If you change a filepath, make sure to

1. delete the ;
2. change the filepath
3. add the ;

because modifying the filepath while keeping the ; will result in e.g. unwanted figures being saved!

Colab 🐌

Since NiftiWidget does not use the GPU (like e.g. ipyniivue) image refreshes in Colab are slow 🐌

However, if used inside a local Jupyter notebook this is not an issue 🐇