jni / napari-vesuvius

napari plugin to work with Vesuvius Challenge data

napari-vesuvius

napari plugin to work with Vesuvius Challenge data

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Current contributions

A reader to read in points and image data from a .volpkg file

Use it with:

napari path/to/data.volpkg

It should prompt you to open the data with the napari-vesuvius plugin and load images as a dask array and point clouds as points layers.

Alternatively, you can use it directly from Python, IPython, or Jupyter:

import napari
viewer = napari.Viewer(ndisplay=3)  # start in 3D view
layers = viewer.open('path/to/data.volpkg', plugin='napari-vesuvius')
napari.run()  # not needed in IPython or Jupyter

Sample data of the vesuvius campfire dataset

You can use napari-vesuvius to quickly have a look at the campfire demo dataset.

To look at the data, you can either use the napari menu at File > Open Sample > napari-vesuvius > [Campfire raw data / Campfire reconstructed data]:

Or you can use the viewer API directly from Python:

import napari
viewer = napari.Viewer(ndisplay=3)  # start in 3D view
layers = viewer.open_sample('napari-vesuvius', 'campfire/raw')
# or
# layers = viewer.open_sample('napari-vesuvius', 'campfire/rec')
napari.run()  # not needed in IPython or Jupyter

(This is the raw x-ray tomography data using the 'minip' projection.)

TODO

• read meshes
• clipping planes
• create and save segmentations
• unfold meshes

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Installation

You can install napari-vesuvius via pip:

pip install git+https://github.com/jni/napari-vesuvius.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the Mozilla Public License 2.0 license, "napari-vesuvius" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.